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PDBsum entry 1h2r

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1h2r
Jmol
Contents
Protein chains
267 a.a. *
534 a.a. *
Ligands
SF4 ×2
F3S
NFE
Metals
_MG
Waters ×577
* Residue conservation analysis
PDB id:
1h2r
Name: Oxidoreductase
Title: Three-dimensional structure of ni-fe hydrogenase from desulfivibrio vulgaris miyazaki f in the reduced form at 1.4 a resolution
Structure: Protein (periplasmic [nife] hydrogenase small subunit). Chain: s. Synonym: hydrogen: ferricytochrome-c3 oxidoreductase. Protein (periplasmic [nife] hydrogenase large subunit). Chain: l. Synonym: hydrogen: ferricytochrome-c3 oxidoreductase. Ec: 1.12.2.1
Source: Desulfovibrio vulgaris str. 'Miyazaki f'. Organism_taxid: 883. Strain: miyazaki f. Atcc: iam 12604. Collection: iam 12604. Cellular_location: periplasmic membrane. Cellular_location: periplasmic membrane
Biol. unit: Dimer (from PQS)
Resolution:
1.40Å     R-factor:   0.218     R-free:   0.254
Authors: Y.Higuchi,H.Ogata
Key ref:
Y.Higuchi et al. (1999). Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure, 7, 549-556. PubMed id: 10378274 DOI: 10.1016/S0969-2126(99)80071-9
Date:
14-Jun-99     Release date:   05-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21853  (PHNS_DESVM) -  Periplasmic [NiFe] hydrogenase small subunit
Seq:
Struc:
317 a.a.
267 a.a.
Protein chain
Pfam   ArchSchema ?
P21852  (PHNL_DESVM) -  Periplasmic [NiFe] hydrogenase large subunit
Seq:
Struc:
 
Seq:
Struc:
567 a.a.
534 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains S, L: E.C.1.12.2.1  - Cytochrome-c3 hydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3
      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   2 terms 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     8 terms  

 

 
    Key reference    
 
 
DOI no: 10.1016/S0969-2126(99)80071-9 Structure 7:549-556 (1999)
PubMed id: 10378274  
 
 
Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution.
Y.Higuchi, H.Ogata, K.Miki, N.Yasuoka, T.Yagi.
 
