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Title: [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

Journal Article · · Biochim Biophys Acta.
; ; ; ; ; ; ;

Research Organization:
Energy Frontier Research Centers (EFRC) (United States); Center for Biological Electron Transfer and Catalysis (BETCy)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
DOE Contract Number:
SC0012518
OSTI ID:
1210612
Journal Information:
Biochim Biophys Acta., Vol. 1853; Related Information: BETCy partners with Montana State University (lead); Arizona State University; National Renewable Energy Laboratory; University of Georgia; University of Kentucky; University of Washington; Utah State University
Country of Publication:
United States
Language:
English

References (245)

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Inactivation of uptake hydrogenase leads to enhanced and sustained hydrogen production with high nitrogenase activity under high light exposure in the cyanobacterium Anabaena siamensis TISTR 8012 journal December 2012
Cloning, sequence determination, and expression of the genes encoding the subunits of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase from Methanobacterium thermoautotrophicum .DELTA.H journal August 1990
The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member journal July 2014
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The Bidirectional NiFe-hydrogenase in Synechocystis sp. PCC 6803 Is Reduced by Flavodoxin and Ferredoxin and Is Essential under Mixotrophic, Nitrate-limiting Conditions journal December 2013
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Methanobacterium thermoautotrophicum encodes two multisubunit membrane-bound [NiFe] hydrogenases . Transcription of the operons and sequence analysis of the deduced proteins journal September 1999
Formate-driven growth coupled with H2 production journal September 2010
Differential expression of hydrogenase isoenzymes in Escherichia coli K-12: evidence for a third isoenzyme. journal January 1985
The Complete Genome Sequence of Thermococcus onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism journal September 2008
Purification and catalytic properties of a CO-oxidizing:H2-evolving enzyme complex from Carboxydothermus hydrogenoformans: CO-oxidizing:H2-evolving enzyme complex journal October 2002
Purification and catalytic properties of Ech hydrogenase from Methanosarcina barkeri journal October 1999
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Characterization of Energy-Conserving Hydrogenase B in Methanococcus maripaludis journal May 2010
Genome Data Mining and Soil Survey for the Novel Group 5 [NiFe]-Hydrogenase To Explore the Diversity and Ecological Importance of Presumptive High-Affinity H 2 -Oxidizing Bacteria journal July 2011
Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase journal March 2010
Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria: Uptake of H journal November 2013
A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases journal March 2014
Structural Studies of the Carbon Monoxide Complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F:  Suggestion for the Initial Activation Site for Dihydrogen journal October 2002
Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases journal April 2005
Activation Process of [NiFe] Hydrogenase Elucidated by High-Resolution X-Ray Analyses: Conversion of the Ready to the Unready State journal November 2005
The Crystal Structure of the [NiFe] Hydrogenase from the Photosynthetic Bacterium Allochromatium vinosum: Characterization of the Oxidized Enzyme (Ni-A State) journal September 2010
Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase journal October 2011
X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli journal March 2012
A Glutamate Is the Essential Proton Transfer Gate during the Catalytic Cycle of the [NiFe] Hydrogenase journal December 2003
Analyses of the Large Subunit Histidine-Rich Motif Expose an Alternative Proton Transfer Pathway in [NiFe] Hydrogenases journal April 2012
Computational Studies of [NiFe] and [FeFe] Hydrogenases journal October 2007
[NiFe] hydrogenases: A common active site for hydrogen metabolism under diverse conditions journal August 2013
