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PDBsum entry 1gx7
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1gx7

 

 

 

 

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Contents
Protein chains
371 a.a. *
88 a.a. *
107 a.a. *
Ligands
SF4 ×3
PDT
CYN ×2
CMO ×2
HEC ×4
Metals
FE2 ×2
* Residue conservation analysis
Theoretical model
PDB id:
1gx7
Name: Oxidoreductase
Title: Best model of the electron transfer complex between cytochrome c3 and [fe]-hydrogenase
Structure: Periplasmic [fe] hydrogenase large subunit. Chain: a. Periplasmic [fe] hydrogenase small subunit. Chain: d. Cytochrome c3. Chain: e
Source: Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough. Strain: hildenborough
NMR struc: 1 models
Authors: L.Elantak,X.Morelli,O.Bornet,C.Hatchikian,M.Czjzek,A.Dolla, F.Guerlesquin
Key ref:
L.ElAntak et al. (2003). The cytochrome c3-[Fe]-hydrogenase electron-transfer complex: structural model by NMR restrained docking. FEBS Lett, 548, 1-4. PubMed id: 12885397 DOI: 10.1016/S0014-5793(03)00718-X
Date:
28-Mar-02     Release date:   31-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07598  (PHFL_DESVH) -  Periplasmic [Fe] hydrogenase large subunit from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
Seq:
Struc: 		421 a.a.
371 a.a.
Protein chain
Pfam   ArchSchema ?
P07603  (PHFS_DESVH) -  Periplasmic [Fe] hydrogenase small subunit from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
Seq:
Struc: 		123 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P00131  (CYC3_DESVH) -  Cytochrome c3 from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
Seq:
Struc: 		129 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, D: E.C.1.12.7.2  - ferredoxin hydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2 + 2 oxidized [2Fe-2S]-[ferredoxin] = 2 reduced [2Fe-2S]-[ferredoxin] + 2 H+
      Cofactor: Iron-sulfur; Ni(2+)
Iron-sulfur
 Ni(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1016/S0014-5793(03)00718-X FEBS Lett 548:1-4 (2003)
PubMed id: 12885397  
 
 
The cytochrome c3-[Fe]-hydrogenase electron-transfer complex: structural model by NMR restrained docking.
L.ElAntak, X.Morelli, O.Bornet, C.Hatchikian, M.Czjzek, A.Dolla, F.Guerlesquin.
 
  ABSTRACT  
 
Cytochrome c(3) (M(r) 13000) is a low redox potential cytochrome specific of the anaerobic metabolism in sulfate-reducing bacteria. This tetrahemic cytochrome is an intermediate between the [Fe]-hydrogenase and the cytochrome Hmc in Desulfovibrio vulgaris Hildenborough strain. The present work describes the structural model of the cytochrome c(3)-[Fe]-hydrogenase complex obtained by nuclear magnetic resonance restrained docking. This model connects the distal cluster of the [Fe]-hydrogenase to heme 4 of the cytochrome, the same heme found in the interaction with cytochrome Hmc. This result gives evidence that cytochrome c(3) is an electron shuttle between the periplasmic hydrogenase and the Hmc membrane-bound complex.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. A: Ribbon representation of the best representative structure of the [Fe]-hydrogenase–cytochrome c[3] complex. The [Fe]-hydrogenase is the left polypeptide chain, the large subunit is colored in beige; the small subunit is colored in yellow and the ferredoxin-like domain in blue, the iron clusters are in green. Cytochrome c[3] is the right polypeptide chain colored in blue, the heme groups are in red. B: Zoom-in view of the interface region, highlighting the residues involved in interatomic contacts within the cytochrome c[3]–[Fe]-hydrogenase complex. Heme 4 and cytochrome c[3] residues are labeled in red, distal [4Fe–4S] cluster and residues of [Fe]-hydrogenase are labeled in green. 		Figure 4.
Fig. 4. A possible mechanism for ALAD in which both A- and P-side substrates form Schiff bases with the enzyme.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2003, 548, 1-4) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19233927 X.Li, Q.Luo, N.Q.Wofford, K.L.Keller, M.J.McInerney, J.D.Wall, and L.R.Krumholz (2009).
A molybdopterin oxidoreductase is involved in H2 oxidation in Desulfovibrio desulfuricans G20.
  J Bacteriol, 191, 2675-2682.  
16964504 R.O.Louro (2007).
Proton thrusters: overview of the structural and functional features of soluble tetrahaem cytochromes c3.
  J Biol Inorg Chem, 12, 1.  
16836469 M.Ihara, H.Nakamoto, T.Kamachi, I.Okura, and M.Maeda (2006).
Photoinduced hydrogen production by direct electron transfer from photosystem I cross-linked with cytochrome c3 to [NiFe]-hydrogenase.
  Photochem Photobiol, 82, 1677-1685.  
16341896 R.E.Di Paolo, P.M.Pereira, I.Gomes, F.M.Valente, I.A.Pereira, and R.Franco (2006).
Resonance Raman fingerprinting of multiheme cytochromes from the cytochrome c3 family.
  J Biol Inorg Chem, 11, 217-224.  
15853810 C.A.Salgueiro, L.Morgado, B.Fonseca, P.Lamosa, T.Catarino, D.L.Turner, and R.O.Louro (2005).
Binding of ligands originates small perturbations on the microscopic thermodynamic properties of a multicentre redox protein.
  FEBS J, 272, 2251-2260.  
15764652 L.Rivas, C.M.Soares, A.M.Baptista, J.Simaan, R.E.Di Paolo, D.H.Murgida, and P.Hildebrandt (2005).
Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies.
  Biophys J, 88, 4188-4199.  
14594815 M.Fournier, Z.Dermoun, M.C.Durand, and A.Dolla (2004).
A new function of the Desulfovibrio vulgaris Hildenborough [Fe] hydrogenase in the protection against oxidative stress.
  J Biol Chem, 279, 1787-1793.  
15386621 M.Prudêncio, and M.Ubbink (2004).
Transient complexes of redox proteins: structural and dynamic details from NMR studies.
  J Mol Recognit, 17, 524-539.  
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.

 

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