Bauke W. Dijkstra

Crystal Structure and Biochemical Properties of a Novel Thermostable Esterase Containing an Immunoglobulin-Like Domain (2009)

Dijkstra, Bauke W., Barendregt, Arjan, Bultema, Jelle B., Akveld, Twan, Swinkels, Peter, ...

Comparative analysis of the genome of the hyperthermophilic bacterium Thermotoga maritima revealed a hypothetical protein (EstA) with typical esterase features. The EstA protein was functionally...

Crystallization and preliminary X-ray analysis of carnein, a serine protease from Ipomoea carnea (2009)

Patel, Ashok Kumar, Oosterwijk, Niels Van, Singh, Vijay Kumar, Rozeboom, Henriëtte J., Kalk, Kor H., Siezen, Roland J., ...

Carnein is an 80 kDa subtilisin-like serine protease from the latex of the plant Ipomoea carnea which displays an exceptional resistance to chemical and thermal denaturation. In order to obtain the...

Biochemical and crystallographic characterization of a glucansucrase from Lactobacillus reuteri 180 (2008)

Pijning, Tjaard, Vujičić-Žagar, Andreja, Kralj, Slavko, Eeuwema, Wieger, Dijkhuizen, Lubbert, Dijkstra, Bauke W.

Glucansucrases are large extracellular transglycosidases secreted by lactic acid bacteria. Using sucrose as a substrate they synthesize high molecular mass α-glucans or, in the presence of suitable...

Structural mimicry for vinculin activation by IpaA, a virulence factor of Shigella flexneri (2006)

Dijkstra, Bauke W., Broos, Jaap, Parsot, Claude, Eerde, André Van, Hamiaux, Cyril

Invasion of epithelial cells by Shigella flexneri is characterized by cytoskeletal rearrangements of the host cell membrane, promoting internalization of the bacterium. The bacterial effector IpaA is...

Degradation of halogenated compounds: structures and catalytic mechanisms of dehalogenases (2006)

Dijkstra, Bauke W.

Directed Evolution of Bacillus subtilis Lipase A by Use of Enantiomeric Phosphonate Inhibitors: Crystal Structures and Phage Display Selection (2006)

Boersma, Ykelien L., Dröge, Melloney J., Pouderoyen, Gertie Van, Vrenken, Titia E., Rüggeberg, Carsten J., Reetz, Manfred T., ...

Phage display can be used as a protein-engineering tool for the selection of proteins with desirable binding properties from a library of mutants. Here we describe the application of this method for...

Fortuitous structure determination of `as-isolated' Escherichia coli bacterioferritin in a novel crystal form (2006)

Eerde, André Van, Oost, John Van Der, Dijkstra, Bauke W.

Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 Å resolution despite a high degree of merohedral...

Acetobacter turbidans α-Amino Acid Ester Hydrolase. How a Single Mutation Improves an Antibiotic-Producing Enzyme (2006)

Jekel, Peter A., Polderman-Tijmes, Jolanda J., Barends, Thomas R.M., Williams, Christopher, Wybenga, Gjalt, Janssen, Dick B., ...

The α-amino acid ester hydrolase (AEH) from Acetobacter turbidans is a bacterial enzyme catalyzing the hydrolysis and synthesis of β-lactam antibiotics. The crystal structures of the native enzyme,...

The X-Ray Structure of the Haloalcohol Dehalogenase HheA from Arthrobacter sp. Strain AD2: Insight into Enantioselectivity and Halide Binding in the Haloalcohol Dehalogenase Family (2006)

Janssen, Dick B., Tang, Lixia, Kalk, Kor H., Jong, René M. De, Dijkstra, Bauke W.

Haloalcohol dehalogenases are bacterial enzymes that cleave the carbon-halogen bond in short aliphatic vicinal haloalcohols, like 1-chloro-2,3-propanediol, some of which are recalcitrant...

Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure (2005)

Straaten, Karin E. Van, Jong, René M. De, Dijkstra, Bauke W., Barends, Thomas R.M.

Crystals were grown of a mutant form of the bacterial cell-wall maintenance protein MltA that diffracted to 2.15 Å resolution. When phasing with molecular replacement using the native structure...

Crystal Structure of MltA from Escherichia coli Reveals a Unique Lytic Transglycosylase Fold (2005)

Vollmer, Waldemar, Dijkstra, Bauke W., Straaten, Karin E. Van

Lytic transglycosylases are bacterial enzymes involved in the maintenance and growth of the bacterial cell-wall peptidoglycan. They cleave the β-(1,4)-glycosidic bonds in peptidoglycan forming...

A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: Structural determinants of redox potential (2005)

Canters, Gerard W., Rossi, Gian Luigi, Cavazzini, Davide, Dijkstra, Bauke W., ...

Flavodoxin II from Azotobacter vinelandii is a ‘‘long-chain’’ flavodoxin and has one of the lowest E1 midpoint potentials found within the flavodoxin family. To better understand the...

An approach to prevent aggregation during the purification and crystallization of wild type acyl coenzyme A: Isopenicillin N acyltransferase from Penicillium chrysogenum (2005)

Dijkstra, Bauke W., Hart, Darren J., Sutherland, John D., Hensgens, Charles M.H., Yoshida, Hiromi

Acyl coenzyme A: isopenicillin N acyltransferase (AT) from Penicillium chrysogenum is an enzyme of interest for the biosynthesis of β-lactam antibiotics. Severe aggregation problems with wild type...

Improved Catalytic Properties of Halohydrin Dehalogenase by Modification of the Halide-Binding Site (2005)

Dijkstra, Bauke W., Jong, René M. De, Fraaije, Marco W., Torres Pazmiño, Daniel E., Tang, Lixia, Janssen, Dick B.

Halohydrin dehalogenase (HheC) from Agrobacterium radiobacter AD1 catalyzes the dehalogenation of vicinal haloalcohols by an intramolecular substitution reaction, resulting in the formation of the...

Structural Basis for the Enantioselectivity of an Epoxide Ring Opening Reaction Catalyzed by Halo Alcohol Dehalogenase HheC (2005)

Dijkstra, Bauke W., Janssen, Dick B., Tang, Lixia, Villa, Alessandra, Tiesinga, Jan J.W., Jong, René M. De

Halo alcohol dehalogenase HheC catalyzes the highly enantioselective dehalogenation of vicinal halo alcohols to epoxides, as well as the reverse reaction, the enantioselective and β-regioselective...

A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: Structural determinants of redox potential (2005)

Alagaratnam, Sharmini, Van Pouderoyen, Gertie, Pijning, Tjaard, Dijkstra, Bauke W., Cavazzini, Davide, Rossi, Gian Luigi, ...

Flavodoxin II from Azotobacter vinelandii is a “long-chain” flavodoxin and has one of the lowest E1 midpoint potentials found within the flavodoxin family. To better understand the relationship...

Purification, crystallization and preliminary X-ray analysis of the lytic transglycosylase MltA from Escherichia coli (2004)

Dijkstra, Bauke W., Straaten, Karin E. Van

The lytic transglycosylase MltA from Escherichia coli with its membrane anchor and signal sequence deleted has been purified to homogeneity by means of cation-exchange chromatography. The enzyme was...

Novel Biocatalysts by Identification and Design (2004)

Jaeger, Karl-Erich, Dijkstra, Bauke W., Pouderoyen, Gertie Van, Streit, Wolfgang, Puls, Michael, Leggewie, Christian, ...

Enzymes produced from bacteria and eukaryotic organisms are presently being used for a large variety of different biotechnological applications. The rapidly increasing demand for enzymes which are...

Three-dimensional structures of enzymes useful for β-lactam antibiotic production (2004)

Dijkstra, Bauke W., Yoshida, Hiromi, Barends, Thomas R.M.

Significant advances have been made in the structure-based engineering of enzymes useful for β-lactam antibiotic production. Structure-based engineering of penicillin G acylase and cephalosporin...

Structure of Spa15, a type III secretion chaperone from Shigella flexneri with broad specificity (2004)

Dijkstra, Bauke W., Parsot, Claude, Pérez, Javier, Hamiaux, Cyril, Eerde, André Van

Type III secretion (TTS) systems are used by many Gram-negative pathogens to inject virulence proteins into the cells of their hosts. Several of these virulence effectors require TTS chaperones that...

The X-ray Structure of trans-3-Chloroacrylic Acid Dehalogenase Reveals a Novel Hydration Mechanism in the Tautomerase Superfamily (2004)

Dijkstra, Bauke W., Whitman, Christian P., Poelarends, Gerrit J., Brugman, Wim, Jong, René M. De

Isomer-specific 3-chloroacrylic acid dehalogenases function in the bacterial degradation of 1,3-dichloropropene, a compound used in agriculture to kill plant-parasitic nematodes. The crystal...

Improved Thermostability of Bacillus circulans Cyclodextrin Glycosyltransferase by the Introduction of a Salt Bridge (2004)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Rozeboom, Henriëtte J., Leemhuis, Hans

Cyclodextrin glycosyltransferase (CGTase) catalyzes the formation of cyclodextrins from starch. Among the CGTases with known three-dimensional structure, Thermoanaerobacterium thermosulfurigenes...

Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase (2004)

Keizer, Evelien, Snijder, Harm J., Hensgens, Charles M.H., Alkema, Wynand B.L., Dijkstra, Bauke W., Janssen, Dick B.

Penicillin acylase catalyses the condensation of Cα-substituted phenylacetic acids with β-lactam nucleophiles, producing semi-synthetic β-lactam antibiotics. For efficient synthesis a low affinity...

Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase (2004)

Alkema, Wynand B.L., Hensgens, Charles M.H., Snijder, Harm J., Keizer, Evelien, Dijkstra, Bauke W., Janssen, Dick B.