Disclosure of Key Stereoelectronic Factors for Efficient H 2 Binding and Cleavage in the Active Site of [NiFe]-Hydrogenases journal January 2014
Density functional theory on the larger active site models for [NiFe] hydrogenases: Two-state reactivity? journal August 2008
Detection and characterization of exchangeable protons bound to the hydrogen-activation nickel site of Desulfovibrio gigas hydrogenase: a proton and deuterium Q-band ENDOR study journal January 1991
Potential Hydrogen Bottleneck in Nickel−Iron Hydrogenase journal July 2010
An orientation-selected ENDOR and HYSCORE study of the Ni-C active state of Desulfovibrio vulgaris Miyazaki F hydrogenase journal December 2004
Computational study of the electronic structure and magnetic properties of the Ni–C state in [NiFe] hydrogenases including the second coordination sphere journal October 2012
The Electronic Structure of the H-Cluster in the [FeFe]-Hydrogenase from Desulfovibrio desulfuricans : A Q-band 57 Fe-ENDOR and HYSCORE Study journal September 2007
Mössbauer Characterization of the Iron−Sulfur Clusters in Desulfovibrio vulgaris Hydrogenase journal March 2001
Electronic Structure of the H Cluster in [Fe]-Hydrogenases journal September 1999
Structural Insights into the Active-Ready Form of [FeFe]-Hydrogenase and Mechanistic Details of Its Inhibition by Carbon Monoxide journal September 2007
On the electronic structure of the hydrogenase H-cluster journal January 2006
Computational Studies of the H-Cluster of Fe-Only Hydrogenases:  Geometric, Electronic, and Magnetic Properties and Their Dependence on the [Fe 4 S 4 ] Cubane journal December 2005
Fundamentals of H 2 Binding and Reactivity on Transition Metals Underlying Hydrogenase Function and H 2 Production and Storage journal October 2007
Functionally Relevant Interplay between the Fe 4 S 4 Cluster and CN − Ligands in the Active Site of [FeFe]-Hydrogenases journal April 2010
Biomimetic assembly and activation of [FeFe]-hydrogenases journal June 2013
Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic journal August 2013
Crystallographic and FTIR Spectroscopic Evidence of Changes in Fe Coordination Upon Reduction of the Active Site of the Fe-Only Hydrogenase from Desulfovibrio d esulfuricans journal February 2001
A Capable Bridging Ligand for Fe-Only Hydrogenase:  Density Functional Calculations of a Low-Energy Route for Heterolytic Cleavage and Formation of Dihydrogen journal April 2001
Insights into [FeFe]-Hydrogenase Structure, Mechanism, and Maturation journal August 2011
Electron and Spin Density Topology of the H-Cluster and Its Biomimetic Complexes journal May 2011
Does the environment around the H-cluster allow coordination of the pendant amine to the catalytic iron center in [FeFe] hydrogenases? Answers from theory journal June 2013
Influence of the [2Fe] H Subcluster Environment on the Properties of Key Intermediates in the Catalytic Cycle of [FeFe] Hydrogenases: Hints for the Rational Design of Synthetic Catalysts journal April 2009
Mechanism of hydrogen production in [Fe–Fe]-hydrogenases: A quantum mechanics/molecular mechanics study journal June 2010
Photochemistry at the Active Site of the Carbon Monoxide Inhibited Form of the Iron-Only Hydrogenase (CpI) journal April 2000
Modeling the Active Sites in Metalloenzymes. 3. Density Functional Calculations on Models for [Fe]-Hydrogenase:  Structures and Vibrational Frequencies of the Observed Redox Forms and the Reaction Mechanism at the Diiron Active Center journal April 2001
Infrared Studies of the CO-Inhibited Form of the Fe-Only Hydrogenase from Clostridium pasteurianum I:  Examination of Its Light Sensitivity at Cryogenic Temperatures † journal February 2002
Mechanistic and Physiological Implications of the Interplay among Iron–Sulfur Clusters in [FeFe]-Hydrogenases. A QM/MM Perspective journal November 2011
EPR and FTIR Analysis of the Mechanism of H 2 Activation by [FeFe]-Hydrogenase HydA1 from Chlamydomonas reinhardtii journal April 2013
The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. II. Redox properties, light sensitivity and CO-ligand exchange as observed by infrared spectroscopy journal December 2005