  ABSTRACT  
 
hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in Desulfovibrio vulgaris Miyazaki F hydrogenase. RESULTS: The X-ray crystal structure of the reduced form hydrogenase has been solved at 1.4 A resolution and refined to a crystallographic R factor of 21.8%. The overall structure is very similar to that of the oxidized form, with the exception that the third monatomic bridge observed at the Ni-Fe site in the oxidized enzyme is absent, leaving this site unoccupied in the reduced form. CONCLUSIONS: The unusual hydrogenase was confirmed in the reduced form of the enzyme, with the exception that the electron density assigned to the monatomic sulfur bridge had almost disappeared. On the basis of this finding, as well as the observation that H2S is liberated from the oxidized enzyme under an atmosphere of H2 in the presence of its electron carrier, it was postulated that the monatomic sulfur bridge must be removed for the enzyme to be activated. A possible mechanism for the catalytic action of the hydrogenase is proposed.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Comparison of the mainchain fold of the D. vulgaris Miyazaki F hydrogenase in the reduced (yellow) and oxidized (green) forms. The overall three-dimensional structure of the reduced form, including the sidechain conformations and spatial arrangement of the five metal centers, is almost identical to that of the oxidized form. The metal centers are depicted in CPK representation. (The figure was generated using the programs MOLSCRIPT [19] and Raster3D [20].)
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 549-556) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20301175 M.E.Pandelia, H.Ogata, and W.Lubitz (2010).
Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site.
  Chemphyschem, 11, 1127-1140.  
20340124 S.Löscher, A.Gebler, M.Stein, O.Sanganas, T.Buhrke, I.Zebger, H.Dau, B.Friedrich, O.Lenz, and M.Haumann (2010).
Protein-protein complex formation affects the Ni-Fe and Fe-S centers in the H2-sensing regulatory hydrogenase from Ralstonia eutropha H16.
  Chemphyschem, 11, 1297-1306.  
20147622 Y.Ohki, K.Yasumura, M.Ando, S.Shimokata, and K.Tatsumi (2010).
A model for the CO-inhibited form of [NiFe] hydrogenase: synthesis of CO3Fe(micro-StBu)3Ni{SC6H3-2,6-(mesityl)2} and reversible CO addition at the Ni site.
  Proc Natl Acad Sci U S A, 107, 3994-3997.  
19173074 A.Perra, Q.Wang, A.J.Blake, E.S.Davies, J.McMaster, C.Wilson, and M.Schröder (2009).
Unusual formation of a [NiSFe(2)(CO)(6)] cluster: a structural model for the inactive form of [NiFe] hydrogenase.
  Dalton Trans, (), 925-931.  
19088963 F.A.Armstrong, N.A.Belsey, J.A.Cracknell, G.Goldet, A.Parkin, E.Reisner, K.A.Vincent, and A.F.Wait (2009).
Dynamic electrochemical investigations of hydrogen oxidation and production by enzymes and implications for future technology.
  Chem Soc Rev, 38, 36-51.  
19801638 F.Germer, I.Zebger, M.Saggu, F.Lendzian, R.Schulz, and J.Appel (2009).
Overexpression, isolation, and spectroscopic characterization of the bidirectional [NiFe] hydrogenase from Synechocystis sp. PCC 6803.
  J Biol Chem, 284, 36462-36472.  
19626348 M.E.Pandelia, H.Ogata, L.J.Currell, M.Flores, and W.Lubitz (2009).
Probing intermediates in the activation cycle of [NiFe] hydrogenase by infrared spectroscopy: the Ni-SIr state and its light sensitivity.
  J Biol Inorg Chem, 14, 1227-1241.  
19088965 M.Rakowski Dubois, and D.L.Dubois (2009).
The roles of the first and second coordination spheres in the design of molecular catalysts for H(2) production and oxidation.
  Chem Soc Rev, 38, 62-72.  
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.  
19583207 Y.Kung, T.I.Doukov, J.Seravalli, S.W.Ragsdale, and C.L.Drennan (2009).
Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.
  Biochemistry, 48, 7432-7440.
PDB codes: 3i01 3i04
18647659 C.J.Chou, F.E.Jenney, M.W.Adams, and R.M.Kelly (2008).
Hydrogenesis in hyperthermophilic microorganisms: implications for biofuels.
  Metab Eng, 10, 394-404.  
18378597 F.E.Jenney, and M.W.Adams (2008).
Hydrogenases of the model hyperthermophiles.
  Ann N Y Acad Sci, 1125, 252-266.  
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.  
18350177 P.Jayapal, D.Robinson, M.Sundararajan, I.H.Hillier, and J.J.McDouall (2008).
High level ab initio and DFT calculations of models of the catalytically active Ni-Fe hydrogenases.
  Phys Chem Chem Phys, 10, 1734-1738.  
18633545 P.Jayapal, M.Sundararajan, I.H.Hillier, and N.A.Burton (2008).
QM/MM studies of Ni-Fe hydrogenases: the effect of enzyme environment on the structure and energies of the inactive and active states.
  Phys Chem Chem Phys, 10, 4249-4257.  
18411840 S.Canaguier, V.Artero, and M.Fontecave (2008).
Modelling NiFe hydrogenases: nickel-based electrocatalysts for hydrogen production.
  Dalton Trans, (), 315-325.  
18511566 Y.Ohki, K.Yasumura, K.Kuge, S.Tanino, M.Ando, Z.Li, and K.Tatsumi (2008).
Thiolate-bridged dinuclear iron(tris-carbonyl)-nickel complexes relevant to the active site of [NiFe] hydrogenase.
  Proc Natl Acad Sci U S A, 105, 7652-7657.  