Penicillin acylase catalyses the condensation of Cα-substituted phenylacetic acids with β-lactam nucleophiles, producing semi-synthetic β-lactam antibiotics. For efficient synthesis a low affinity...

Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase (2004)

Alkema, Wynand B. L., Hensgens, Charles M. H., Snijder, Harm J., Keizer, Evelien, Dijkstra, Bauke W., Janssen, Dick B.

Penicillin acylase catalyses the condensation of Cα-substituted phenylacetic acids with β-lactam nucleophiles, producing semi-synthetic β-lactam antibiotics. For efficient synthesis a low affinity...

Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase (2004)

Alkema, Wynand B. L., Hensgens, Charles M. H., Snijder, Harm J., Keizer, Evelien, Dijkstra, Bauke W., Janssen, Dick B.

Penicillin acylase catalyses the condensation of Cα-substituted phenylacetic acids with β-lactam nucleophiles, producing semi-synthetic β-lactam antibiotics. For efficient synthesis a low affinity...

X-ray analysis of two antibiotic-synthesizing bacterial ester hydrolases: preliminary results (2003)

Dijkstra, Bauke W., Janssen, Dick B., Vries, Erik De, Jekel, Peter A., Polderman-Tijmes, Jolanda J., Hensgens, Charles M.H., ...

α-Amino-acid ester hydrolases are multimeric enzymes of potential use in antibiotic production. Knowledge of their structure could help to engineer these enzymes into economically viable...

Oils used in microbatch crystallization do not remove a detergent from the drops they cover (2003)

Dijkstra, Bauke W., Barends, Thomas R.M.

In microbatch crystallizations, a small volume of protein solution is placed in contact with a large volume of oil. Detergents present in the water phase may be expected to migrate into the oil...

Directed Evolution of an Enantioselective Bacillus subtilis Lipase (2003)

Eggert, Thorsten, Jaeger, Karl-Erich, Eipper, Andreas, Thiel, Walter, Otte, Nikolaj, Reetz, Manfred T., ...

Chiral compounds are of steadily increasing importance to the chemical industry, in particular for the production of pharmaceuticals. Where do these compounds come from? Apart from natural resources,...

Conversion of Cyclodextrin Glycosyltransferase into a Starch Hydrolase by Directed Evolution: The Role of Alanine 230 in Acceptor Subsite +1 (2003)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Euverink, Gert-Jan W., Wilbrink, Maarten, Rozeboom, Henriëtte J., Leemhuis, Hans

Cyclodextrin glycosyltransferase (CGTase) preferably catalyzes transglycosylation reactions, whereas many other α-amylase family enzymes are hydrolases. Despite the availability of three-dimensional...

Single-Crystal EPR Study at 95 GHz of the Type 2 Copper Site of the Inhibitor-Bound Quercetin 2,3-Dioxygenase (2003)

Huber, Martina, Groenen, Edgar J.J., Dijkstra, Bauke W., Matsushita, Michio, Steiner, Roberto A., Fittipaldi, Maria

An electron-spin-echo-detected, electron-paramagnetic-resonance study has been performed on the type 2 copper site of quercetin 2,3-dioxygenase from Aspergillus japonicus. In the protein, copper is...

Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon–halogen bond (2003)

Dijkstra, Bauke W., Jong, René M. De

The dehalogenases make use of fundamentally different strategies to cleave carbon–halogen bonds. The structurally characterized haloalkane dehalogenases, haloacid dehalogenases and...

Catalysis and regulation — from structure to function (2003)

Matthews, Rowena G., Dijkstra, Bauke W.

Thermoanaerobacterium thermosulfurigenes cyclodextrin glycosyltransferase. Mechanism and kinetics of inhibition by acarbose and cyclodextrins (2003)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Leemhuis, Hans

Cyclodextrin glycosyltransferase (CGTase) uses an α-retaining double displacement mechanism to catalyze three distinct transglycosylation reactions. To investigate these reactions as catalyzed by...

Engineering cyclodextrin glycosyltransferase into a starch hydrolase with a high exo-specificity (2003)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Kragh, Karsten M., Leemhuis, Hans

Cyclodextrin glycosyltransferase (CGTase) enzymes from various bacteria catalyze the formation of cyclodextrins from starch. The Bacillus stearothermophilus maltogenic α-amylase (G2-amylase is...

The fully conserved Asp residue in conserved sequence region I of the α-amylase family is crucial for the catalytic site architecture and activity (2003)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Rozeboom, Henriëtte J., Leemhuis, Hans

The α-amylase family is a large group of starch processing enzymes. It is characterized by four short sequence motifs that contain the seven fully conserved amino acid residues in this family: two...

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger (2003)

Dijkstra, Bauke W., Benen, Jacques A.E., Snijder, Harm J., Pouderoyen, Gertie Van

Endopolygalacturonase I is a processive enzyme, while the 60% sequence identical endopolygalacturonase II is not. The 1.70 Å resolution crystal structure of endopolygalacturonase I reveals a...

Crystal Structure and Carbohydrate-binding Properties of the Human Cartilage Glycoprotein-39 (2003)

Dijkstra, Bauke W., Bos, Ebo, Kalk, Kor H., Pijning, Tjaard, Fusetti, Fabrizia

The human cartilage glycoprotein-39 (HCgp-39 or YKL40) is expressed by synovial cells and macrophages during inflammation. Its precise physiological role is unknown. However, it has been proposed...

Crystal Structures of the ATPase Subunit of the Glucose ABC Transporter from Sulfolobus solfataricus: Nucleotide-free and Nucleotide-bound Conformations (2003)

Dijkstra, Bauke W., Albers, Sonja V., Driessen, Arnold J.M., Verdon, Grégory

The ABC-ATPase GlcV energizes a binding protein-dependent ABC transporter that mediates glucose uptake in Sulfolobus solfataricus. Here, we report high-resolution crystal structures of GlcV in...

Formation of the Productive ATP-Mg2+-bound Dimer of GlcV, an ABC-ATPase from Sulfolobus solfataricus (2003)

Driessen, Arnold J.M., Dijkstra, Bauke W., Oosterwijk, Niels Van, Albers, Sonja-Verena, Verdon, Grégory

The ABC-ATPase GlcV from Sulfolobus solfataricus energizes an ABC transporter mediating glucose uptake. In ABC transporters, two ABC-ATPases are believed to form a head-to-tail dimer, with both...

Acetobacter turbidans α-amino acid ester hydrolase: merohedral twinning in P21 obscured by pseudo-translational NCS (2003)

Dijkstra, Bauke W., Barends, Thomas R.M.

The structure elucidation of the α-amino acid ester hydrolase from Acetobacter turbidans by molecular replacement is described. In the monoclinic crystal, the molecules are related by both...

The Sequence and Crystal Structure of the α-Amino Acid Ester Hydrolase from Xanthomonas citri Define a New Family of β-Lactam Antibiotic Acylases (2003)

Polderman-Tijmes, Jolanda J., Barends, Thomas R.M., Jekel, Peter A., Hensgens, Charles M.H., Vries, Erik J. De, Janssen, Dick B., ...

α-Amino acid ester hydrolases (AEHs) catalyze the hydrolysis and synthesis of esters and amides with an α-amino group. As such, they can synthesize β-lactam antibiotics from acyl compounds and...

Purification, crystallization and preliminary X-ray diffraction of Cys103Ala acyl coenzyme A: isopenicillin N acyltransferase from Penicillium chrysogenum (2002)

Dijkstra, Bauke W., Montfort, Bart A. Van, Kroezinga, Els A., Hensgens, Charles M.H., Sutherland, John D.

Penicillins and cephalosporins are an efficacious group of antibiotics produced by fungi such as Penicillium chrysogenum and Acremonium chrysogenum. The last step in their biosynthesis is catalyzed...

Purification, crystallization and preliminary X-ray diffraction analysis of an archaeal ABC-ATPase (2002)

Driessen, Arnold J.M., Dijkstra, Bauke W., Albers, Sonja-V., Verdon, Grégory

In the archaeon Sulfolobus solfataricus glucose uptake is mediated by an ABC transport system. The ABC-ATPase of this transporter (GlcV) has been overproduced in Escherichia coli and purified....

Functional Analysis of the Copper-Dependent Quercetin 2,3-Dioxygenase. 1. Ligand-Induced Coordination Changes Probed by X-ray Crystallography: Inhibition, Ordering Effect, and Mechanistic Insights (2002)

Dijkstra, Bauke W., Kooter, Ingeborg M., Steiner, Roberto A.

The crystal structures of the copper-dependent Aspergillus japonicus quercetin 2,3-dioxygenase (2,3QD) complexed with the inhibitors diethyldithiocarbamate (DDC) and kojic acid (KOJ) are reported at...

Functional Analysis of the Copper-Dependent Quercetin 2,3-Dioxygenase. 2. X-ray Absorption Studies of Native Enzyme and Anaerobic Complexes with the Substrates Quercetin and Myricetin (2002)

Dijkstra, Bauke W., Meyer-Klaucke, Wolfram, Steiner, Roberto A.

Quercetin 2,3-dioxygenase (2,3QD) is a mononuclear copper-dependent dioxygenase which catalyzes the cleavage of the heterocyclic ring of the flavonol quercetin (5,7,3',4'-tetrahydroxy flavonol) to...

Functional importance of calcium binding sites in outer membrane phospholipase A (2002)

Egmond, Maarten R., Dekker, Niek, Dijkstra, Bauke W., Snijder, Harm J., Kingma, Roelie L.

Outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that hydrolyses phospholipids requiring Ca2+ as cofactor. In vitro studies have shown that OMPLA is only active as a dimer. The...

