Rebecca D. Miles, Prabha P. Iyer, James G. Ferry, Chcocoa Pi, Chcopo Coa
Acetate kinase catalyzes the magnesium-dependent transfer of the γ-phosphate of ATP to acetate. The recently determined crystal structure of the M. thermophila enzyme identifies it as a member of...
The Stepwise Evolution of Early Life Driven by Energy Conservation (2006)
Ferry, James G., House, Christopher H.
Two main theories have emerged for the origin and early evolution of life based on heterotrophic versus chemoautotrophic metabolisms. With the exception of a role for CO, the theories have little...
The Step-Wise Evolution of Early Life Driven by Energy Conservation (2006)
Ferry, James G., House, Christopher H.
Two main theories have emerged for the origin and early evolution of life based on heterotrophic versus chemoautotrophic metabolisms. With the exception of a role for CO, the theories have little...
Andrade, Susana L. A., Cruz, Francisco, Drennan, Catherine L., Ramakrishnan, Vijay, Rees, Douglas C., Ferry, James G., ...
Iron-sulfur flavoproteins (ISF) constitute a widespread family of redox-active proteins in anaerobic prokaryotes. Based on sequence homologies, their overall structure is expected to be similar to...
Trace methane oxidation studied in several Euryarchaeota under diverse conditions (2005)
James J. Moran, Christopher H. House, Katherine H. Freeman, James G. Ferry
We used 13C-labeled methane to document the extent of trace methane oxidation by Archaeoglobus fulgidus, Archaeoglobus lithotrophicus, Archaeoglobus profundus, Methanobacterium thermoautotrophicum,...
Carbonic anhydrase is an ancient enzyme widespread in prokaryotes
Smith, Kerry S., Jakubzick, Claudia, Whittam, Thomas S., Ferry, James G.
Carbonic anhydrases catalyze the reversible hydration of CO2 and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (γ class) in a...
O-Acetylserine Sulfhydrylase from Methanosarcina thermophila
Borup, Birthe, Ferry, James G.
Cysteine is the major source of fixed sulfur for the synthesis of sulfur-containing compounds in organisms of the Bacteria and Eucarya domains. Though pathways for cysteine biosynthesis have been...
Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases
Buss, Kathryn A., Cooper, David R., Ingram-Smith, Cheryl, Ferry, James G., Sanders, David Avram, Hasson, Miriam S.
Acetate kinase, an enzyme widely distributed in the Bacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina...
Iyer, Prabha P., Ferry, James G.
Phosphotransacetylase (EC 2.3.1.8) catalyzes the reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA): CH3COOPO32− + CoASH ⇆ CH3COSCoA + HPO42−. The role of...
Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases
Buss, Kathryn A., Cooper, David R., Ingram-Smith, Cheryl, Ferry, James G., Sanders, David Avram, Hasson, Miriam S.
Zhao, Tong, Cruz, Francisco, Ferry, James G.
A total of 35 homologs of the iron-sulfur flavoprotein (Isf) from Methanosarcina thermophila were identified in databases. All three domains were represented, and multiple homologs were present in...
Smith, Kerry S., Ferry, James G.
Carbonic anhydrase, a zinc enzyme catalyzing the interconversion of carbon dioxide and bicarbonate, is nearly ubiquitous in the tissues of highly evolved eukaryotes. Here we report on the first known...
Identification of Essential Glutamates in the Acetate Kinase from Methanosarcina thermophila
Singh-Wissmann, Kavita, Ingram-Smith, Cheryl, Miles, Rebecca D., Ferry, James G.
Acetate kinase catalyzes the reversible phosphorylation of acetate (CH3COO− + ATP⇄CH3CO2PO32− + ADP). A mechanism which involves a covalent phosphoryl-enzyme intermediate has been proposed, and...
Maupin-Furlow, Julie A., Aldrich, Henry C., Ferry, James G.
The 20S proteasome from the methanoarchaeon Methanosarcina thermophila was produced in Escherichia coli and characterized. The biochemical properties revealed novel features of the archaeal 20S...
Identification of Essential Glutamates in the Acetate Kinase from Methanosarcina thermophila
Singh-Wissmann, Kavita, Ingram-Smith, Cheryl, Miles, Rebecca D., Ferry, James G.
Leartsakulpanich, Ubolsree, Antonkine, Mikhail L., Ferry, James G.