Identification and Characterization of the “Super-Reduced” State of the H-Cluster in [FeFe] Hydrogenase: A New Building Block for the Catalytic Cycle? journal October 2012
Structure–function relationships of anaerobic gas-processing metalloenzymes journal August 2009
New Redox States Observed in [FeFe] Hydrogenases Reveal Redox Coupling Within the H-Cluster journal July 2014
Spectroelectrochemical Characterization of the Active Site of the [FeFe] Hydrogenase HydA1 from Chlamydomonas reinhardtii journal August 2009
Identification of Global Ferredoxin Interaction Networks in Chlamydomonas reinhardtii journal October 2013
[NiFe] and [FeFe] Hydrogenases Studied by Advanced Magnetic Resonance Techniques journal October 2007
Redox properties of the iron-sulfur clusters in activated Fe-hydrogenase from Desulfovibrio vulgaris (Hildenborough) journal October 1992
Desulfovibrio vulgaris hydrogenase: a nonheme iron enzyme lacking nickel that exhibits anomalous EPR and Mossbauer spectra. journal June 1984
FeFe hydrogenase reductive inactivation and implication for catalysis journal January 2014
Covalent Attachment of FeFe Hydrogenases to Carbon Electrodes for Direct Electron Transfer journal August 2012
Electrochemical Investigations of the Interconversions between Catalytic and Inhibited States of the [FeFe]-Hydrogenase from Desulfovibrio desulfuricans journal December 2006
The HydG Enzyme Generates an Fe(CO)2(CN) Synthon in Assembly of the FeFe Hydrogenase H-Cluster journal January 2014
Combining acid–base, redox and substrate binding functionalities to give a complete model for the [FeFe]-hydrogenase journal October 2011
Investigations on the Role of Proton-Coupled Electron Transfer in Hydrogen Activation by [FeFe]-Hydrogenase journal October 2014
The [NiFe]-Hydrogenase of the Cyanobacterium Synechocystis sp. PCC 6803 Works Bidirectionally with a Bias to H 2 Production journal July 2011
Electrocatalytic mechanism of reversible hydrogen cycling by enzymes and distinctions between the major classes of hydrogenases journal July 2012
Electrochemical Definitions of O 2 Sensitivity and Oxidative Inactivation in Hydrogenases journal December 2005
Iron-sulfur clusters of hydrogenase I and hydrogenase II of Clostridium pasteurianum. journal July 1989
Understanding and Tuning the Catalytic Bias of Hydrogenase journal May 2012
The organometallic active site of [Fe]hydrogenase: Models and entatic states journal March 2003
Structural and Functional Analogues of the Active Sites of the [Fe]-, [NiFe]-, and [FeFe]-Hydrogenases † journal June 2009
Development of Molecular Electrocatalysts for Energy Storage journal February 2014
Analysis of the hydA locus of Escherichia coli : two genes (hydN and hypF) involved in formate and hydrogen metabolism journal May 1996
Molecular characterization of an operon ( hyp ) necessary for the activity of the three hydrogenase isoenzymes in Escherichia coli journal January 1991
Taming of a Poison: Biosynthesis of the NiFe-Hydrogenase Cyanide Ligands journal February 2003
Analysis of the transcarbamoylation-dehydration reaction catalyzed by the hydrogenase maturation proteins HypF and HypE: Hydrogenase maturation protein HypE journal July 2004
Structural Basis for the Reaction Mechanism of S-Carbamoylation of HypE by HypF in the Maturation of [NiFe]-Hydrogenases* journal August 2012
Structure of Hydrogenase Maturation Protein HypF with Reaction Intermediates Shows Two Active Sites journal December 2011
An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro journal August 2007
Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex journal August 2008
The O -Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction journal March 2012
X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 Å resolution journal September 1999
Domain Organization of Salmonella typhimurium Formylglycinamide Ribonucleotide Amidotransferase Revealed by X-ray Crystallography † , ‡ journal August 2004
Structure of [NiFe] Hydrogenase Maturation Protein HypE from Escherichia coli and Its Interaction with HypF journal December 2007
Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation journal December 2013
Interaction of the Hydrogenase Accessory Protein HypC with HycE, the Large Subunit of Escherichia coli Hydrogenase 3 during Enzyme Maturation † journal March 1998
