PDBsum entry 1hfe

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protein ligands metals Protein-protein interface(s) links
Hydrogenase PDB id
Protein chains
88 a.a. *
397 a.a. *
CYN ×4
SF4 ×6
PDT ×2
CMO ×4
CYS ×2
FE2 ×4
Waters ×1211
* Residue conservation analysis
PDB id:
Name: Hydrogenase
Title: 1.6 a resolution structure of the fe-only hydrogenase from desulfovibrio desulfuricans
Structure: Protein (fe-only hydrogenase (smaller subunit)). Chain: s, t. Other_details: the fe-only hydrogenase from desulfovibrio desulfuricans has exactly the same sequence as the fe-only hydrogenase from desulfovibrio vulgaris (strain hildenborough). Protein (fe-only hydrogenase (larger subunit)).
Source: Desulfovibrio vulgaris subsp. Vulgaris str. Hildenborough. Organism_taxid: 882. Strain: hildenborough / atcc 29579 / ncimb 8303. Atcc: 7757. Cellular_location: periplasm. Cellular_location: periplasm
Biol. unit: Dimer (from PQS)
1.60Å     R-factor:   0.158     R-free:   0.182
Authors: Y.Nicolet,C.Piras,P.Legrand,E.C.Hatchikian,J.C.Fontecilla- Camps
Key ref:
Y.Nicolet et al. (1999). Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. Structure, 7, 13-23. PubMed id: 10368269 DOI: 10.1016/S0969-2126(99)80005-7
11-Nov-98     Release date:   20-Apr-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P07603  (PHFS_DESVH) -  Periplasmic [Fe] hydrogenase small subunit
123 a.a.
88 a.a.
Protein chains
Pfam   ArchSchema ?
P07598  (PHFL_DESVH) -  Periplasmic [Fe] hydrogenase large subunit
421 a.a.
397 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains S, L, T, M: E.C.  - Ferredoxin hydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2 + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H+
      Cofactor: Iron-sulfur; Ni(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     7 terms  


    Key reference    
DOI no: 10.1016/S0969-2126(99)80005-7 Structure 7:13-23 (1999)
PubMed id: 10368269  
Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.
Y.Nicolet, C.Piras, P.Legrand, C.E.Hatchikian, J.C.Fontecilla-Camps.
BACKGROUND: Many microorganisms have the ability to either oxidize molecular hydrogen to generate reducing power or to produce hydrogen in order to remove low-potential electrons. These reactions are catalyzed by two unrelated enzymes: the Ni-Fe hydrogenases and the Fe-only hydrogenases. RESULTS: We report here the structure of the heterodimeric Fe-only hydrogenase from Desulfovibrio desulfuricans - the first for this class of enzymes. With the exception of a ferredoxin-like domain, the structure represents a novel protein fold. The cubane bridged to a binuclear active site Fe center containing putative CO and CN ligands and one bridging 1, 3-propanedithiol molecule. The conformation of the subunits can be explained by the evolutionary changes that have transformed monomeric cytoplasmic enzymes into dimeric periplasmic enzymes. Plausible electron- and proton-transfer pathways and a putative channel for the access of hydrogen to the active site have been identified. CONCLUSIONS: The unrelated active sites of Ni-Fe and Fe-only hydrogenases have several common features: coordination of diatomic ligands to an Fe ion; a vacant coordination site on one of the metal ions representing a possible substrate-binding site; a thiolate-bridged binuclear center; and plausible proton- and electron-transfer pathways and substrate channels. The diatomic coordination to Fe ions makes them low spin and favors low redox states, which may be required for catalysis. Complex electron paramagnetic resonance signals typical of Fe-only hydrogenases cluster and the active site binuclear center. The paucity of protein ligands to this center suggests that it was imported from the inorganic world as an already functional unit.
  Selected figure(s)  
Figure 6.
Figure 6. Interactions of the binuclear Fe center with the protein. Besides the bridging Cys382 residue, two of the putative ligands form hydrogen bonds (dashed lines) with the protein (see text for details). (The figure was prepared using the program TURBO-FRODO [39].)
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 13-23) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

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20162194 C.Zheng, K.Kim, T.Matsumoto, and S.Ogo (2010).
The useful properties of H2O as a ligand of a hydrogenase mimic.
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20418861 D.W.Mulder, E.S.Boyd, R.Sarma, R.K.Lange, J.A.Endrizzi, J.B.Broderick, and J.W.Peters (2010).