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.  
17609782 M.Razavet, V.Artero, C.Cavazza, Y.Oudart, C.Lebrun, J.C.Fontecilla-Camps, and M.Fontecave (2007).
Tricarbonylmanganese(I)-lysozyme complex: a structurally characterized organometallic protein.
  Chem Commun (Camb), (), 2805-2807.
PDB code: 2q0m
17082918 O.Schröder, B.Bleijlevens, T.E.de Jongh, Z.Chen, T.Li, J.Fischer, J.Förster, C.G.Friedrich, K.A.Bagley, S.P.Albracht, and W.Lubitz (2007).
Characterization of a cyanobacterial-like uptake [NiFe] hydrogenase: EPR and FTIR spectroscopic studies of the enzyme from Acidithiobacillus ferrooxidans.
  J Biol Inorg Chem, 12, 212-233.  
16511689 A.Pardo, A.L.De Lacey, V.M.Fernández, H.J.Fan, Y.Fan, and M.B.Hall (2006).
Density functional study of the catalytic cycle of nickel-iron [NiFe] hydrogenases and the involvement of high-spin nickel(II).
  J Biol Inorg Chem, 11, 286-306.  
16514453 A.Perra, E.S.Davies, J.R.Hyde, Q.Wang, J.McMaster, and M.Schröder (2006).
Electrocatalytic production of hydrogen by a synthetic model of [NiFe] hydrogenases.
  Chem Commun (Camb), (), 1103-1105.  
16418856 E.van der Linden, T.Burgdorf, A.L.de Lacey, T.Buhrke, M.Scholte, V.M.Fernandez, B.Friedrich, and S.P.Albracht (2006).
An improved purification procedure for the soluble [NiFe]-hydrogenase of Ralstonia eutropha: new insights into its (in)stability and spectroscopic properties.
  J Biol Inorg Chem, 11, 247-260.  
16292669 M.van Gastel, M.Stein, M.Brecht, O.Schröder, F.Lendzian, R.Bittl, H.Ogata, Y.Higuchi, and W.Lubitz (2006).
A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.
  J Biol Inorg Chem, 11, 41-51.  
17028697 P.Jayapal, M.Sundararajan, I.H.Hillier, and N.A.Burton (2006).
How are the ready and unready states of nickel-iron hydrogenase activated by H2? A density functional theory study.
  Phys Chem Chem Phys, 8, 4086-4094.  
15803334 A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, and J.C.Fontecilla-Camps (2005).
Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
  J Biol Inorg Chem, 10, 239-249.
PDB codes: 1yq9 1yqw 1yrq
16271886 H.Ogata, S.Hirota, A.Nakahara, H.Komori, N.Shibata, T.Kato, K.Kano, and Y.Higuchi (2005).
Activation process of [NiFe] hydrogenase elucidated by high-resolution X-ray analyses: conversion of the ready to the unready state.
  Structure, 13, 1635-1642.
PDB codes: 1wui 1wuj 1wuk 1wul
16045760 O.Duché, S.Elsen, L.Cournac, and A.Colbeau (2005).
Enlarging the gas access channel to the active site renders the regulatory hydrogenase HupUV of Rhodobacter capsulatus O2 sensitive without affecting its transductory activity.
  FEBS J, 272, 3899-3908.  
15611882 S.Foerster, M.van Gastel, M.Brecht, and W.Lubitz (2005).
An orientation-selected ENDOR and HYSCORE study of the Ni-C active state of Desulfovibrio vulgaris Miyazaki F hydrogenase.
  J Biol Inorg Chem, 10, 51-62.  
15764814 T.Buhrke, S.Löscher, O.Lenz, E.Schlodder, I.Zebger, L.K.Andersen, P.Hildebrandt, W.Meyer-Klaucke, H.Dau, B.Friedrich, and M.Haumann (2005).
Reduction of unusual iron-sulfur clusters in the H2-sensing regulatory Ni-Fe hydrogenase from Ralstonia eutropha H16.
  J Biol Chem, 280, 19488-19495.  
15342627 B.Bleijlevens, T.Buhrke, E.van der Linden, B.Friedrich, and S.P.Albracht (2004).
The auxiliary protein HypX provides oxygen tolerance to the soluble [NiFe]-hydrogenase of ralstonia eutropha H16 by way of a cyanide ligand to nickel.
  J Biol Chem, 279, 46686-46691.  
15211513 L.L.Videau, W.B.Arendall, and J.S.Richardson (2004).
The cis-Pro touch-turn: a rare motif preferred at functional sites.
  Proteins, 56, 298-309.  
15365900 M.Bruschi, L.De Gioia, G.Zampella, M.Reiher, P.Fantucci, and M.Stein (2004).
A theoretical study of spin states in Ni-S4 complexes and models of the [NiFe] hydrogenase active site.
  J Biol Inorg Chem, 9, 873-884.  
14688251 S.Dementin, B.Burlat, A.L.De Lacey, A.Pardo, G.Adryanczyk-Perrier, B.Guigliarelli, V.M.Fernandez, and M.Rousset (2004).
A glutamate is the essential proton transfer gate during the catalytic cycle of the [NiFe] hydrogenase.
  J Biol Chem, 279, 10508-10513.  
12829270 S.B.Mulrooney, and R.P.Hausinger (2003).
Nickel uptake and utilization by microorganisms.
  FEMS Microbiol Rev, 27, 239-261.  
11857710 D.Sellmann, F.Geipel, and F.W.Heinemann (2002).
(NEt(4))(2)[Fe(CN)(2)(CO)('S(3)')]: an iron thiolate complex modeling the [Fe(CN)(2)(CO)(S-Cys)(2)] site of [NiFe] hydrogenase centers.
  Chemistry, 8, 958-966.  
12039011 M.Stein, and W.Lubitz (2002).
Quantum chemical calculations of [NiFe] hydrogenase.
  Curr Opin Chem Biol, 6, 243-249.  
12399498 T.Burgdorf, A.L.De Lacey, and B.Friedrich (2002).
Functional analysis by site-directed mutagenesis of the NAD(+)-reducing hydrogenase from Ralstonia eutropha.
  J Bacteriol, 184, 6280-6288.  
11524134 P.M.Vignais, B.Billoud, and J.Meyer (2001).
Classification and phylogeny of hydrogenases.
  FEMS Microbiol Rev, 25, 455-501.  
10607666 J.W.Peters (1999).
Structure and mechanism of iron-only hydrogenases.
  Curr Opin Struct Biol, 9, 670-676.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.