Isf (iron-sulfur flavoprotein) from Methanosarcina thermophila has been produced in Escherichia coli as a dimer containing two 4Fe-4S clusters and two FMN (flavin mononucleotide) cofactors. The...
Structural and Kinetic Characterization of an Archaeal β-Class Carbonic Anhydrase
Smith, Kerry S., Cosper, Nathaniel J., Stalhandske, Christina, Scott, Robert A., Ferry, James G.
The β-class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum (Cab) was structurally and kinetically characterized. Analytical ultracentrifugation experiments show that Cab...
Smith, Kerry S., Ingram-Smith, Cheryl, Ferry, James G.
The roles of an aspartate and an arginine, which are completely conserved in the active sites of β-class carbonic anhydrases, were investigated by steady-state kinetic analyses of replacement...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Production and Consumption of H2 during Growth of Methanosarcina spp. on Acetate
Lovley, Derek R., Ferry, James G.
Methanosarcina sp. strain TM-1 and Methanosarcina acetivorans produced and consumed H2 to maintain H2 partial pressures of 16 to 92 Pa in closed cultures during growth on acetate. Strain TM-1...
Sowers, Kevin R., Baron, Stephen F., Ferry, James G.
A new acetotrophic marine methane-producing bacterium that was isolated from the methane-evolving sediments of a marine canyon is described. Exponential phase cultures grown with sodium acetate...
Effect of Monensin on Growth and Methanogenesis of Methanobacterium formicicum
Dellinger, Carole A., Ferry, James G.
Monensin inhibited methanogenesis from formate but not from H2-CO2 by resting-cell suspensions of Methanobacterium formicicum. The antibiotic severely inhibited growth on formate. The lag phase of...
Kinetics of Formate Metabolism in Methanobacterium formicicum and Methanospirillum hungatei
Schauer, Neil L., Brown, David P., Ferry, James G.
The kinetics of formate metabolism in Methanobacterium formicicum and Methanospirillum hungatei were studied with log-phase formate-grown cultures. The progress of formate degradation was followed by...
Sowers, Kevin R., Ferry, James G.
A new genus of marine methanogenic bacteria is described that utilizes trimethylamine, diethylamine, monomethylamine, and methanol as substrates for growth and methanogenesis. Methane was not...
Flavin Mononucleotide-Binding Flavoprotein Family in the Domain Archaea
Ding, Yan-Huai R., Ferry, James G.
The protein (AfpA, for archaeoflavoprotein) encoded by AF1518 in the genome of Archaeoglobus fulgidus was produced in Escherichia coli and characterized. AfpA was found to be a homodimer with a...
Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase
Ingram-Smith, Cheryl, Gorrell, Andrea, Lawrence, Sarah H., Iyer, Prabha, Smith, Kerry, Ferry, James G.
Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP γ-phosphoryl group to acetate. Inspection of the crystal structure of the...
Andrade, Susana L. A., Cruz, Francisco, Drennan, Catherine L., Ramakrishnan, Vijay, Rees, Douglas C., Ferry, James G., ...
Iron-sulfur flavoproteins (ISF) constitute a widespread family of redox-active proteins in anaerobic prokaryotes. Based on sequence homologies, their overall structure is expected to be similar to...
Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase
Ingram-Smith, Cheryl, Gorrell, Andrea, Lawrence, Sarah H., Iyer, Prabha, Smith, Kerry, Ferry, James G.
Li, Qingbo, Li, Lingyun, Rejtar, Tomas, Lessner, Daniel J., Karger, Barry L., Ferry, James G.
A liquid chromatography-hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometry approach was used to determine the differential abundance of proteins in acetate-grown cells...
Lawrence, Sarah H., Luther, Kelvin B., Schindelin, Hermann, Ferry, James G.
Phosphotransacetylase (EC 2.3.1.8) catalyzes reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. Two crystal structures of...
Steady-State Kinetic Analysis of Phosphotransacetylase from Methanosarcina thermophila
Lawrence, Sarah H., Ferry, James G.
Phosphotransacetylase (EC 2.3.1.8) catalyzes the reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. A steady-state kinetic...
WrbA from Escherichia coli and Archaeoglobus fulgidus Is an NAD(P)H:Quinone Oxidoreductase
Patridge, Eric V., Ferry, James G.
