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PDBsum entry 3oma

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3oma
Jmol
Contents
Protein chains
535 a.a. *
256 a.a. *
Ligands
_OH ×2
DMU ×11
TRD ×9
HEA ×4
HTH
Metals
_CA ×2
_CD ×4
_CU ×4
_MG ×2
CU1 ×2
Waters ×452
* Residue conservation analysis
PDB id:
3oma
Name: Oxidoreductase
Title: Catalytic core subunits (i and ii) of cytochromE C oxidase f rhodobacter sphaeroides with k362m mutation
Structure: CytochromE C oxidase, aa3 type, subunit i. Chain: a, c. Fragment: unp residues 17-551. Engineered: yes. Mutation: yes. CytochromE C oxidase subunit 2. Chain: b, d. Fragment: unp residues 30-281. Engineered: yes
Source: Rhodobacter sphaeroides 2.4.1. Organism_taxid: 272943. Strain: atcc 17023/2.4.1/ncib 8253/dsm 158. Gene: coxi, ctad, rhos4_04590, rsp_1877. Expressed in: rhodobacter sphaeroides. Expression_system_taxid: 1063. Gene: coxii, ctab, ctac, rhos4_04060, rsp_1826.
Resolution:
2.30Å     R-factor:   0.192     R-free:   0.219
Authors: J.Liu,L.Qin,S.Ferguson-Miller
Key ref: J.Liu et al. (2011). Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump. Proc Natl Acad Sci U S A, 108, 1284-1289. PubMed id: 21205904
Date:
26-Aug-10     Release date:   02-Feb-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q3J5A7  (Q3J5A7_RHOS4) -  Cytochrome c oxidase, aa3 type, subunit I
Seq:
Struc:
 
Seq:
Struc:
566 a.a.
535 a.a.*
Protein chains
Pfam   ArchSchema ?
Q3J5G0  (Q3J5G0_RHOS4) -  Cytochrome c oxidase subunit 2
Seq:
Struc:
303 a.a.
256 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.1.9.3.1  - Cytochrome-c oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
4 × ferrocytochrome c
Bound ligand (Het Group name = HEA)
matches with 50.60% similarity
+ O(2)
+ 4 × H(+)
= 4 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     electron carrier activity     7 terms  

 

 
    reference    
 
 
Proc Natl Acad Sci U S A 108:1284-1289 (2011)
PubMed id: 21205904  
 
 
Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.
J.Liu, L.Qin, S.Ferguson-Miller.
 
  ABSTRACT  
 
Crystal structures in both oxidized and reduced forms are reported for two bacterial cytochrome c oxidase mutants that define the D and K proton paths, showing conformational change in response to reduction and the loss of strategic waters that can account for inhibition of proton transfer. In the oxidized state both mutants of the Rhodobacter sphaeroides enzyme, D132A and K362M, show overall structures similar to wild type, indicating no long-range effects of mutation. In the reduced state, the mutants show an altered conformation similar to that seen in reduced wild type, confirming this reproducible, reversible response to reduction. In the strongly inhibited D132A mutant, positions of residues and waters in the D pathway are unaffected except in the entry region close to the mutation, where a chloride ion replaces the missing carboxyl and a 2-Å shift in N207 results in loss of its associated water. In K362M, the methionine occupies the same position as the original lysine, but K362- and T359-associated waters in the wild-type structure are missing, likely accounting for the severe inhibition. Spectra of oxidized frozen crystals taken during X-ray radiation show metal center reduction, but indicate development of a strained configuration that only relaxes to a native form upon annealing. Resistance of the frozen crystal to structural change clarifies why the oxidized conformation is observable and supports the conclusion that the reduced conformation has functional significance. A mechanism is described that explains the conformational change and the incomplete response of the D-path mutant.