Biochemical properties and three-dimensional structures of two extracellular lipolytic enzymes from Bacillus subtilis (2002)

Verger, Robert, Douchet, Isabelle, Pencreac’h, Gaëlle, Pouderoyen, Gertie Van, Jaeger, Karl-Erich, Dijkstra, Bauke W., ...

This article reviews our present knowledge on the extracellular lipolytic enzymes LipA and LipB from Bacillus subtilis. Growth of B. subtilis to the late logarithmic growth phase results in a total...

Catalytic mechanism and product specificity of cyclodextrin glycosyltransferase, a prototypical transglycosylase from the α-amylase family (2002)

Dijkstra, Bauke W., Dijkhuizen, Lubbert, Uitdehaag, Joost C.M.

The catalytic mechanism of cyclodextrin glycosyltransferase, a member of the α-amylase family, is reviewed. The focus is put on the bond cleavage mechanism, the nature of the transition state and of...

Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis (2002)

Dijkstra, Bauke W., Sibbald, Mark, Rozeboom, Henriëtte J., Beintema, Jaap J., Bokma, Evert

Hevamine is a chitinase from the rubber tree Hevea brasiliensis. Its active site contains Asp125, Glu127, and Tyr183, which interact with the -1 sugar residue of the substrate. To investigate their...

EPR characterization of the mononuclear Cu-containing Aspergillus japonicus quercetin 2,3-dioxygenase reveals dramatic changes upon anaerobic binding of substrates (2002)

Dijkstra, Bauke W., Steiner, Roberto A., Huber, Martina, Egmond, Maarten R., Noort, Paula I. Van, Kooter, Ingeborg M.

Quercetin 2,3-dioxygenase (2,3QD) is a copper-containing dioxygenase that catalyses the oxidation of the flavonol quercetin to 2-protocatechuoylphloroglucinol carboxylic acid with concomitant...

Mutations converting cyclodextrin glycosyltransferase from a transglycosylase into a starch hydrolase (2002)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Leemhuis, Hans

Cyclodextrin glycosyltransferase (CGTase) efficiently catalyzes transglycosylation of oligo-maltodextrins, although the enzyme also has a low hydrolytic activity. Its +2 substrate binding subsite,...

Structure of Human Chitotriosidase. Implications for Specific Inhibitor Design and Function of Mammalian Chitinase-like Lectins (2002)

Boot, Rolf G., Dijkstra, Bauke W., Rozeboom, Henriëtte J., Houston, Douglas, Moeller, Holger Von, ...

Chitin hydrolases have been identified in a variety of organisms ranging from bacteria to eukaryotes. They have been proposed to be possible targets for the design of novel chemotherapeutics against...

The Remote Substrate Binding Subsite -6 in Cyclodextrin-glycosyltransferase Controls the Transferase Activity of the Enzyme via an Induced-fit Mechanism (2002)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Rozeboom, Henriëtte J., Uitdehaag, Joost C.M., Leemhuis, Hans

Cyclodextrin-glycosyltransferase (CGTase) catalyzes the formation of α-, β-, and γ-cyclodextrins (cyclic α-(1,4)-linked oligosaccharides of 6, 7, or 8 glucose residues, respectively) from starch....

Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroni. Structural Basis for Substrate Oxidation and Electron Transfer (2002)

Dijkstra, Bauke W., Huizinga, Eric G., Kalk, Kor H., Rozeboom, Henriëtte J., Oubrie, Arthur

Quinoprotein alcohol dehydrogenases are redox enzymes that participate in distinctive catabolic pathways that enable bacteria to grow on various alcohols as the sole source of carbon and energy. The...

Anaerobic enzyme·substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase (2002)

Dijkstra, Bauke W., Kalk, Kor H., Steiner, Roberto A.

Quercetin 2,3-dioxygenase (2,3QD) is the only firmly established copper dioxygenase known so far. Depending solely on a mononuclear Cu center, it catalyzes the breakage of the O-heterocycle of...

Crystal Structure of the Copper-Containing Quercetin 2,3-Dioxygenase from Aspergillus japonicus (2002)

Schröter, Klaus H., Fusetti, Fabrizia, Steiner, Roberto A., Noort, Paula I. Van, Pijning, Tjaard, Rozeboom, Henriëtte J., ...

Quercetin 2,3-dioxygenase is a copper-containing enzyme that catalyzes the insertion of molecular oxygen into polyphenolic flavonols. Dioxygenation catalyzed by iron-containing enzymes has been...

Crystallization and preliminary X-ray analysis of an enantioselective halohydrin dehalogenase from Agrobacterium radiobacter AD1 (2002)

Janssen, Dick B., Tang, Lixia, Kalk, Kor H., Rozeboom, Henriëtte J., Jong, René M. De, Dijkstra, Bauke W.

Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. Crystals of the enantioselective halohydrin dehalogenase HheC from...

Crystallization of quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni: crystals with unique optical properties (2001)

Duine, Johannis A., Kalk, Kor H., Rozeboom, Henriëtte J., Huizinga, Eric G., Oubrie, Arthur, ...

Quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni is a functional electron-transfer protein containing both a haem c and a pyrroloquinoline quinone cofactor. The enzyme has been...

X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution (2001)

Murshudov, Garib N., Kalk, Kor H., Vries, André De, Rozeboom, Henriëtte J., Steiner, Roberto A., Wilson, Keith S., ...

Using synchrotron radiation and a CCD camera, X-ray data have been collected from wild-type bovine pancreatic phospholipase A2 at 100 K to 0.97 Å resolution allowing full anisotropic refinement. The...

Lipolytic enzymes LipA and LipB from Bacillus subtilis differ in regulation of gene expression, biochemical properties, and three-dimensional structure (2001)

Jaeger, Karl-Erich, Dijkstra, Bauke W., Pouderoyen, Gertie Van, Eggert, Thorsten

Bacillus subtilis secretes the lipolytic enzymes LipA and LipB. We show here that they are differentially expressed depending on the composition of the growth medium: LipA is produced in rich and in...

Hydrophobic Amino Acid Residues in the Acceptor Binding Site Are Main Determinants for Reaction Mechanism and Specificity of Cyclodextrin-glycosyltransferase (2001)

Dijkstra, Bauke W., Uitdehaag, Joost C.M., Kralj, Slavko, Leemhuis, Hans, Dijkhuizen, Lubbert

Cyclodextrin-glycosyltransferases (CGTases) (EC 2.4.1.19) preferably catalyze transglycosylation reactions with glucosyl residues as acceptor, whereas the homologous α-amylases catalyze hydrolysis...

The Crystal Structure of Bacillus subtilis Lipase: A Minimal α/β Hydrolase Fold Enzyme (2001)

Jaeger, Karl-Erich, Eggert, Thorsten, Pouderoyen, Gertie Van, Dijkstra, Bauke W.

The X-ray structure of the lipase LipA from Bacillus subtilis has been determined at 1.5 Å resolution. It is the first structure of a member of homology family I.4 of bacterial lipases. The lipase...

Enzymatic Circularization of a Malto-octaose Linear Chain Studied by Stochastic Reaction Path Calculations on Cyclodextrin Glycosyltransferase (2001)

Elber, Ron, Dijkhuizen, Lubbert, Uitdehaag, Joost C.M., Dijkstra, Bauke W.

Cyclodextrin glycosyltransferase (CGTase) is an enzyme belonging to the α-amylase family that forms cyclodextrins (circularly linked oligosaccharides) from starch. X-ray work has indicated that this...

Structure and mechanism of the epoxide hydrolase from Agrobacterium radiobacter AD1 (2001)

Dijkstra, Bauke W., Janssen, Dick B., Rink, Rick, Nardini, Marco

The X-ray structure of the epoxide hydrolase from Agrobacterium radiobacter AD1 has been determined by isomorphous replacement at 2.1 Å resolution. The enzyme shows a two-domain structure, with the...

Unusual Catalytic Triad of Escherichia coli Outer Membrane Phospholipase A (2000)

Dijkstra, Bauke W., Snijder, Harm J., Fragiathaki, Maria, Kingma, Roelie L., Verheij, Hubertus M., Dekker, Niek, ...

Escherichia coli outer membrane phospholipase A (OMPLA) is an integral membrane enzyme. OMPLA is active as a homodimer and requires calcium as a cofactor. The crystal structures of the monomeric and...

Structures of Maltohexaose and Maltoheptaose Bound at the Donor Sites of Cyclodextrin Glycosyltransferase Give Insight into the Mechanisms of Transglycosylation Activity and Cyclodextrin Size Specificity (2000)

Dijkhuizen, Lubbert, Uitdehaag, Joost C.M., Dijkstra, Bauke W.

The enzymes from the α-amylase family all share a similar α-retaining catalytic mechanism but can have different reaction and product specificities. One family member, cyclodextrin...

Crystallographic Studies of the Interactions of Escherichia coli Lytic Transglycosylase Slt35 with Peptidoglycan (2000)

Dijkstra, Bauke W., Kalk, Kor H., Asselt, Erik J. Van

Lytic transglycosylases catalyze the cleavage of the β-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan with concomitant formation of a...

Engineering of cyclodextrin glycosyltransferase reaction and product specificity (2000)

Dijkstra, Bauke W., Uitdehaag, Joost C.M., Dijkhuizen, Lubbert

Directed evolution of an enantioselective lipase (2000)

Nardini, Marco, Schimossek, Klaus, Zonta, Albin, Liebeton, Klaus, Lang, Dietmar, Dijkstra, Bauke W., ...

Background: The biocatalytic production of enantiopure compounds is of steadily increasing importance to the chemical and biotechnological industry. In most cases, however, it is impossible to...

The three transglycosylation reactions catalyzed by cyclodextrin glycosyltransferase from Bacillus circulans (strain 251) proceed via different kinetic mechanisms (2000)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Uitdehaag, Joost C.M.

