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PDBsum entry 1hfe

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protein ligands metals Protein-protein interface(s) links
Hydrogenase PDB id
1hfe
Jmol
Contents
Protein chains
88 a.a. *
397 a.a. *
Ligands
CYN ×4
SF4 ×6
PDT ×2
CMO ×4
CYS ×2
Metals
_ZN
FE2 ×4
Waters ×1211
* Residue conservation analysis
PDB id:
1hfe
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)
Resolution:
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
Date:
11-Nov-98     Release date:   20-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: Chains S, L, T, M: E.C.1.12.7.2  - Ferredoxin hydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2 + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H+
      Cofactor: Iron-sulfur; Ni(2+)
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.
 
  ABSTRACT  
 
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

  PubMed id Reference
22412465 S.Gao, D.Y.Jiang, Q.C.Liang, and Q.Duan (2012).
Bis{μ-[4-(1,3-benzothia-zol-2-yl)phen-yl]methane-thiol-ato-κS,S':S,S'}bis-[tricarbonyl-iron(I)](Fe-Fe).
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22412407 S.Gao, Q.Duan, and D.Y.Jiang (2012).
{μ-2-[4-(1,3-Benzothia-zol-2-yl)phen-yl]-2-aza-propane-1,3-dithiol-ato-κS,S':S,S'}bis-[tricarbonyl-iron(I)].
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22412455 S.Gao, Q.Duan, and D.Y.Jiang (2012).
{μ-2-[4-(Benzothia-zol-2-yl)benz-yl]-2-aza-propane-1,3-dithiol-ato-1:2κS,S':S,S'}bis-[tricarbonyl-iron(I)].
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21274947 C.Greco, M.Bruschi, P.Fantucci, U.Ryde, and L.De Gioia (2011).
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21296047 G.Hong, A.J.Cornish, E.L.Hegg, and R.Pachter (2011).
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Penta-carbonyl-1κC,2κC-(4-iodo-phenyl isocyanide-1κC)(μ-propane-1,3-dithiol-ato-1:2κS,S':S,S')iron(I)(Fe-Fe).
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21063595 S.Lounissi, J.F.Capon, F.Gloaguen, F.Matoussi, F.Y.Pétillon, P.Schollhammer, and J.Talarmin (2011).
Diiron species containing a cyclic P(Ph)2N(Ph)2 diphosphine related to the [FeFe]H2ases active site.
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21293817 Y.C.Liu, L.K.Tu, T.H.Yen, G.H.Lee, and M.H.Chiang (2011).
Influences on the rotated structure of diiron dithiolate complexes: electronic asymmetry vs. secondary coordination sphere interaction.
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21394351 Z.Xiao, Z.Wei, L.Long, Y.Wang, D.J.Evans, and X.Liu (2011).
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  Dalton Trans, 40, 4291-4299.  
20830602 A.Grigoropoulos, and R.K.Szilagyi (2010).
Evaluation of biosynthetic pathways for the unique dithiolate ligand of the FeFe hydrogenase H-cluster.
  J Biol Inorg Chem, 15, 1177-1182.  
20221536 A.Jablonskyte, J.A.Wright, and C.J.Pickett (2010).
Mechanistic aspects of the protonation of [FeFe]-hydrogenase subsite analogues.
  Dalton Trans, 39, 3026-3034.  
20593098 C.Greco, P.Fantucci, L.De Gioia, R.Suarez-Bertoa, M.Bruschi, J.Talarmin, and P.Schollhammer (2010).
Electrocatalytic dihydrogen evolution mechanism of [Fe2(CO)4(kappa(2)-Ph2PCH2CH2PPh2)(mu-S(CH2)3S)] and related models of the [FeFe]-hydrogenases active site: a DFT investigation.
  Dalton Trans, 39, 7320-7329.  
20967337 C.Zhan, X.Wang, Z.Wei, D.J.Evans, X.Ru, X.Zeng, and X.Liu (2010).
Synthesis and characterisation of polymeric materials consisting of {Fe2(CO)5}-unit and their relevance to the diiron sub-unit of [FeFe]-hydrogenase.