Maturation of [NiFe]-hydrogenases in Escherichia coli: The HypC Cycle journal November 2002
The Complex Between Hydrogenase-maturation Proteins HypC and HypD is an Intermediate in the Supply of Cyanide to the Active Site Iron of [NiFe]-Hydrogenases journal November 2004
[NiFe]-hydrogenase maturation: Isolation of a HypC-HypD complex carrying diatomic CO and CN − ligands journal September 2012
Crystal Structures of the HypCD Complex and the HypCDE Ternary Complex: Transient Intermediate Complexes during [NiFe] Hydrogenase Maturation journal December 2012
A Universal Scaffold for Synthesis of the Fe(CN)2(CO) Moiety of [NiFe] Hydrogenase* journal November 2012
Solution structure of Escherichia coli HypC journal September 2007
Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling journal July 2007
Properties of the [NiFe]-hydrogenase maturation protein HypD journal June 2006
Structural basis of [NiFe] hydrogenase maturation by Hyp proteins journal October 2012
HypD Is the Scaffold Protein for Fe-(CN) 2 CO Cofactor Assembly in [NiFe]-Hydrogenase Maturation journal April 2013
The [NiFe]-hydrogenase accessory chaperones HypC and HybG of Escherichia coli are iron- and carbon dioxide-binding proteins journal July 2013
The biosynthetic routes for carbon monoxide and cyanide in the Ni-Fe active site of hydrogenases are different journal December 2004
Pleiotropic hydrogenase mutants of Escherichia coli K12: growth in the presence of nickel can restore hydrogenase activity journal January 1986
Requirement of nickel metabolism proteins HypA and HypB for full activity of both hydrogenase and urease in Helicobacter pylori journal January 2001
Maturation of [NiFe]-hydrogenases in Escherichia coli journal January 2007
Crystal Structure of HypA, a Nickel-Binding Metallochaperone for [NiFe] Hydrogenase Maturation journal December 2009
Characterization of Helicobacter pylori Nickel Metabolism Accessory Proteins Needed for Maturation of both Urease and Hydrogenase journal February 2003
HybF, a Zinc-Containing Protein Involved in NiFe Hydrogenase Maturation journal May 2004
GTP Hydrolysis by HypB is Essential for Nickel Insertion into Hydrogenases of Escherichia Coli journal May 1995
Roles of conserved nucleotide-binding domains in accessory proteins, HypB and UreG, in the maturation of nickel-enzymes required for efficient Helicobacter pylori colonization journal November 2003
Metal Binding Activity of the Escherichia coli Hydrogenase Maturation Factor HypB † journal September 2005
Structural Insights into HypB, a GTP-binding Protein That Regulates Metal Binding journal June 2006
Microbial nickel proteins journal January 2010
Effects of Metal on the Biochemical Properties of Helicobacter pylori HypB, a Maturation Factor of [NiFe]-Hydrogenase and Urease journal January 2011
Relationship between Ni(II) and Zn(II) Coordination and Nucleotide Binding by the Helicobacter pylori [NiFe]-Hydrogenase and Urease Maturation Factor HypB journal December 2013
Relationship between the GTPase, metal-binding, and dimerization activities of E. coli HypB journal May 2011
Protein Interactions and Localization of the Escherichia coli Accessory Protein HypA during Nickel Insertion to [NiFe] Hydrogenase* journal December 2011
Metallo-GTPase HypB from Helicobacter pylori and Its Interaction with Nickel Chaperone Protein HypA journal February 2012
In Vivo Interactome of Helicobacter pylori Urease Revealed by Tandem Affinity Purification journal December 2008
Interaction of SlyD with HypB of Helicobacter pylori facilitates nickel trafficking journal January 2013
Metal Transfer within the Escherichia coli HypB–HypA Complex of Hydrogenase Accessory Proteins journal August 2013
Escherichia coli SlyD, More Than a Ni(II) Reservoir journal December 2011
[NiFe]-Hydrogenase maturation endopeptidase: structure and function journal February 2005
Characterisation of a Protease from Escherichia coli Involved in Hydrogenase Maturation journal January 1995
Carboxyl-terminal processing may be essential for production of active NiFe hydrogenase in Azotobacter vinelandii journal September 1992
A novel very small subunit of a selenium containing [NiFe] hydrogenease of Methanococcus voltae is postranslationally processed by cleavage at a defined position journal May 1993