Cyclodextrin glycosyltransferase (CGTase) catalyzes three transglycosylation reactions via a double displacement mechanism involving a covalent enzyme-intermediate complex (substituted-enzyme...

The role of arginine 47 in the cyclization and coupling reactions of cyclodextrin glycosyltransferase from Bacillus circulans strain 251. Implications for product inhibition and product specificity (2000)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Uitdehaag, Joost C.M.

Cyclodextrin glycosyltransferase (CGTase) (EC 2.4.1.19) is used for the industrial production of cyclodextrins. Its application, however, is hampered by the limited cyclodextrin product specificity...

Enzyme kinetics of hevamine, a chitinase from the rubber tree Hevea brasiliensis (2000)

Terwisscha Van Scheltinga, Anke C., Barends, Thomas, Bokma, Evert, Dijkstra, Bauke W., Beintema, Jaap J.

The enzyme kinetics of hevamine, a chitinase from the rubber tree Hevea brasiliensis, were studied in detail with a new enzyme assay. In this assay, the enzyme reaction products were derivatized by...

The Active Site Topology of Aspergillus niger Endopolygalacturonase II as Studied by Site-directed Mutagenesis (2000)

Kester, Harry C.M., Sánchez-Torres, Paloma, Wagemaker, Matthé J.M., Armand, Sylvie, Santen, Yovka Van, Dijkstra, Bauke W., ...

Strictly conserved charged residues among polygalacturonases (Asp-180, Asp-201, Asp-202, His-223, Arg-256, and Lys-258) were subjected to site-directed mutagenesis in Aspergillus niger...

Crystal Structure of Pseudomonas aeruginosa Lipase in the Open Conformation. The Prototype for Family I.1 of Bacterial Lipases (2000)

Dijkstra, Bauke W., Jaeger, Karl-Erich, Liebeton, Klaus, Lang, Dietmar A., Nardini, Marco

The x-ray structure of the lipase from Pseudomonas aeruginosa PAO1 has been determined at 2.54 Å resolution. It is the first structure of a member of homology family I.1 of bacterial lipases. The...

Rational Design of Cyclodextrin Glycosyltransferase from Bacillus circulans Strain 251 to Increase α-Cyclodextrin Production (2000)

Penninga, Dirk, Uitdehaag, Joost C.M., Smith, Loraine M., Dijkstra, Bauke W., ...

Cyclodextrin glycosyltransferases (CGTase) (EC 2.4.1.19) are extracellular bacterial enzymes that generate cyclodextrins from starch. All known CGTases produce mixtures of α, β, and...

Structural requirements of pyrroloquinoline quinone dependent enzymatic reactions (2000)

Dijkstra, Bauke W., Oubrie, Arthur

On the basis of crystal structures of the pyrroloquinoline quinone (PQQ) dependent enzymes methanol dehydrogenase (MDH) and soluble glucose dehydrogenase (s-GDH), different catalytic mechanisms have...

Characterization of the β-lactam binding site of penicillin acylase of Escherichia coli by structural and site-directed mutagenesis studies (2000)

Vries, Erik De, Kroezinga, Els H., Hensgens, Charles M.H., Alkema, Wynand B.L., Floris, René, ...

The binding of penicillin to penicillin acylase was studied by X-ray crystallography. The structure of the enzyme–substrate complex was determined after soaking crystals of an inactive βN241A...

Characterization of the {beta}-lactam binding site of penicillin acylase of Escherichia coli by structural and site-directed mutagenesis studies (2000)

Alkema, Wynand B.L., Hensgens, Charles M.H., Kroezinga, Els H., De Vries, Erik, Floris, René, Van Der Laan, Jan-Metske, ...

The binding of penicillin to penicillin acylase was studied by X-ray crystallography. The structure of the enzyme–substrate complex was determined after soaking crystals of an inactive βN241A...

Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 Å resolution (1999)

Rozeboom, Henriëtte J., Dijkstra, Bauke W., Ridder, Ivo S.

Crystals of the 35 kDa protein haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 diffract to 1.15 Å resolution at cryogenic temperature using synchrotron radiation. Blocked anisotropic...

Identification of the Mg2+-binding site in the P-type ATPase and phosphatase members of the HAD (haloacid dehalogenase) superfamily by structural similarity to the response regulator protein CheY (1999)

Dijkstra, Bauke W., Ridder, Ivo S.

The large HAD (haloacid dehalogenase) superfamily of hydrolases comprises P-type ATPases, phosphatases, epoxide hydrolases and L-2-haloacid dehalogenases. A comparison of the three-dimensional...

Structure and mechanism of soluble quinoprotein glucose dehydrogenase (1999)

Duine, Johannis A., Olsthoorn, Arjen J.J., Kalk, Kor H., Rozeboom, Henriëtte J., Oubrie, Arthur, Dijkstra, Bauke W.

Soluble glucose dehydrogenase (s-GDH; EC 1.1.99.17) is a classical quinoprotein which requires the cofactor pyrroloquinoline quinone (PQQ) to oxidize glucose to gluconolactone. The reaction mechanism...

α/β Hydrolase fold enzymes: the family keeps growing (1999)

Dijkstra, Bauke W., Nardini, Marco

The α/β hydrolase fold is a typical example of a tertiary fold adopted by proteins that have no obvious sequence similarity, but nevertheless, in the course of evolution, diverged from a common...

Binding of calcium in the EF-hand of Escherichia coli lytic transglycosylase Slt35 is important for stability (1999)

Dijkstra, Bauke W., Asselt, Erik J. Van

The Escherichia coli lytic transglycosylase Slt35 contains a single metal ion-binding site that resembles EF-hand calcium-binding sites. The Slt35 EF-hand is only the second observation of such a...

Crystal Structures of Intermediates in the Dehalogenation of Haloalkanoates by L-2-Haloacid Dehalogenase (1999)

Dijkstra, Bauke W., Kalk, Kor H., Rozeboom, Henriëtte J., Ridder, Ivo S.

The L-2-haloacid dehalogenase from the 1,2-dichloroethane-degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoates to their...

The Cyclization Mechanism of Cyclodextrin Glycosyltransferase (CGTase) as Revealed by a γ-Cyclodextrin-CGTase Complex at 1.8-Å Resolution (1999)

Dijkhuizen, Lubbert, Kalk, Kor H., Uitdehaag, Joost C.M., Dijkstra, Bauke W.

The enzyme cyclodextrin glycosyltransferase is closely related to α-amylases but has the unique ability to produce cyclodextrins (circular α(1→4)-linked glucoses) from starch. To characterize...

1.68-Å Crystal Structure of Endopolygalacturonase II from Aspergillus niger and Identification of Active Site Residues by Site-directed Mutagenesis (1999)

Dijkstra, Bauke W., Visser, Jaap, Kalk, Kor H., Schröter, Klaus-Hasso, Armand, Sylvie, Benen, Jacques A.E., ...

Polygalacturonases specifically hydrolyze polygalacturonate, a major constituent of plant cell wall pectin. To understand the catalytic mechanism and substrate and product specificity of these...

The 1.7 Å Crystal Structure of the Apo Form of the Soluble Quinoprotein Glucose Dehydrogenase from Acinetobacter calcoaceticus Reveals a Novel Internal Conserved Sequence Repeat (1999)

Dijkstra, Bauke W., Duine, Johannis A., Kalk, Kor H., Rozeboom, Henriëtte J., Oubrie, Arthur

The crystal structure of a dimeric apo form of the soluble quinoprotein glucose dehydrogenase (s-GDH) from Acinetobacter calcoaceticus has been solved by multiple isomorphous replacement followed by...

High Resolution Crystal Structures of the Escherichia coli Lytic Transglycosylase Slt70 and its Complex with a Peptidoglycan Fragment (1999)

Dijkstra, Bauke W., Asselt, Erik J. Van

The 70 kDa soluble lytic transglycosylase (Slt70) from Escherichia coli is an exo-muramidase, that catalyses the cleavage of the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine...

X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the α-amylase family (1999)

Dijkstra, Bauke W., Dijkhuizen, Lubbert, Kalk, Kor H., Withers, Stephen G., Mosi, Renée, ...

Cyclodextrin glycosyltransferase (CGTase) is an enzyme of the α-amylase family, which uses a double displacement mechanism to process α-linked glucose polymers. We have determined two X-ray...

Active-site structure of the soluble quinoprotein glucose dehydrogenase complexed with methylhydrazine: A covalent cofactor-inhibitor complex (1999)

Dijkstra, Bauke W., Rozeboom, Henriëtte J., Oubrie, Arthur

Soluble glucose dehydrogenase (s-GDH) from the bacterium Acinetobacter calcoaceticus is a classical quinoprotein. It requires the cofactor pyrroloquinoline quinone (PQQ) to catalyze the oxidation of...

Crystal structure of Escherichia coli lytic transglycosylase Slt35 reveals a lysozyme-like catalytic domain with an EF-hand (1999)

Takacs, Bela, Kalk, Kor H., Dijkstra, Arnoud J., Dijkstra, Bauke W., Keck, Wolfgang, Asselt, Erik J. Van

Background: Lytic transglycosylases are bacterial muramidases that catalyse the cleavage of the β-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in...

Crystallographic and Kinetic Evidence of a Collision Complex Formed during Halide Import in Haloalkane Dehalogenase (1999)

Rozeboom, Henriëtte J., Ridder, Ivo S., Pikkemaat, Mariël G., Kalk, Kor H., Dijkstra, Bauke W., Janssen, Dick B.

Haloalkane dehalogenase (DhlA) converts haloalkanes to their corresponding alcohols and halide ions. The rate-limiting step in the reaction of DhlA is the release of the halide ion. The kinetics of...