  Dalton Trans, 39, 11255-11262.  
20162194 C.Zheng, K.Kim, T.Matsumoto, and S.Ogo (2010).
The useful properties of H2O as a ligand of a hydrogenase mimic.
  Dalton Trans, 39, 2218-2225.  
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).
  Nature, 465, 248-251.
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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  Proc Natl Acad Sci U S A, 107, 10448-10453.  
20148213 H.Zhang, D.Chen, Y.Zhang, G.Zhang, and J.Liu (2010).
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High-yield expression of heterologous [FeFe] hydrogenases in Escherichia coli.
  PLoS One, 5, e15491.  
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20544787 W.G.Wang, F.Wang, H.Y.Wang, G.Si, C.H.Tung, and L.Z.Wu (2010).
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.
  Chemistry, 16, 2537-2546.  
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.
  J Biol Inorg Chem, 14, 301-313.  
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.
  Phys Chem Chem Phys, 11, 6592-6599.  
  20160838 D.Dogaru, S.Motiu, and V.Gogonea (2009).
Inactivation of [Fe-Fe]-Hydrogenase by O(2). Thermodynamics and Frontier Molecular Orbitals Analyses.
  Int J Quantum Chem, 109, 876-889.  
  20485511 D.Dogaru, S.Motiu, and V.Gogonea (2009).
Residue Mutations in [Fe-Fe]-hydrogenase Impedes O(2) Binding: A QM/MM Investigation.
  Int J Quantum Chem, 110, 1784-1792.  
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.
  Appl Environ Microbiol, 75, 4620-4623.  
19855833 J.M.Kuchenreuther, J.A.Stapleton, and J.R.Swartz (2009).
Tyrosine, cysteine, and S-adenosyl methionine stimulate in vitro [FeFe] hydrogenase activation.
  PLoS One, 4, e7565.  
19088964 M.L.Ghirardi, A.Dubini, J.Yu, and P.C.Maness (2009).
Photobiological hydrogen-producing systems.
  Chem Soc Rev, 38, 52-61.  
19672488 M.Wang, Y.Na, M.Gorlov, and L.Sun (2009).
Light-driven hydrogen production catalysed by transition metal complexes in homogeneous systems.
  Dalton Trans, (), 6458-6467.  
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Characterization of the key step for light-driven hydrogen evolution in green algae.
  J Biol Chem, 284, 36620-36627.  
19259561 P.Li, M.Wang, L.Chen, J.Liu, Z.Zhao, and L.Sun (2009).
Structures, protonation, and electrochemical properties of diiron dithiolate complexes containing pyridyl-phosphine ligands.
  Dalton Trans, (), 1919-1926.  
19575350 R.J.Wright, C.Lim, and T.D.Tilley (2009).
Diiron proton reduction catalysts possessing electron-rich and electron-poor naphthalene-1,8-dithiolate ligands.
  Chemistry, 15, 8518-8525.  
19503862 S.Ogo (2009).
Electrons from hydrogen.
  Chem Commun (Camb), (), 3317-3325.  
19130447 S.Pal, Y.Ohki, T.Yoshikawa, K.Kuge, and K.Tatsumi (2009).
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.
  Chem Asian J, 4, 961-968.  
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.
  Dalton Trans, (), 2712-2720.  
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.
  Chem Commun (Camb), (), 1563-1565.  
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.
  Chem Biodivers, 5, 2023-2041.  
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.
  Dalton Trans, (), 2379-2381.  
18729093 M.S.Koay, M.L.Antonkine, W.Gärtner, and W.Lubitz (2008).
Modelling low-potential [Fe4S4] clusters in proteins.
  Chem Biodivers, 5, 1571-1587.  
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.
  J Am Chem Soc, 130, 12021-12030.  
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.
  Inorg Chem, 47, 645-655.  
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.
  Chem Commun (Camb), (), 2547-2549.  