Carboxy-terminal processing of the large subunit of [NiFe] hydrogenases journal September 1993
Maturation of the large subunit (HYCE) of Escherichia coli hydrogenase 3 requires nickel incorporation followed by C-terminal processing at Arg537 journal March 1994
Nickel serves as a substrate recognition motif for the endopeptidase involved in hydrogenase maturation: Nickel recognition by maturation endopeptidase journal April 2000
Crystal structure of hydrogenase maturating endopeptidase HycI from Escherichia coli journal November 2009
Functional Studies of [FeFe] Hydrogenase Maturation in an Escherichia coli Biosynthetic System journal March 2006
Biochemical characterization of the HydE and HydG iron-only hydrogenase maturation enzymes from Thermatoga maritima journal August 2005
The [Fe-Fe]-Hydrogenase Maturation Protein HydF from Thermotoga maritima Is a GTPase with an Iron-Sulfur Cluster journal November 2005
Activation of HydA ΔEFG Requires a Preformed [4Fe-4S] Cluster journal July 2009
Nuclear Resonance Vibrational Spectroscopy and Electron Paramagnetic Resonance Spectroscopy of 57 Fe-Enriched [FeFe] Hydrogenase Indicate Stepwise Assembly of the H-Cluster journal January 2013
Emerging Paradigms for Complex Iron-Sulfur Cofactor Assembly and Insertion journal July 2012
Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold journal May 2010
Crystal Structure of HydF Scaffold Protein Provides Insights into [FeFe]-Hydrogenase Maturation journal November 2011
HydF as a scaffold protein in [FeFe] hydrogenase H-cluster biosynthesis journal May 2008
The [FeFe]-hydrogenase maturase HydF from Clostridium acetobutylicum contains a CO and CN − ligated iron cofactor journal December 2009
The [FeFe]-hydrogenase maturation protein HydF contains a H-cluster like [4Fe4S]-2Fe site journal December 2010
Iron-sulfur cluster coordination in the [FeFe]-hydrogenase H cluster biosynthetic factor HydF journal October 2012
New Insights into [FeFe] Hydrogenase Activation and Maturase Function journal September 2012
The [4Fe–4S]-cluster coordination of [FeFe]-hydrogenase maturation protein HydF as revealed by EPR and HYSCORE spectroscopies journal December 2012
The proton iron-sulfur cluster environment of the [FeFe]-hydrogenase maturation protein HydF from Thermotoga neapolitana journal October 2014
An EPR/HYSCORE, Mössbauer, and resonance Raman study of the hydrogenase maturation enzyme HydF: a model for N-coordination to [4Fe–4S] clusters journal November 2013
[FeFe]-Hydrogenase Maturation journal June 2014
Biochemical Analysis of the Interactions between the Proteins Involved in the [FeFe]-Hydrogenase Maturation Process journal August 2012
Radical S -Adenosylmethionine Enzymes journal January 2014
Thiamine Biosynthesis inEscherichia coli: Identification of the Intermediate and By-Product Derived from Tyrosine journal December 2007
The role of the maturase HydG in [FeFe]‐hydrogenase active site synthesis and assembly journal January 2009
[FeFe]-Hydrogenase Maturation: HydG-Catalyzed Synthesis of Carbon Monoxide journal July 2010
A glycyl free radical as the precursor in the synthesis of carbon monoxide and cyanide by the [FeFe]-hydrogenase maturase HydG journal September 2010
Biochemical and Kinetic Characterization of Radical S -Adenosyl- l -methionine Enzyme HydG journal November 2013
Further Characterization of the [FeFe]-Hydrogenase Maturase HydG journal February 2011
A Radical Intermediate in Tyrosine Scission to the CO and CN- Ligands of FeFe Hydrogenase journal October 2013
Cell-free H-cluster Synthesis and [FeFe] Hydrogenase Activation: All Five CO and CN− Ligands Derive from Tyrosine journal May 2011
Crystal Structure of Methylornithine Synthase (PylB): Insights into the Pyrrolysine Biosynthesis journal November 2011
Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins journal August 2009
X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters journal April 2013
Structure of the [NiFe] Hydrogenase Active Site:  Evidence for Biologically Uncommon Fe Ligands ⊥ journal January 1996
Dithiomethylether as a Ligand in the Hydrogenase H-Cluster journal April 2008

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