Mutation of Tyrosine Residues Involved in the Alkylation Half Reaction of Epoxide Hydrolase from Agrobacterium radiobacter AD1 Results in Improved Enantioselectivity (1999)

Kingma, Jaap, Pieters, Roland J., Lutje Spelberg, Jeffrey H., Rink, Rick, Nardini, Marco, Kellogg, Richard M., ...

The X-ray Structure of Epoxide Hydrolase from Agrobacterium radiobacter AD1. An Enzyme to Detoxify Harmful Epoxides (1999)

Rozeboom, Henriëtte J., Ridder, Ivo S., Nardini, Marco, Kalk, Kor H., Rink, Rick, Janssen, Dick B., ...

Epoxide hydrolases catalyze the cofactor-independent hydrolysis of reactive and toxic epoxides. They play an essential role in the detoxification of various xenobiotics in higher organisms and in the...

Accelerated X-ray Structure Elucidation of a 36 kDa Muramidase/Transglycosylase Using wARP (1998)

Dijkstra, Bauke W., Lamzin, Victor S., Kalk, Kor H., Perrakis, Anastassis, Asselt, Erik J. Van

The X-ray structure of the 36kDa soluble lytic transglycosylase from Escherichia coli has been determined starting with the multiple isomorphous replacement method with inclusion of anomalous...

Reassessment of Acarbose as a Transition State Analogue Inhibitor of Cyclodextrin Glycosyltransferase (1998)

Withers, Stephen G., Dijkstra, Bauke W., Ruiterkamp, Richard, Uitdehaag, Joost C.M., Sham, Howard, Mosi, Renee

The binding of several different active site mutants of Bacillus circulans cyclodextrin glycosyltransferase to the inhibitor acarbose has been investigated through measurement of Ki values. The...

Structural investigations of the regio- and enantioselectivity of lipases (1998)

Dijkstra, Bauke W., Lang, Dietmar A.

Although lipases are widely applied for the stereospecific resolution of racemic mixtures of esters, the atomic details of the factors that are responsible for their stereospecificity are largely...

Structural basis of the chiral selectivity of Pseudomonas cepacia lipase (1998)

Dijkstra, Bauke W., Verheij, Hubertus M., Haas, Gerard H. De, Mannesse, Maurice L.M., Lang, Dietmar A.

To investigate the enantioselectivity of Pseudomonas cepacia lipase, inhibition studies were performed with SC- and RC-(RP,SP)-1,2-dialkylcarbamoylglycero-3-O-p-nitrophenyl alkylphosphonates of...

Crystal structure of a murine α-class glutathione S-transferase involved in cellular defense against oxidative stress (1998)

Dijkstra, Bauke W., Zimniak, Piotr, Kalk, Kor H., Arkema, Anita, Hoier, Helga, Schröter, Klaus-Hasso, ...

Glutathione S-transferases (GSTs) are ubiquitous multifunctional enzymes which play a key role in cellular detoxification. The enzymes protect the cells against toxicants by conjugating them to...

Engineering of Cyclodextrin Product Specificity and pH Optima of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1 (1998)

Dijkstra, Bauke W., Buitelaar, Reinetta M., Uitdehaag, Joost C.M., Wind, Richèle D., Dijkhuizen, Lubbert

The product specificity and pH optimum of the thermostable cyclodextrin glycosyltransferase (CGTase) from Thermoanaerobacterium thermosulfurigenes EM1 was engineered using a combination of x-ray...

The Three-dimensional Structure of the Nitrogen Regulatory Protein IIANtr from Escherichia coli (1998)

Reizer, Jonathan, Kalk, Kor H., Pijning, Tjaard, Bordo, Domenico, Saier Jr., Milton H., ...

The bacterial rpoN operon codes for σ54, which is the key σ factor that, under nitrogen starvation conditions, activates the transcription of genes needed to assimilate ammonia and glutamate. The...

The functional importance of structural differences between the mannitol-specific IIAmannitol and the regulatory IIAnitrogen (1998)

Dijkstra, Bauke W.

The three-dimensional structures of the IIA domain of the mannitol-specific phosphoenol-pyruvate dependent phosphotransferase system (PTS) of Escherichia coli and the regulatory IIAntr enzyme have...

The structure of the Escherichia coli phosphotransferase IIAmannitol reveals a novel fold with two conformations of the active site (1998)

Hangyi, Ilona, Kalk, Kor H., Pijning, Tjaard, Robillard, George T., ...

Background: The bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS) catalyses the cellular uptake and subsequent phosphorylation of carbohydrates. Moreover, the PTS plays a...

Kinetic Analysis and X-ray Structure of Haloalkane Dehalogenase with a Modified Halide-Binding Site (1998)

Ridder, Ivo S., Krooshof, Geja H., Vos, Gerda J., Rozeboom, Henriëtte J., Kalk, Kor H., ...

Haloalkane dehalogenase (DhlA) catalyzes the hydrolysis of haloalkanes via an alkyl-enzyme intermediate. Trp175 forms a halogen/halide-binding site in the active-site cavity together with Trp125. To...

Trapping and Characterization of the Reaction Intermediate in Cyclodextrin Glycosyltransferase by Use of Activated Substrates and a Mutant Enzyme (1997)

Withers, Stephen G., Dijkstra, Bauke W., Uitdehaag, Joost, He, Shouming, Mosi, Renee

Cyclodextrin glycosyltransferases (CGTases) catalyze the degradation of starch into linear or cyclic oligosaccharides via a glycosyl transfer reaction occurring with retention of anomeric...

X-ray structure of antistasin at 1.9 Å resolution and its modelled complex with blood coagulation factor Xa (1997)

Schreuder, Herman A., Krengel, Ute, Lapatto, Risto, Arkema, Anita, Boer, Bijtske De, Kalk, Kor H., ...

The three-dimensional structure of antistasin, a potent inhibitor of blood coagulation factor Xa, from the Mexican leech Haementeria officinalis was determined at 1.9 Å resolution by X-ray...

Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes (1997)

Dijkstra, Bauke W., Wilson, Keith S., Perrakis, Anastassis, Terwisscha Van Scheltinga, Anke C., Tews, Ivo

Hen egg-white lysozyme has long been the paradigm for enzymatic glycosyl hydrolysis with retention of configuration, with a protonated carboxylic acid and a deprotonated carboxylate participating in...

Extreme Stabilization of a Thermolysin-like Protease by an Engineered Disulfide Bond (1997)

Ulbrich-Hofmann, Renate, Venema, Gerard, Burg, Bertus Van Den, Veltman, O. Rob, Dijkstra, Bauke W., Vriend, Gert, ...

The thermal inactivation of broad specificity proteases such as thermolysin and subtilisin is initiated by partial unfolding processes that render the enzyme susceptible to autolysis. Previous...

Bacterial lipases for biotechnological applications (1997)

Reetz, Manfred T., Zonta, Albin, Schimossek, Klaus, Werner, Michael, Rosenau, Frank, Dijkstra, Bauke W., ...

Lipase genes originating from the Gram-negative bacteria Serrutiu marcescens and Pseudomonus urruginosa were cloned. S. marcescens lipase was overexpressed in Escherichia coli yielding inclusion...

The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases (1997)

Saier Jr., Milton H., Reizer, Jonathan, Kalk, Kor H., Pijning, Tjaard, ...

Background: The bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS) mediates the energy-driven uptake of carbohydrates and their concomitant phosphorylation. In addition, the PTS...

Three-dimensional Structure of L-2-Haloacid Dehalogenase from Xanthobacter autotrophicus GJ10 Complexed with the Substrate-analogue Formate (1997)

Dijkstra, Bauke W., Janssen, Dick B., Kalk, Kor H., Rozeboom, Henriëtte J., Ridder, Ivo S.

The L-2-haloacid dehalogenase from the 1,2-dichloroethane degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the...

Crystallization and preliminary crystallographic analysis of endo-1,4-β-xylanase I from Aspergillus niger (1996)

Dijkstra, Bauke W., Kalk, Kor H., Rozeboom, Henriëtte J., Krengel, Ute

A family G xylanase from Aspergillus niger has been crystallized using the vapor-diffusion method. Several crystal forms could be obtained using various sodium salts as precipitants. Three of the...

Structure of Cyclodextrin Glycosyltransferase Complexed with a Maltononaose Inhibitor at 2.6 Å Resolution. Implications for Product Specificity (1996)

Dijkhuizen, Lubbert, Kalk, Kor H., Rozeboom, Henriëtte J., Penninga, Dirk, Dijkstra, Bauke W., Knegtel, Ronald M.A., ...

Crystals of the Y195F mutant of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 were subjected to a double soaking procedure, in which they were first soaked in a solution...

The Raw Starch Binding Domain of Cyclodextrin Glycosyltransferase from Bacillus circulans Strain 251 (1996)

Dijkhuizen, Lubbert, Dijkstra, Bauke W., Kalk, Kor H., Rozeboom, Henriëtte J., Knegtel, Ronald M.A., ...

The E-domain of cyclodextrin glycosyltransferase (CGTase) (EC 2.4.1.19) from Bacillus circulans strain 251 is a putative raw starch binding domain. Analysis of the maltose-dependent CGTase crystal...

Crystal Structure at 2.3 Å Resolution and Revised Nucleotide Sequence of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1 (1996)

Buitelaar, Reinetta M., Kalk, Kor H., Rozeboom, Henriëtte J., Wind, Richèle D., Knegtel, Ronald M.A., Dijkhuizen, Lubbert, ...

The crystal structure of the cyclodextrin glycosyltransferase (CGTase) from the thermophilic microorganism Thermoanaerobacterium thermosulfurigenes EM1 has been elucidated at 2.3 Å resolution. The...