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG).
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PDB code: 3lx4
20498089 E.M.Shepard, S.E.McGlynn, A.L.Bueling, C.S.Grady-Smith, S.J.George, M.A.Winslow, S.P.Cramer, J.W.Peters, and J.B.Broderick (2010).
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20165762 M.Saggu, C.Teutloff, M.Ludwig, M.Brecht, M.E.Pandelia, O.Lenz, B.Friedrich, W.Lubitz, P.Hildebrandt, F.Lendzian, and R.Bittl (2010).
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20376875 M.Saggu, M.Ludwig, B.Friedrich, P.Hildebrandt, R.Bittl, F.Lendzian, O.Lenz, and I.Zebger (2010).
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Photocatalytic hydrogen evolution by [FeFe] hydrogenase mimics in homogeneous solution.
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20077533 W.Gao, J.Sun, T.Akermark, M.Li, L.Eriksson, L.Sun, and B.Akermark (2010).
Attachment of a hydrogen-bonding carboxylate side chain to an [FeFe]-hydrogenase model complex: influence on the catalytic mechanism.
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19011912 A.Silakov, B.Wenk, E.Reijerse, S.P.Albracht, and W.Lubitz (2009).
Spin distribution of the H-cluster in the H(ox)-CO state of the [FeFe] hydrogenase from Desulfovibrio desulfuricans: HYSCORE and ENDOR study of (14)N and (13)C nuclear interactions.
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19639134 A.Silakov, B.Wenk, E.Reijerse, and W.Lubitz (2009).
(14)N HYSCORE investigation of the H-cluster of [FeFe] hydrogenase: evidence for a nitrogen in the dithiol bridge.
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Inactivation of [Fe-Fe]-Hydrogenase by O(2). Thermodynamics and Frontier Molecular Orbitals Analyses.
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Residue Mutations in [Fe-Fe]-hydrogenase Impedes O(2) Binding: A QM/MM Investigation.
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19429563 E.S.Boyd, J.R.Spear, and J.W.Peters (2009).
[FeFe] hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community.
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19855833 J.M.Kuchenreuther, J.A.Stapleton, and J.R.Swartz (2009).
Tyrosine, cysteine, and S-adenosyl methionine stimulate in vitro [FeFe] hydrogenase activation.
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Photobiological hydrogen-producing systems.
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Light-driven hydrogen production catalysed by transition metal complexes in homogeneous systems.
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Characterization of the key step for light-driven hydrogen evolution in green algae.
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Diiron proton reduction catalysts possessing electron-rich and electron-poor naphthalene-1,8-dithiolate ligands.
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Electrons from hydrogen.
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Dithiolate-bridged Fe-Ni-Fe trinuclear complexes consisting of Fe(CO)(3-n)(CN)(n) (n = 0, 1) components relevant to the active site of [NiFe] hydrogenase.
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19805068 S.T.Stripp, G.Goldet, C.Brandmayr, O.Sanganas, K.A.Vincent, M.Haumann, F.A.Armstrong, and T.Happe (2009).
How oxygen attacks [FeFe] hydrogenases from photosynthetic organisms.
  Proc Natl Acad Sci U S A, 106, 17331-17336.  
19333494 W.G.Wang, H.Y.Wang, G.Si, C.H.Tung, and L.Z.Wu (2009).
Fluorophenyl-substituted Fe-only hydrogenases active site ADT models: different electrocatalytic process for proton reduction in HOAc and HBF4/Et2O.
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18354800 C.M.Thomas, T.Liu, M.B.Hall, and M.Y.Darensbourg (2008).
Regioselective (12)CO/(13)CO exchange activity of a mixed-valent Fe(ii)Fe(i) model of the H(ox) state of [FeFe]-hydrogenase.
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18412257 I.Fdez Galván, A.Volbeda, J.C.Fontecilla-Camps, and M.J.Field (2008).
A QM/MM study of proton transport pathways in a [NiFe] hydrogenase.
  Proteins, 73, 195-203.  
18563582 J.J.Mansure, and P.C.Hallenbeck (2008).
Desulfovibrio vulgaris Hildenborough HydE and HydG interact with the HydA subunit of the [FeFe] hydrogenase.
  Biotechnol Lett, 30, 1765-1769.  
