spacer
spacer

PDBsum entry 1e08
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrogenase PDB id
1e08

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
371 a.a. *
88 a.a. *
78 a.a. *
Ligands
SF4 ×3
PDT
CYN ×2
CMO ×2
HEC
Metals
_ZN
FE2 ×2
Waters ×3
* Residue conservation analysis
Theoretical model
PDB id:
1e08
Name: Hydrogenase
Title: Structural model of the [fe]-hydrogenase/cytochrome c553 complex combining nmr and soft-docking
Structure: [Fe]-hydrogenase (large subunit). Chain: a. [Fe]-hydrogenase (small subunit). Chain: d. Cytochrome c553. Chain: e
Source: Desulfovibrio desulfuricans. Organism_taxid: 876. Atcc: 7757. Cellular_location: periplasm. Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough. Cellular_location: periplasm
NMR struc: 1 models
Authors: X.Morelli,M.Czjzek,C.E.Hatchikian,O.Bornet,J.C.Fontecilla-Camps, N.P.Palma,J.J.G.Moura,F.Guerlesquin
Key ref:
X.Morelli et al. (2000). Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations. J Biol Chem, 275, 23204-23210. PubMed id: 10748163 DOI: 10.1074/jbc.M909835199
Date:
13-Mar-00     Release date:   25-Aug-00    
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 ?
P04032  (CY553_DESVH) -  Cytochrome c-553 from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
Seq:
Struc: 		103 a.a.
78 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: 10.1074/jbc.M909835199 J Biol Chem 275:23204-23210 (2000)
PubMed id: 10748163  
 
 
Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations.
X.Morelli, M.Czjzek, C.E.Hatchikian, O.Bornet, J.C.Fontecilla-Camps, N.P.Palma, J.J.Moura, F.Guerlesquin.
 
  ABSTRACT  
 
Fe-hydrogenase is a 54-kDa iron-sulfur enzyme essential for hydrogen cycling in sulfate-reducing bacteria. The x-ray structure of Desulfovibrio desulfuricans Fe-hydrogenase has recently been solved, but structural information on the recognition of its redox partners is essential to understand the structure-function relationships of the enzyme. In the present work, we have obtained a structural model of the complex of Fe-hydrogenase with its redox partner, the cytochrome c(553), combining docking calculations and NMR experiments. The putative models of the complex demonstrate that the small subunit of the hydrogenase has an important role in the complex formation with the redox partner; 50% of the interacting site on the hydrogenase involves the small subunit. The closest contact between the redox centers is observed between Cys-38, a ligand of the distal cluster of the hydrogenase and Cys-10, a ligand of the heme in the cytochrome. The electron pathway from the distal cluster of the Fe-hydrogenase to the heme of cytochrome c(553) was investigated using the software Greenpath and indicates that the observed cysteine/cysteine contact has an essential role. The spatial arrangement of the residues on the interface of the complex is very similar to that already described in the ferredoxin-cytochrome c(553) complex, which therefore, is a very good model for the interacting domain of the Fe-hydrogenase-cytochrome c(553).
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. A, 1H and 15N chemical shift variations of cytochrome c[553] NH groups observed in TROSY experiments. B, mapping of the hydrogenase interacting site on the cytochrome c[553], obtained by heteronuclear experiments. In the top figure, the heme is colored in red, the NH groups whose resonances undergo chemical shift variations are in green, unassigned residues are in blue, and unaffected residues are in white. The bottom figure shows a 180° rotation along the x axis and represents the "back side" of the molecule. 		Figure 5.
Fig. 5. Model of fam1 solution 3 using Grasp software. A, ribbon model of the cytochrome c[553]-hydrogenase complex. For hydrogenase, the ferredoxin-like domain is in green, the large subunit is in blue, and the small subunit is in yellow. The cytochrome c[553] is in red. B, view of interface in the cytochrome c[553]-ferredoxin complex (a) and in the cytochrome c[553]-hydrogenase complex (b).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 23204-23210) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16060674 S.Deep, S.C.Im, E.R.Zuiderweg, and L.Waskell (2005).
Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data.
  Biochemistry, 44, 10654-10668.  
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.  
12784362 L.Krippahl, J.J.Moura, and P.N.Palma (2003).
Modeling protein complexes with BiGGER.
  Proteins, 52, 19-23.  
14528294 P.Arnoux, M.Sabaty, J.Alric, B.Frangioni, B.Guigliarelli, J.M.Adriano, and D.Pignol (2003).
Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase.
  Nat Struct Biol, 10, 928-934.
PDB code: 1ogy
12165429 J.Simon (2002).
Enzymology and bioenergetics of respiratory nitrite ammonification.
  FEMS Microbiol Rev, 26, 285-309.  
11320307 M.Czjzek, P.Arnoux, R.Haser, and W.Shepard (2001).
Structure of cytochrome c7 from Desulfuromonas acetoxidans at 1.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 670-678.
PDB code: 1hh5
11524134 P.M.Vignais, B.Billoud, and J.Meyer (2001).
Classification and phylogeny of hydrogenases.
  FEMS Microbiol Rev, 25, 455-501.  
11567104 X.J.Morelli, P.N.Palma, F.Guerlesquin, and A.C.Rigby (2001).
A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
  Protein Sci, 10, 2131-2137.  
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 code is shown on the right.

 

spacer
spacer