Three-dimensional Structure of Endo-1,4-β-xylanase I from Aspergillus niger: Molecular Basis for its Low pH Optimum (1996)

Dijkstra, Bauke W., Krengel, Ute

The crystal structure of endo-1,4-β-xylanase I from Aspergillus niger has been solved by molecular replacement and was refined to 2.4 Å resolution. The final R-factor for all data from 6 to 2.4 Å...

The 1.8 Å Resolution Structure of Hevamine, a Plant Chitinase/Lysozyme, and Analysis of the Conserved Sequence and Structure Motifs of Glycosyl Hydrolase Family 18 (1996)

Dijkstra, Bauke W., Hennig, Michael, Terwisscha Van Scheltinga, Anke C.

The three-dimensional structure of hevamine, a plant enzyme with chitinase and lysozyme activity, has been refined at 1.8 Å resolution to an R-factor of 14.9% and a free R-factor of 19.6%. The final...

Cure for a crisis? (1996)

Dijkstra, Bauke W.

The first look at the three-dimensional structure of an essential penicillin binding protein from a human pathogen, and its complex with a β-lactam antibiotic provides hope for the future design of...

Kinetic Characterization and X-ray Structure of a Mutant of Haloalkane Dehalogenase with Higher Catalytic Activity and Modified Substrate Range (1996)

Poelarends, Gerrit J., Rink, Rick, Ridder, Ivo S., Schanstra, Joost P., Heimeriks, Gaston J., Kalk, Kor H., ...

Conversion of halogenated aliphatics by haloalkane dehalogenase proceeds via the formation of a covalent alkyl-enzyme intermediate which is subsequently hydrolyzed by water. In the wild type enzyme,...

Site-Directed Mutations in Tyrosine 195 of Cyclodextrin Glycosyltransferase from Bacillus circulans Strain 251 Affect Activity and Product Specificity (1995)

Dijkstra, Bauke W., Lawson, Catherine L., Rozeboom, Henriëtte J., Strokopytov, Boris, Penninga, Dirk, Bergsma, Jack, ...

Tyrosine 195 is located in the center of the active site cleft of cyclodextrin glycosyltransferase (EC 2.4.1.19) from Bacillus circulans strain 251. Alignment of amino acid sequences of CGTases and...

X-ray Structure of Cyclodextrin Glycosyltransferase Complexed with Acarbose. Implications for the Catalytic Mechanism of Glycosidases (1995)

Dijkstra, Bauke W., Dijkhuizen, Lubbert, Kalk, Kor H., Rozeboom, Henriëtte J., Penninga, Dirk, Strokopytov, Boris

Crystals of cyclodextrin glycosyltransferase (CGTase) from Bacillus circulans strain 251 were soaked in buffer solutions containing the pseudotetrasaccharide acarbose, a strong amylase- and CGTase...

Stereochemistry of Chitin Hydrolysis by a Plant Chitinase/Lysozyme and X-ray Structure of a Complex with Allosamidin: Evidence for Substrate Assisted Catalysis (1995)

Henrissat, Bernard, Isogai, Akira, Kalk, Kor H., Armand, Sylvie, Terwisscha Van Scheltinga, Anke C., Dijkstra, Bauke W.

The plant enzyme hevamine has both chitinase and lysozyme activity. HPLC analysis of the products of the hydrolysis of chitopentaose shows that hevamine acts with retention of the configuration,...

Structure of the 70-kDa Soluble Lytic Transglycosylase Complexed with Bulgecin A. Implications for the Enzymatic Mechanism (1995)

Dijkstra, Bauke W., Kalk, Kor H., Rozeboom, Henriëtte J.

Bulgecins are O-sulfonated glycopeptides that are able to enhance the antibacterial activity of β-lactam antibiotics. The 70-kDa soluble lytic transglycosylase (SLT70) from Escherichia coli forms a...

Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli (1995)

Verheij, Hubertus M., Dekker, Niek, Blaauw, Mieke, Kalk, Kor H., Dijkstra, Bauke W.

The outer membrane phospholipase A (OMPLA) of Escherichia coli is one of the few integral outer membrane proteins displaying enzymatic activity. It is encoded as a mature protein of 269 amino acids...

Crystallographic Studies of the Interaction of Cyclodextrin Glycosyltransferase from Bacillus circulans Strain 251 with Natural Substrates and Products (1995)

Penninga, Dirk, Strokopytov, Boris, Knegtel, Ronald M.A., Faber, Onno G., Rozeboom, Henriëtte J., Kalk, Kor H., ...

Asp-229, Glu-257, and Asp-328 constitute the catalytic residues in cyclodextrin glycosyl transferase from Bacillus circulans strain 251. Via site-directed mutagenesis constructed D229N, E257Q, and...

Crystal Structure of Concanavalin B at 1.65 Å Resolution. An ‘‘Inactivated’’ Chitinase from Seeds of Canavalia ensiformis (1995)

Schlesier, Bernhard, Dijkstra, Bauke W., Terwisscha Van Scheltinga, Anke C., Jansonius, Johan N., Hennig, Michael

Seeds of Canavalia ensiformis (jack bean) contain besides large amounts of canavalin and concanavalin A, a protein with a molecular mass of 33,800 which has been named concanavalin B. Although...

Purification, Crystallisation and Preliminary X-ray Analysis of Penicillin Binding Protein 4 from Escherichia coli, a Protein Related to Class A β-Lactamases (1995)

Dijkstra, Bauke W., Boer, Bijtske De, Fusetti, Fabrizia

Crystals of the penicillin binding protein 4 (PBP4) from Escherichia coli have been obtained at 37°C from liquid to liquid diffusion experiments in capillaries. PBP4 was dissolved in a 1.0 M...

Crystallization and Preliminary X-Ray Analysis of a Lipase from Staphylococcus hyicus (1995)

Boots, Jan-Willem P., Slotboom, Arend J., Dijkstra, Bauke W., Blaauw, Mieke, Ransac, Stéphane, Verheij, Hubertus M.

Single crystals of a lipase from Staphylococcus hyicus have been obtained using a combination of 18 to 24% dimethylsulfoxide and 10% isopropanol as a precipitant. The crystals grow at 4°C in 2–3...

Drug or tool, design or serendipity? (1995)

Dijkstra, Bauke W.

Iterative protein structure-based ligand design has led to a 'selective' inhibitor of human non-pancreatic secretory phospholipase A2 which provides a new tool for probing metabolic pathways and may...

The Catalytic Domain of a Bacterial Lytic Transglycosylase Defines a Novel Class of Lysozymes (1995)

Dijkstra, Bauke W., Isaacs, Neil W.

The 70-kDa soluble lytic transglycosylase (SLT70) from Escherichia coli is a bacterial exo-muramidase that cleaves the cell wall peptidoglycan, producing 1,6-anhydro-muropeptides. The X-ray structure...

Crystallization and preliminary X-ray analysis of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 (1995)

Dijkstra, Bauke W., Janssen, Dick B., Kingma, Jaap, Rozeboom, Henriëtte J., Ridder, Ivo S.

Haloacid dehalogenases are enzymes that cleave carbon-chlorine or carbon-bromine bonds of 2-haloalkanoates. X-ray-quality crystals of L-2-haloacid dehalogenase from the 1,2-dichloroethane-degrading...

'Holy' proteins II: the soluble lytic transglycosylase (1994)

Dijkstra, Bauke W.

Enzymes involved in the metabolism of the bacterial cell wall peptidoglycan are excellent targets for antibiotics. Penicillins and related β-lactam antibiotics inhibit the enzymes that act on the...

Protein stabilization by hydrophobic interactions at the surface (1994)

Eijsink, Vincent G.H., Venema, Gerard, Dijkstra, Bauke W., Vinne, Bernard Van Der, Vriend, Gert, Burg, Bertus Van Den

The contribution of the solvent-exposed residue 63 to thermal stability of the thermolysin-like neutral protease of Bacillus stearothermophilus was studied by analyzing the effect of twelve different...

Bacterial lipases (1994)

Misset, Onno, Heuvel, Margreet Van, Colson, Charles, Dijkstra, Bauke W., Ransac, Stéphane, Jaeger, Karl-Erich

Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a...

An Optimal Strategy for X-ray Data Collection on Macromolecular Crystals with Position-Sensitive Detectors (1994)

Dijkstra, Bauke W., Drenth, Jan, Kalk, Kor H., Vicković, Ivan

X-ray data collection on macromolecular crystals is preferably done with minimum exposure time and high completeness. A Fortran procedure - DCS - has been written in the environment of the MADNES...

Nucleotide Sequence and X-ray Structure of Cyclodextrin Glycosyltransferase from Bacillus circulans Strain 251 in a Maltose-dependent Crystal Form (1994)

Montfort, Rob Van, Lawson, Catherine L., Strokopytov, Boris, Rozeboom, Henriette J., Kalk, Kor H., Vries, Gert E. De, ...

The cyclodextrin glycosyltransferase (CGTase, EC 2.4.1.19) gene from Bacillus circulans strain 251 was cloned and sequenced. It was found to code for a mature protein of 686 amino acid residues,...

Crystallization and Preliminary X-ray Analysis of a Lipase from Bacillus subtilis (1994)

Dijkstra, Bauke W., Colson, Charles, Schanck, Karin, Lesuisse, Emmanuel, Blaauw, Mieke, Ransac, Stéphane

Single crystals of the lipase from Bacillus subtilis have been obtained using a mixture of polyethylene glycol 4000 and sodium sulphate solution as the precipitant. The crystals grow at room...

Crystallization of Enzyme IIB of the Cellobiose-specific Phosphotransferase System of Escherichia coli (1994)

Reizer, Jonathan, Schuurman-Wolters, Gea K., Kalk, Kor H., Pijning, Tjaard, Safer Jr., Milton H., ...

