The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism

Gibson, Marcus I.; Brignole, Edward J.; Pierce, Elizabeth; Can, Mehmet; Ragsdale, Stephen W.; Drennan, Catherine L.

doi:10.1021/acs.biochem.5b00521

Title: The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism

Authors:

Gibson, Marcus I. ^[1]; Brignole, Edward J. ^[2]; Pierce, Elizabeth ^[3]; Can, Mehmet ^[3]; Ragsdale, Stephen W. ^[3]; Drennan, Catherine L. ^[4]

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States, Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States

Publication Date:: Wed Jun 24 00:00:00 EDT 2015

Research Org.:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Org.:: USDOE; NSFNIHHHMI

OSTI Identifier:: 1188511

Alternate Identifier(s):: OSTI ID: 1194213

Grant/Contract Number:: AC02-06CH11357

Resource Type:: Published Article

Journal Name:: Biochemistry

Additional Journal Information:: Journal Name: Biochemistry Journal Volume: 54 Journal Issue: 26; Journal ID: ISSN 0006-2960

Publisher:: American Chemical Society

Country of Publication:: United States

Language:: English

Citation Formats


                    Gibson, Marcus I., Brignole, Edward J., Pierce, Elizabeth, Can, Mehmet, Ragsdale, Stephen W., and Drennan, Catherine L. The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism.  United States: N. p., 2015. 
Web.  doi:10.1021/acs.biochem.5b00521.

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                    Gibson, Marcus I., Brignole, Edward J., Pierce, Elizabeth, Can, Mehmet, Ragsdale, Stephen W., & Drennan, Catherine L. The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism.  United States.  https://doi.org/10.1021/acs.biochem.5b00521

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                    Gibson, Marcus I., Brignole, Edward J., Pierce, Elizabeth, Can, Mehmet, Ragsdale, Stephen W., and Drennan, Catherine L. Wed .  
"The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism".  United States.  https://doi.org/10.1021/acs.biochem.5b00521.

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@article{osti_1188511,

  title        = {The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism},

  author       = {Gibson, Marcus I. and Brignole, Edward J. and Pierce, Elizabeth and Can, Mehmet and Ragsdale, Stephen W. and Drennan, Catherine L.},

  abstractNote = {},

  doi          = {10.1021/acs.biochem.5b00521},

  journal      = {Biochemistry},

  number       = 26,

  volume       = 54,

  place        = {United States},

  year         = {Wed Jun 24 00:00:00 EDT 2015},

  month        = {Wed Jun 24 00:00:00 EDT 2015}

}

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Title: The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism

Citation Formats

Bioenergetic Strategies of the Sulfate-Reducing Bacteria book, January 1993

Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate journal, February 2006

CHAINSAW : a program for mutating pdb files used as templates in molecular replacement journal, April 2008

Bacillus subtilis YvrK Is an Acid-Induced Oxalate Decarboxylase journal, January 2000

The inactivation of yeast enolase by 2,3-butanedione journal, September 1978

A single eubacterial origin of eukaryotic pyruvate: ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes journal, September 1999

Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation journal, May 2009

Burst Kinetics and Redox Transformations of the Active Site Manganese Ion in Oxalate Oxidase journal, March 2007

A new least-squares refinement technique based on the fast Fourier transform algorithm journal, September 1978

Oxalate Oxidase from Barley Roots: Purification to Homogeneity and Study of Some Molecular, Catalytic, and Binding Properties journal, April 1997

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage journal, May 2012

Molecular Characterization of the Oxalate Oxidase Involved in the Response of Barley to the Powdery Mildew Fungus1 journal, May 1998

Autotrophic CO2 fixation in Chlorobium limicola. Evidence for the operation of a reductive tricarboxylic acid cycle in growing cells journal, November 1980

Reduction of nitroimidazole derivatives by hydrogenosomal extracts of Trichomonas vaginalis journal, January 1985

Evolutionary Analysis of the TPP-Dependent Enzyme Family journal, November 2007

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life? journal, October 2011

Oxalate metabolism by the acetogenic bacterium Moorella thermoacetica journal, February 2004

Carbon Assimilation by Pseudomonas Oxalaticus (ox 1). 7. Decarboxylation of Oxalyl-Coenzyme a to Formyl-Coenzyme a journal, December 1963

Pulsed Electron Paramagnetic Resonance Experiments Identify the Paramagnetic Intermediates in the Pyruvate Ferredoxin Oxidoreductase Catalytic Cycle journal, March 2006

Characterization of recombinant barley oxalate oxidase expressed by Pichia pastoris journal, July 2001

Enzymatic Decarboxylation of Oxalic acid journal, September 1956

More examples of the 15-crown-5...H 2 O— M —OH 2 ...15-crown-5 motif, M = Al 3+ , Cr 3+ and Pd 2+ journal, March 2010

Crystallographic Snapshots of Cyanide- and Water-Bound C-Clusters from Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase , journal, August 2009

A stable free radical intermediate in the reaction of 2-oxoacid:ferredoxin oxidoreductases of Halobacterium halobium journal, September 1980

Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima. journal, January 1996

Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase journal, December 2001

Is a Hydrophobic Amino Acid Required To Maintain the Reactive V Conformation of Thiamin at the Active Center of Thiamin Diphosphate-Requiring Enzymes? Experimental and Computational Studies of Isoleucine 415 of Yeast Pyruvate Decarboxylase † journal, September 1998

Consistent Estimation of Gibbs Energy Using Component Contributions journal, July 2013

Evidence for the key position of pyruvate synthase in the assimilation of CO 2 by Chlorobium journal, April 1978

Influence of nitrate on oxalate- and glyoxylate-dependent growth and acetogenesis by Moorella thermoacetica journal, December 2002

Clostridial pyruvate oxidoreductase and the pyruvate-oxidizing enzyme specific to nitrogen fixation in Klebsiella pneumoniae are similar enzymes. journal, August 1987

Improved Fourier coefficients for maps using phases from partial structures with errors journal, May 1986

[20] Processing of X-ray diffraction data collected in oscillation mode book, January 1997

Identification and Characterization of Oxalate Oxidoreductase, a Novel Thiamine Pyrophosphate-dependent 2-Oxoacid Oxidoreductase That Enables Anaerobic Growth on Oxalate journal, October 2010

Phaser crystallographic software journal, July 2007

Bioenergetic Strategies of the Sulfate-Reducing Bacteria
book, January 1993

Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate
journal, February 2006

CHAINSAW : a program for mutating pdb files used as templates in molecular replacement
journal, April 2008

Bacillus subtilis YvrK Is an Acid-Induced Oxalate Decarboxylase
journal, January 2000

The inactivation of yeast enolase by 2,3-butanedione
journal, September 1978

A single eubacterial origin of eukaryotic pyruvate: ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes
journal, September 1999

Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation
journal, May 2009

Burst Kinetics and Redox Transformations of the Active Site Manganese Ion in Oxalate Oxidase
journal, March 2007

A new least-squares refinement technique based on the fast Fourier transform algorithm
journal, September 1978

Oxalate Oxidase from Barley Roots: Purification to Homogeneity and Study of Some Molecular, Catalytic, and Binding Properties
journal, April 1997

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
journal, May 2012

Molecular Characterization of the Oxalate Oxidase Involved in the Response of Barley to the Powdery Mildew Fungus1
journal, May 1998

Autotrophic CO2 fixation in Chlorobium limicola. Evidence for the operation of a reductive tricarboxylic acid cycle in growing cells
journal, November 1980

Reduction of nitroimidazole derivatives by hydrogenosomal extracts of Trichomonas vaginalis
journal, January 1985

Evolutionary Analysis of the TPP-Dependent Enzyme Family
journal, November 2007

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?
journal, October 2011

Oxalate metabolism by the acetogenic bacterium Moorella thermoacetica
journal, February 2004

Carbon Assimilation by Pseudomonas Oxalaticus (ox 1). 7. Decarboxylation of Oxalyl-Coenzyme a to Formyl-Coenzyme a
journal, December 1963

Pulsed Electron Paramagnetic Resonance Experiments Identify the Paramagnetic Intermediates in the Pyruvate Ferredoxin Oxidoreductase Catalytic Cycle
journal, March 2006

Characterization of recombinant barley oxalate oxidase expressed by Pichia pastoris
journal, July 2001

Enzymatic Decarboxylation of Oxalic acid
journal, September 1956

More examples of the 15-crown-5...H ₂ O— M —OH ₂ ...15-crown-5 motif, M = Al ³⁺ , Cr ³⁺ and Pd ²⁺
journal, March 2010

Crystallographic Snapshots of Cyanide- and Water-Bound C-Clusters from Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase ^,
journal, August 2009

A stable free radical intermediate in the reaction of 2-oxoacid:ferredoxin oxidoreductases of Halobacterium halobium
journal, September 1980

Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima.
journal, January 1996

Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase
journal, December 2001

Is a Hydrophobic Amino Acid Required To Maintain the Reactive V Conformation of Thiamin at the Active Center of Thiamin Diphosphate-Requiring Enzymes? Experimental and Computational Studies of Isoleucine 415 of Yeast Pyruvate Decarboxylase ^†
journal, September 1998

Consistent Estimation of Gibbs Energy Using Component Contributions
journal, July 2013

Evidence for the key position of pyruvate synthase in the assimilation of CO ₂ by Chlorobium
journal, April 1978

Influence of nitrate on oxalate- and glyoxylate-dependent growth and acetogenesis by Moorella thermoacetica
journal, December 2002

Clostridial pyruvate oxidoreductase and the pyruvate-oxidizing enzyme specific to nitrogen fixation in Klebsiella pneumoniae are similar enzymes.
journal, August 1987

Improved Fourier coefficients for maps using phases from partial structures with errors
journal, May 1986

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997

Identification and Characterization of Oxalate Oxidoreductase, a Novel Thiamine Pyrophosphate-dependent 2-Oxoacid Oxidoreductase That Enables Anaerobic Growth on Oxalate
journal, October 2010

Phaser crystallographic software
journal, July 2007