WrbA (tryptophan [W] repressor-binding protein) was discovered in Escherichia coli, where it was proposed to play a role in regulation of the tryptophan operon; however, this has been put in...
Carbonic anhydrase is an ancient enzyme widespread in prokaryotes
Smith, Kerry S., Jakubzick, Claudia, Whittam, Thomas S., Ferry, James G.
Carbonic anhydrases catalyze the reversible hydration of CO2 and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (γ class) in a...
O-Acetylserine Sulfhydrylase from Methanosarcina thermophila
Borup, Birthe, Ferry, James G.
Cysteine is the major source of fixed sulfur for the synthesis of sulfur-containing compounds in organisms of the Bacteria and Eucarya domains. Though pathways for cysteine biosynthesis have been...
Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases
Buss, Kathryn A., Cooper, David R., Ingram-Smith, Cheryl, Ferry, James G., Sanders, David Avram, Hasson, Miriam S.
Acetate kinase, an enzyme widely distributed in the Bacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina...
Iyer, Prabha P., Ferry, James G.
Phosphotransacetylase (EC 2.3.1.8) catalyzes the reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA): CH3COOPO32− + CoASH ⇆ CH3COSCoA + HPO42−. The role of...
Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases
Buss, Kathryn A., Cooper, David R., Ingram-Smith, Cheryl, Ferry, James G., Sanders, David Avram, Hasson, Miriam S.
Zhao, Tong, Cruz, Francisco, Ferry, James G.
A total of 35 homologs of the iron-sulfur flavoprotein (Isf) from Methanosarcina thermophila were identified in databases. All three domains were represented, and multiple homologs were present in...
Smith, Kerry S., Ferry, James G.
Carbonic anhydrase, a zinc enzyme catalyzing the interconversion of carbon dioxide and bicarbonate, is nearly ubiquitous in the tissues of highly evolved eukaryotes. Here we report on the first known...
Identification of Essential Glutamates in the Acetate Kinase from Methanosarcina thermophila
Singh-Wissmann, Kavita, Ingram-Smith, Cheryl, Miles, Rebecca D., Ferry, James G.
Acetate kinase catalyzes the reversible phosphorylation of acetate (CH3COO− + ATP⇄CH3CO2PO32− + ADP). A mechanism which involves a covalent phosphoryl-enzyme intermediate has been proposed, and...
Maupin-Furlow, Julie A., Aldrich, Henry C., Ferry, James G.
The 20S proteasome from the methanoarchaeon Methanosarcina thermophila was produced in Escherichia coli and characterized. The biochemical properties revealed novel features of the archaeal 20S...
Identification of Essential Glutamates in the Acetate Kinase from Methanosarcina thermophila
Singh-Wissmann, Kavita, Ingram-Smith, Cheryl, Miles, Rebecca D., Ferry, James G.
Leartsakulpanich, Ubolsree, Antonkine, Mikhail L., Ferry, James G.
Isf (iron-sulfur flavoprotein) from Methanosarcina thermophila has been produced in Escherichia coli as a dimer containing two 4Fe-4S clusters and two FMN (flavin mononucleotide) cofactors. The...
Structural and Kinetic Characterization of an Archaeal β-Class Carbonic Anhydrase
Smith, Kerry S., Cosper, Nathaniel J., Stalhandske, Christina, Scott, Robert A., Ferry, James G.
The β-class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum (Cab) was structurally and kinetically characterized. Analytical ultracentrifugation experiments show that Cab...
Smith, Kerry S., Ingram-Smith, Cheryl, Ferry, James G.
The roles of an aspartate and an arginine, which are completely conserved in the active sites of β-class carbonic anhydrases, were investigated by steady-state kinetic analyses of replacement...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Production and Consumption of H2 during Growth of Methanosarcina spp. on Acetate
Lovley, Derek R., Ferry, James G.
Methanosarcina sp. strain TM-1 and Methanosarcina acetivorans produced and consumed H2 to maintain H2 partial pressures of 16 to 92 Pa in closed cultures during growth on acetate. Strain TM-1...
Sowers, Kevin R., Baron, Stephen F., Ferry, James G.
A new acetotrophic marine methane-producing bacterium that was isolated from the methane-evolving sediments of a marine canyon is described. Exponential phase cultures grown with sodium acetate...
Effect of Monensin on Growth and Methanogenesis of Methanobacterium formicicum
Dellinger, Carole A., Ferry, James G.