Crystals of enzyme IIB of the cellobiose-specific phosphotransferase system have been obtained from 15% polyethylene glycol 4000 using both streak-seeding and macroseeding techniques at 4°. Crystals...

Doughnut-shaped structure of a bacterial muramidase revealed by X-ray crystallography (1994)

Keck, Wolfgang, Engel, Henk, Rozeboom, Henriëtte J., Kalk, Kor H., Dijkstra, Arnoud J., ...

The integrity of the bacterial cell wall depends on the balanced action of several peptidoglycan (murein) synthesizing and degrading enzymes. Penicillin inhibits the enzymes responsible for peptide...

Crystal structures of hevamine, a plant defence protein with chitinase and lysozyme activity, and its complex with an inhibitor (1994)

Dijkstra, Bauke W., Beintema, Jaap J., Kalk, Kor H., Terwisscha Van Scheltinga, Anke C.

Background: Hevamine is a member of one of several families of plant chitinases and lysozymes that are important for plant defence against pathogenic bacteria and fungi. The enzyme can hydrolyze the...

The structure-function relationship of the lipases from Pseudomonas aeruginosa and Bacillus subtilis (1994)

Colson, Charles, Winkler, Ulrich, Jaeger, Karl-Erich, Gerritse, Gijs, Misset, Onno, Schanck, Karin, ...

Within the BRIDGE T-project on lipases we investigate the structure-function relationships of the lipases from Bacillus subtilis and Pseudomonas aeruginosa. Construction of an overproducing Bacillus...

The structure-function relationship of the lipases from Pseudomonas aeruginosa and Bacillus subtilis (1994)

Misset, Onno, Gerritse, Gijs, Jaeger, Karl-Erich, Winkler, Ulrich, Colson, Charles, Schanck, Karin, ...

Within the BRIDGE T-project on lipases we investigate the structure-function relationships of the lipases from Bacillus subtilis and Pseudomonas aeruginosa. Construction of an overproducing Bacillus....

Catalytic Mechanism of Haloalkane Dehalogenase: Crystal Structures of Enzyme-Substrate, Alkyl-Enzyme and Enzyme-Product Complexes (1993)

Rozeboom, Henriette, Kalk, Kor H., Verschueren, Koen H.G., Dijkstra, Bauke W.

Topological characterization and modeling of the 3D structure of lipase from Pseudomonas aeruginosa (1993)

Ferrato, Francine, Koch, Heinrich B., Ransac, Stéphane, Dijkstra, Bauke W., Jaeger, Karl-Erich

Lipase from Pseudomonas aeruginosa is a Mr 29 kDa protein with a single functional disulfide bond as shown by a shift in electrophoretic mobility after treatment with dithiothreitol and...

Crystallization of Porcine Liver Ribonuclease Inhibitor a Member of the Family of Proteins Containing Leucine-rich Repeats (1993)

Dijkstra, Bauke W., Arkema, Anita H., Hofsteenge, Jan, Neumann, Ulf

Single crystals of the RNase inhibitor from porcine liver have been obtained from 30 to 34 % saturated ammonium sulphate solutions at pH 6.0 to 7.2, containing 20 mM dithiothreitol, at room...

Crystal Structure of a Porcine Pancreatic Phospholipase A2 Mutant. A Large Conformational Change Caused by the F63V Point Mutation (1993)

Haas, Gerard H. De, Franken, Peet A., Verheij, Hubertus M., Kalk, Kor H., Drenth, Jan, ...

The highly homologous bovine and porcine pancreatic phospholipases A2 (85% amino acid residue identity) show a large conformational difference in the loop from residue 59 to 71. In bovine...

Refined X-ray Structures of Haloalkane Dehalogenase at pH 6.2 and pH 8.2 and Implications for the Reaction Mechanism (1993)

Kalk, Kor H., Rozeboom, Henriëtte J., Franken, Sybille M., Verschueren, Koen H.G., Dijkstra, Bauke W.

The crystal structure of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 has been refined at 1.9 Å resolution at two different pH values, the pH of crystallization (pH 6.2) and the pH...

Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase (1993)

Dijkstra, Bauke W., Kalk, Kor H., Rozeboom, Henriëtte J., Seljée, Frank, Verschueren, Koen H.G.

Crystal structures of haloalkane dehalogenase were determined in the presence of the substrate 1,2-dichloroethane. At pH 5 and 4 °C, substrate is bound in the active site without being converted;...

Introduction of disulfide bonds into Bacillus subtilis neutral protease (1993)

Vinne, Bernard Van Der, Dijkstra, Bauke W., Burg, Bertus Van Den, Stulp, Ben K., Eijsink, Vincent G.H., Venema, Gerard

The effects of engineered disulfide bonds on autodigestion and thermostability of Bacillus subtilis neutral protease (NP-sub) were studied using site-directed mutagenesis. After modelling studies two...

Crystal Structure of a Bacterial Muramidase: The Soluble Lytic Transglycosylase from E. Coli (1993)

Dijkstra, Bauke W., Keck, Wolfgang, Kalk, Kor H., Rozeboom, Henriette, Dijkstra, Arnoud, Thunnissen, Andy-Mark

Crystallographic and Fluorescence Studies of the Interaction of Haloalkane Dehalogenase with Halide Ions. Studies with Halide Compounds Reveal a Halide Binding Site in the Active Site (1993)

Rozeboom, Henriëtte J., Kingma, Jaap, Verschueren, Koen H.G., Kalk, Kor H., Janssen, Dick B., Dijkstra, Bauke W.

Haloalkane dehalogenase from Xanthobacter autotrophicus GJ 10 catalyzes the conversion of 1,2-dichloroethane to 2-chloroethanol and chloride without use of oxygen or cofactors. The active site is...

Introduction of disulfide bonds into Bacillus subtilis neutral protease (1993)

Van Den Burg, Bertus, Dijkstra, Bauke W., Van Der Vinne, Bernard, Stulp, Ben K., Eijsink, Vincent G.H., Venema, Gerard

The effects of engineered disulfide bonds on autodigestion and thermostability of Bacillus subtilis neutral protease (NP-sub) were studied using site-directed mutagenesis. After modelling studies two...

Crystallization of the A-Domain of the Mannitol Transport Protein Enzyme IImtl (1992)

Robillard, George T., Pas, Hendri H., Weeghel, Rob P. Van, Dijkstra, Bauke W., Lammers, Leidy A.

The A-domain of the mannitol transport protein enzyme IImtl from Escherichia coli (relative molecular mass 16,300) was crystallized, both at room temperature and 4°C, from 40% polyethylene glycol...

The effect of cavity-filling mutations on the thermostability of Bacillus stearothermophilus neutral protease (1992)

Veltman, Oene R., Vriend, Gerrit, Dijkstra, Bauke W., Eijsink, Vincent G.H., Vinne, B. Van Der, ...

Cavities in the hydrophobic core of the neutral protease of Bacillus stearothermophilus were analyzed using a three-dimensional model that was inferred from the crystal structure of thermolysin, the...

Site-directed mutagenesis and X-ray crystallography of two phospholipase A2 mutants: Y52F and Y73F (1992)

Verheij, Hubertus M., Kalk, Kor H., Drenth, Jan, Haas, Gerard H. De, Dijkstra, Bauke W., Franken, Peet A., ...

Tyr52 and Tyr73 are conserved amino acid residues throughout all vertebrate phospholipases A2. They are part of an extended hydrogen bonding system that links the N-terminal α-NH3+-group to the...

The effect of cavity-filling mutations on the thermostability of Bacillus stearothermophilus neutral protease (1992)

Eijsink, Vincent G.H., Dijkstra, Bauke W., Vriend, Gerrit, Van Der Zee, J.Rob, Vettman, Oene R., ...

Cavities in the hydrophobic core of the neutral protease of Bacillus stearothermophilus were analyzed using a threedimensional model that was inferred from the crystal structure of thermolysin, the...

Crystal structure of haloalkane dehalogenase: an enzyme to detoxify halogenated alkanes (1991)

Dijkstra, Bauke W., Kalk, Kor H., Rozeboom, Henriette J., Franken, Sybille M.

Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 converts 1-haloalkanes to the corresponding alcohols and halide ions with water as the sole cosubstrate and without any need for oxygen or...

Homology modelling and protein engineering strategy of subtilases, the family of subtilisin-like serine proteinases (1991)

Leunissen, Jack A.M., Vos, Willem M. De, Dijkstra, Bauke W., Siezen, Roland J.

Subtilases are members of the family of subtilisin-like serine proteases. Presently, >50 subtilases are known, >40 of which with their complete amino acid sequences. We have compared these sequences...

Homology modelling and protein engineering strategy of subtilases, the family of subtilisin-like serine proteinases (1991)

Siezen, Roland J., De Vos, William M., Leunissen, Jack A.M., Dijkstra, Bauke W.

Subtilases are members of the family of subtilisin-like serine proteases. Presently, ≥50 subtilases are known, ≥40 of which with their complete amino acid sequences. We have compared these...

Maltodextrin-dependent Crystallization of Cyclomaltodextrin Glucanotransferase from Bacillus circulans (1990)

Bruinenberg, Peter M., Bergsma, Jack, Lawson, Catherine L., Vries, Gert De, Dijkhuizen, Lubbert, Dijkstra, Bauke W.

Crystals of cyclomaltodextrin glucanotransferase from Bacillus circulans (EC 2.4.1.19) suitable for high-resolution X-ray analysis were obtained by vapor diffusion against 60% (v/v) 2-methyl...