18398538 S.Gao, J.Fan, S.Sun, X.Peng, X.Zhao, and J.Hou (2008).
Selenium-bridged diiron hexacarbonyl complexes as biomimetic models for the active site of Fe-Fe hydrogenases.
  Dalton Trans, (), 2128-2135.  
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.
  Science, 321, 572-575.
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.
  Acta Crystallogr Sect E Struct Rep Online, 64, m1557-m1558.  
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.
  Acta Crystallogr Sect E Struct Rep Online, 65, m77-m78.  
21580868 Y.F.Tang, and J.L.Zhu (2008).
Penta-carbonyl-1κC,2κC-(ferrocenyl-diphenyl-phosphine-1κP)[μ-2-(4-methyl-phen-yl)-2-aza-propane-1,3-dithiol-ato-1:2κS,S':S,S']diiron(I)(Fe-Fe).
  Acta Crystallogr Sect E Struct Rep Online, 64, m1423.  
18400755 Y.Nicolet, J.K.Rubach, M.C.Posewitz, P.Amara, C.Mathevon, M.Atta, M.Fontecave, and J.C.Fontecilla-Camps (2008).
X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima.
  J Biol Chem, 283, 18861-18872.
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.
  Dalton Trans, (), 2400-2406.  
  17615612 A.K.Justice, T.B.Rauchfuss, and S.R.Wilson (2007).
Unsaturated, mixed-valence diiron dithiolate model for the H(ox) state of the [FeFe] hydrogenase.
  Angew Chem Int Ed Engl, 46, 6152-6154.  
17660315 C.H.Chang, P.W.King, M.L.Ghirardi, and K.Kim (2007).
Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii.
  Biophys J, 93, 3034-3045.  
17712448 F.Wang, M.Wang, X.Liu, K.Jin, W.Dong, and L.Sun (2007).
Protonation, electrochemical properties and molecular structures of halogen-functionalized diiron azadithiolate complexes related to the active site of iron-only hydrogenases.
  Dalton Trans, (), 3812-3819.  
17766465 J.Inoue, K.Saita, T.Kudo, S.Ui, and M.Ohkuma (2007).
Hydrogen production by termite gut protists: characterization of iron hydrogenases of Parabasalian symbionts of the termite Coptotermes formosanus.
  Eukaryot Cell, 6, 1925-1932.  
17372642 L.Duan, M.Wang, P.Li, Y.Na, N.Wang, and L.Sun (2007).
Carbene-pyridine chelating 2Fe2S hydrogenase model complexes as highly active catalysts for the electrochemical reduction of protons from weak acid (HOAc).
  Dalton Trans, (), 1277-1283.  
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.
  Biotechnol Lett, 29, 421-430.  
17216401 L.Forzi, and R.G.Sawers (2007).
Maturation of [NiFe]-hydrogenases in Escherichia coli.
  Biometals, 20, 565-578.  
17150028 M.L.Ghirardi, M.C.Posewitz, P.C.Maness, A.Dubini, J.Yu, and M.Seibert (2007).
Hydrogenases and hydrogen photoproduction in oxygenic photosynthetic organisms.
  Annu Rev Plant Biol, 58, 71-91.  
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.
  J Biol Inorg Chem, 12, 62-78.  
17297518 S.Jiang, J.Liu, Y.Shi, Z.Wang, B.Akermark, and L.Sun (2007).
Fe-S complexes containing five-membered heterocycles: novel models for the active site of hydrogenases with unusual low reduction potential.
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Escherichia coli hydrogenase 3 is a reversible enzyme possessing hydrogen uptake and synthesis activities.
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Bis(mu4-butane-1,4-dithiolato)bis[hexacarbonyldiiron(II)(Fe-Fe)].
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16898857 A.Badura, B.Esper, K.Ataka, C.Grunwald, C.Wöll, J.Kuhlmann, J.Heberle, and M.Rögner (2006).
Light-driven water splitting for (bio-)hydrogen production: photosystem 2 as the central part of a bioelectrochemical device.
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PDB code: 1dwl
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