Monensin inhibited methanogenesis from formate but not from H2-CO2 by resting-cell suspensions of Methanobacterium formicicum. The antibiotic severely inhibited growth on formate. The lag phase of...
Kinetics of Formate Metabolism in Methanobacterium formicicum and Methanospirillum hungatei
Schauer, Neil L., Brown, David P., Ferry, James G.
The kinetics of formate metabolism in Methanobacterium formicicum and Methanospirillum hungatei were studied with log-phase formate-grown cultures. The progress of formate degradation was followed by...
Sowers, Kevin R., Ferry, James G.
A new genus of marine methanogenic bacteria is described that utilizes trimethylamine, diethylamine, monomethylamine, and methanol as substrates for growth and methanogenesis. Methane was not...
Flavin Mononucleotide-Binding Flavoprotein Family in the Domain Archaea
Ding, Yan-Huai R., Ferry, James G.
The protein (AfpA, for archaeoflavoprotein) encoded by AF1518 in the genome of Archaeoglobus fulgidus was produced in Escherichia coli and characterized. AfpA was found to be a homodimer with a...
Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase
Ingram-Smith, Cheryl, Gorrell, Andrea, Lawrence, Sarah H., Iyer, Prabha, Smith, Kerry, Ferry, James G.
Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP γ-phosphoryl group to acetate. Inspection of the crystal structure of the...
Andrade, Susana L. A., Cruz, Francisco, Drennan, Catherine L., Ramakrishnan, Vijay, Rees, Douglas C., Ferry, James G., ...
Iron-sulfur flavoproteins (ISF) constitute a widespread family of redox-active proteins in anaerobic prokaryotes. Based on sequence homologies, their overall structure is expected to be similar to...
Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase
Ingram-Smith, Cheryl, Gorrell, Andrea, Lawrence, Sarah H., Iyer, Prabha, Smith, Kerry, Ferry, James G.
Li, Qingbo, Li, Lingyun, Rejtar, Tomas, Lessner, Daniel J., Karger, Barry L., Ferry, James G.
A liquid chromatography-hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometry approach was used to determine the differential abundance of proteins in acetate-grown cells...
Lawrence, Sarah H., Luther, Kelvin B., Schindelin, Hermann, Ferry, James G.
Phosphotransacetylase (EC 2.3.1.8) catalyzes reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. Two crystal structures of...
Steady-State Kinetic Analysis of Phosphotransacetylase from Methanosarcina thermophila
Lawrence, Sarah H., Ferry, James G.
Phosphotransacetylase (EC 2.3.1.8) catalyzes the reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. A steady-state kinetic...
WrbA from Escherichia coli and Archaeoglobus fulgidus Is an NAD(P)H:Quinone Oxidoreductase
Patridge, Eric V., Ferry, James G.
WrbA (tryptophan [W] repressor-binding protein) was discovered in Escherichia coli, where it was proposed to play a role in regulation of the tryptophan operon; however, this has been put in...
Lessner, Daniel J., Li, Lingyun, Li, Qingbo, Rejtar, Tomas, Andreev, Victor P., Reichlen, Matthew, ...
Methanosarcina acetivorans produces acetate, formate, and methane when cultured with CO as the growth substrate [Rother M, Metcalf WW (2004) Proc Natl Acad Sci USA 101:16929–16934], which suggests...
Lessner, Daniel J., Ferry, James G.
Methanosarcina acetivorans, a strictly anaerobic methane-producing species belonging to the domain Archaea, contains a gene cluster annotated with homologs encoding oxidative stress proteins. One of...
Crystal Structure of the NADH:Quinone Oxidoreductase WrbA from Escherichia coli▿
Andrade, Susana L. A., Patridge, Eric V., Ferry, James G., Einsle, Oliver
The flavoprotein WrbA, originally described as a tryptophan (W) repressor-binding protein in Escherichia coli, has recently been shown to exhibit the enzymatic activity of a NADH:quinone...
Trace methane oxidation studied in several Euryarchaeota under diverse conditions
Moran, James J., House, Christopher H., Freeman, Katherine H., Ferry, James G.
We used 13C-labeled methane to document the extent of trace methane oxidation by Archaeoglobus fulgidus, Archaeoglobus lithotrophicus, Archaeoglobus profundus, Methanobacterium thermoautotrophicum,...