Crystallization of Hevamine, an Enzyme with Lysozyme/Chitinase Activity from Hevea brasiliensis Latex (1990)

Dijkstra, Bauke W., Beintema, Jaap J., Budiani, Asmini, Rozeboom, Henriëtte J.

Hevamine, an enzyme with both lysozyme and chitinase activity, was isolated and purified from Hevea brasiliensis (rubber tree) latex. The enzyme (molecular weight 29,000) is homologous to certain...

Crystallization of the Soluble Lytic Transglycosylase from Escherichia coli K12 (1990)

Dijkstra, Bauke W., Rozeboom, Henriette J., Engel, Henk, Keck, Wolfgang

Lytic transglycosylases degrade the murein polymer of the bacterial cell wall to 1,6-anhydromuropeptides. These enzymes are of significant medical interest, not only because they are ideal targets...

Structure of an Engineered Porcine Phospholipase A2 with Enhanced Activity at 2.1 Å Resolution. Comparison with the Wild-type Porcine and Crotalus atrox Phospholipase A2 (1990)

Drenth, Jan, Kalk, Kor H., Dijkstra, Bauke W.

The crystal structure of an engineered phospholipase A2 with enhanced activity has been refined to an R-factor of 18.6% at 2.1 Å resolution using a combination of molecular dynamics refinement by...

X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor (1990)

Kalk, Kor H., AB, Eiso, Drenth, Jan, Dijkstra, Bauke W., Kuipers, Oscar P., ...

Phospholipases A2 play a part in a number of physiologically important cellular processes such as inflammation, blood platelet aggregation and acute hypersensitivity. These processes are all...

Crystallographic Refinement by Incorporation of Molecular Dynamics: Thermostable Serine Protease Thermitase Complexed with Eglin c (1989)

Hol, Wim G.J., Kalk, Kor H., Dijkstra, Bauke W., Fujinaga, Masao, Gros, Piet

In order to investigate the principles of protein thermostability, the crystal structure of thermitase from Thermoactinomyces vulgaris, a thermostable member of the subtilisin family of serine...

Use of electron microscopy in the examination of lattice defects in crystals of alcohol oxidase (1989)

Rozeboom, Henriëtte, Lawson, Catherine L., Dijkstra, Bauke W., Veenhuis, Marten, Harder, Wim, ...

Alcohol oxidase, purified from the yeast Hansenula polymorpha, was crystallized in vitro for the purpose of determining its structure at atomic resolution by X-ray diffraction methods. The crystals...

Enhanced Activity and Altered Specificity of Phospholipase A2 by Deletion of a Surface Loop (1989)

Dijkstra, Bauke W., Geus, Pieter De, Kuipers, Oscar P., Drenth, Jan, Verheij, Hubertus M., ...

Protein engineering and x-ray crystallography have been used to study the role of a surface loop that is present in pancreatic phospholipases but is absent in snake venom phospholipases. Removal of...

Crystal Structure of Bovine Pancreatic Phospholipase A2 Covalently Inhibited by p-Bromo-phenacyl-bromide (1988)

Drenth, Jan, Kalk, Kor H., Huizinga, Kees, Dijkstra, Bauke W., Renetseder, Roland

Bovine pancreatic phospholipase A2 covalently inhibited by p-bromo-phenacyl-bromide was crystallized from 50% (v/v) 2-methyl-2,4-pentanediol. The space group was P3121 with cell dimensions a = b =...

Model building of disulfide bonds in proteins with known three-dimensional structure (1988)

Dijkstra, Bauke W., Hazes, Bart

As an aid in the selection of sites in a protein where a disulfide bond might be engineered, a computer program has been developed. The algorithm starts with the generation of Cβ positions from the...

Crystallization of Haloalkane Dehalogenase from Xanthobacter autotrophicus GJ10 (1988)

Dijkstra, Bauke W., Janssen, Dick B., Kingma, Jaap, Rozeboom, Henriëtte J.

Haloalkane dehalogenases are enzymes that release chloride or bromide from n-halogenated alkanes. X-ray quality crystals of haloalkane dehalogenase from the 1,2-dichloroethane-degrading bacterium...

Model building of disulfide bonds in proteins with known three-dimensional structure (1988)

Hazes, Bart, Dijkstra, Bauke W.

As an aid in the selection of sites in a protein where a disulfide bond might be engineered, a computer program has been developed. The algorithm starts with the generation of Cβ positions from the...

Bovine Phospholipase A2 Crystals Soaked in 30% Methanol: the First Structure Determination with a FAST Diffractometer at High Resolution (1986)

Drenth, Jan, Kalk, Kor H., Dijkstra, Bauke W., Renetseder, Roland, Verpoorte, Jaap

Data collection has always been a time-consuming operation in protein X-ray crystallography. This situation drastically changed with the introduction of two-dimensional area detectors. In this...

A Comparison of the Crystal Structures of Phospholipase A2 from Bovine Pancreas and Crotalus atrox Venom (1985)

Sigler, Paul B., Drenth, Jan, Dijkstra, Bauke W., Brunie, Simone, Renetseder, Roland

The refined high resolution crystal structure of the bovine phospholipase A2 was compared with its counterpart from the venom of Crotalus atrox, the western diamondbacked rattlesnake. The strong...

Role of the N-Terminus in the Interaction of Pancreatic Phospholipase A2 with Aggregated Substrates. Properties and Crystal Structure of Transaminated Phospholipase A2 (1984)

Haas, Gerard H. De, Drenth, Jan, Kalk, Kor H., Dijkstra, Bauke W., Egmond, Maarten R., Slotboom, Arend J.

A free N-terminal α-NH3+ group is absolutely required for full catalytic activity of phospholipase A2 on aggregated substrates. To elucidate how this α-NH3+ group triggers catalytic activity, we...

Natural-Abundance 13C-NMR Spectroscopy of Two Glyco-asparagines Derived from the Core of N-Glycosidic Carbohydrate Chains (1983)

Montreuil, Jean, Strecker, Gérard, Vliegenthart, Johannes F.G., Dijkstra, Bauke W.

13C-NMR spectroscopic studies were carried out on Manα(1→6)Manβ(1→4)GlcNAcβ(1→4)GlcNAcβ(1→N)Asn and Manα(1→6)Manβ(1→4)GlcNAcβ(1→4)[Fucα(1→6)]GlcNAcβ(1→N)Asn, which are part...

Polypeptide chains with similar amino acid sequences but a distinctly different conformation. Bovine and porcine phospholipase A2 (1983)

Wierenga, Rik K., Weijer, Wicher J., Dijkstra, Bauke W.

The primary structures of bovine and porcine pancreatic phospholipase A2 differ only by about 15%. Nevertheless, a 12 residue loop, with only one substitution (Val→Phe) has a quite different...

Structure of Porcine Pancreatic Phospholipase A2 at 2.6 Å Resolution and Comparison with Bovine Phospholipase A2 (1983)

Hol, Wim G.J., Kalk, Kor H., Renetseder, Roland, Dijkstra, Bauke W., Drenth, Jan

The previously published three-dimensional structure of porcine pancreatic prophospholipase A2 at 3 Å resolution was found to be incompatible with the structures of bovine phospholipase A2 and...

The Structure of Bovine Pancreatic Prophospholipase A2 at 3.0 Å Resolution (1982)

Kalk, Kor H., Dijkstra, Bauke W., Brandenburg, Niko P., Hol, Wim G.J., Drenth, Jan

Bovine pancreatic prophospholipase A2, the precursor of the lipolytic enzyme phospholipase A2, crystallizes in space group P3121 with cell dimensions a = b = 46.95, c = 102.0 Å. The structure was...

Structure of Bovine Pancreatic Phospholipase A2 at 1.7Å Resolution (1981)

Hol, Wim G.J., Kalk, Kor H., Dijkstra, Bauke W., Drenth, Jan

The crystal structure of bovine pancreatic phospholipase A2 has been refined to 1.7 Å resolution. The starting model for this refinement was the previously published structure at a resolution of 2.4...

Active site and catalytic mechanism of phospholipase A2 (1981)

Kalk, Kor H., Dijkstra, Bauke W., Drenth, Jan

The esterolytic enzyme phospholipase A2 specifically splits the 2-acyl linkage of phosphoglycerides in a calcium-dependent reaction. In the pancreas the enzyme occurs as a zymogen which is activated...

Three-dimensional Structure and Disulfide Bond Connections in Bovine Pancreatic Phospholipase A2 (1978)

Vandermaelen, Philip J., Kalk, Kor H., Drenth, Jan, Dijkstra, Bauke W.

Bovine pancreatic phospholipase A2 (Mr = 14,000) has been crystallized and its three-dimensional structure determined by X-ray diffraction analysis to a resolution of 2.4 Å. Three heavy-atom...

Crystallization and preliminary crystallographic analysis of an esterase with a novel domain from the hyperthermophile Thermotoga maritima

Sun, Lei, Levisson, Mark, Hendriks, Sjon, Akveld, Twan, Kengen, Servé W. M., Dijkstra, Bauke W., ...

A thermostable esterase (EstA) from Thermotoga maritima was cloned and purified. Crystals of EstA and its selenomethionine derivative were grown and diffract to beyond 2.6 Å resolution at 100 K...

Purification, crystallization and preliminary X-ray analysis of a thermostable glycoside hydrolase family 43 β-xylosidase from Geobacillus thermoleovorans IT-08

Rohman, Ali, Van Oosterwijk, Niels, Kralj, Slavko, Dijkhuizen, Lubbert, Dijkstra, Bauke W., Puspaningsih, Ni Nyoman Tri

The β-xylosidase was crystallized using PEG 6000 as precipitant. 5% PEG 6000 yielded bipyramid-shaped tetragonal crystals diffracting to 1.55 Å resolution, and 13% PEG 6000 gave rectangular...