18972523 J.Windhager, R.A.Seidel, U.P.Apfel, H.Görls, G.Linti, and W.Weigand (2008).
Oxidation of diiron and triiron sulfurdithiolato complexes: mimics for the active site of [FeFe]-hydrogenase.
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18461189 L.Schwartz, L.Eriksson, R.Lomoth, F.Teixidor, C.Viñas, and S.Ott (2008).
Influence of an electron-deficient bridging o-carborane on the electronic properties of an [FeFe] hydrogenase active site model.
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18729093 M.S.Koay, M.L.Antonkine, W.Gärtner, and W.Lubitz (2008).
Modelling low-potential [Fe4S4] clusters in proteins.
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18700771 M.T.Olsen, M.Bruschi, L.De Gioia, T.B.Rauchfuss, and S.R.Wilson (2008).
Nitrosyl derivatives of diiron(I) dithiolates mimic the structure and Lewis acidity of the [FeFe]-hydrogenase active site.
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18078337 P.Baran, R.Boca, I.Chakraborty, J.Giapintzakis, R.Herchel, Q.Huang, J.E.McGrady, R.G.Raptis, Y.O.Sanakis, and A.Simopouloso (2008).
Synthesis, characterization, and study of octanuclear iron-oxo clusters containing a redox-active Fe4O4-cubane core.
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18506239 S.Ezzaher, P.Y.Orain, J.F.Capon, F.Gloaguen, F.Y.Pétillon, T.Roisnel, P.Schollhammer, and J.Talarmin (2008).
First insights into the protonation of dissymetrically disubstituted di-iron azadithiolate models of the [FeFe]H2ases active site.
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18398538 S.Gao, J.Fan, S.Sun, X.Peng, X.Zhao, and J.Hou (2008).
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18653896 S.Shima, O.Pilak, S.Vogt, M.Schick, M.S.Stagni, W.Meyer-Klaucke, E.Warkentin, R.K.Thauer, and U.Ermler (2008).
The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site.
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PDB codes: 3daf 3dag
21581166 T.Yamaguchi, S.Masaoka, and K.Sakai (2008).
Diaqua-(1,4,7,10,13-penta-oxacyclo-penta-deca-ne)iron(II) bis-(μ-cis-1,2-dicyano-1,2-ethyl-enedithiol-ato)bis-[(cis-1,2-dicyano-1,2-ethyl-enedithiol-ato)ferrate(III)] 1,4,7,10,13-penta-oxacyclo-penta-decane disolvate.
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21581543 T.Yamaguchi, S.Masaoka, and K.Sakai (2008).
Bis(triethyl-ammonium) bis-(μ-pyrazine-2,3-dithiol-ato)bis-(pyrazine-2,3-dithio-lato)diferrate(III) methanol disolvate.
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X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima.
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PDB codes: 3ciw 3cix
18461194 Z.Yu, M.Wang, P.Li, W.Dong, F.Wang, and L.Sun (2008).
Diiron dithiolate complexes containing intra-ligand NH ... S hydrogen bonds: [FeFe] hydrogenase active site models for the electrochemical proton reduction of HOAc with low overpotential.
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Unsaturated, mixed-valence diiron dithiolate model for the H(ox) state of the [FeFe] hydrogenase.
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Protonation, electrochemical properties and molecular structures of halogen-functionalized diiron azadithiolate complexes related to the active site of iron-only hydrogenases.
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17766465 J.Inoue, K.Saita, T.Kudo, S.Ui, and M.Ohkuma (2007).
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Carbene-pyridine chelating 2Fe2S hydrogenase model complexes as highly active catalysts for the electrochemical reduction of protons from weak acid (HOAc).
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17195059 L.E.Nagy, J.E.Meuser, S.Plummer, M.Seibert, M.L.Ghirardi, P.W.King, D.Ahmann, and M.C.Posewitz (2007).
Application of gene-shuffling for the rapid generation of novel [FeFe]-hydrogenase libraries.
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17216401 L.Forzi, and R.G.Sawers (2007).
Maturation of [NiFe]-hydrogenases in Escherichia coli.
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16969669 M.Long, J.Liu, Z.Chen, B.Bleijlevens, W.Roseboom, and S.P.Albracht (2007).
Characterization of a HoxEFUYH type of [NiFe] hydrogenase from Allochromatium vinosum and some EPR and IR properties of the hydrogenase module.
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Escherichia coli hydrogenase 3 is a reversible enzyme possessing hydrogen uptake and synthesis activities.
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