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PDBsum entry 3hb3

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3hb3
Jmol
Contents
Protein chains
529 a.a. *
252 a.a. *
118 a.a. *
108 a.a. *
Ligands
HEA ×2
LDA ×10
LMT ×14
PEO
Metals
CU1 ×3
_MN
_CA
Waters ×554
* Residue conservation analysis
PDB id:
3hb3
Name: Oxidoreductase
Title: High resolution crystal structure of paracoccus denitrificans cytochromE C oxidase
Structure: CytochromE C oxidase subunit 1-beta. Chain: a. Synonym: cytochromE C oxidase polypeptide i-beta, cytochrome aa3 subunit 1-beta. Engineered: yes. CytochromE C oxidase subunit 2. Chain: b. Synonym: cytochromE C oxidase polypeptide ii, cytochrome aa3 subunit 2, oxidase aa(3) subunit 2.
Source: Paracoccus denitrificans. Organism_taxid: 266. Gene: ctadii. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ctac, coii, ctab. Mus musculus. Mouse. Organism_taxid: 10090.
Resolution:
2.25Å     R-factor:   0.220     R-free:   0.280
Authors: J.Koepke,H.Angerer,G.Peng
Key ref: J.Koepke et al. (2009). High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways. Biochim Biophys Acta, 1787, 635-645. PubMed id: 19374884
Date:
04-May-09     Release date:   23-Jun-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P98002  (COX1B_PARDE) -  Cytochrome c oxidase subunit 1-beta
Seq:
Struc:
 
Seq:
Struc:
558 a.a.
529 a.a.
Protein chain
Pfam   ArchSchema ?
P08306  (COX2_PARDE) -  Cytochrome c oxidase subunit 2
Seq:
Struc:
298 a.a.
252 a.a.
Protein chain
Pfam   ArchSchema ?
P18525  (HVM54_MOUSE) -  Ig heavy chain V region 5-84
Seq:
Struc:
117 a.a.
118 a.a.*
Protein chain
Pfam   ArchSchema ?
P01636  (KV5A4_MOUSE) -  Ig kappa chain V-V region MOPC 149
Seq:
Struc:
108 a.a.
108 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 20 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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 50.00% similarity
+
O(2)
Bound ligand (Het Group name = PEO)
corresponds exactly
+ 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   4 terms 
  Biological process     oxidation-reduction process   8 terms 
  Biochemical function     electron carrier activity     8 terms  

 

 
    reference    
 
 
Biochim Biophys Acta 1787:635-645 (2009)
PubMed id: 19374884  
 
 
High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways.
J.Koepke, E.Olkhova, H.Angerer, H.Müller, G.Peng, H.Michel.
 
  ABSTRACT  
 
The structure of the two-subunit cytochrome c oxidase from Paracoccus denitrificans has been refined using X-ray cryodata to 2.25 A resolution in order to gain further insights into its mechanism of action. The refined structural model shows a number of new features including many additional solvent and detergent molecules. The electron density bridging the heme a(3) iron and Cu(B) of the active site is fitted best by a peroxo-group or a chloride ion. Two waters or OH(-) groups do not fit, one water (or OH(-)) does not provide sufficient electron density. The analysis of crystals of cytochrome c oxidase isolated in the presence of bromide instead of chloride appears to exclude chloride as the bridging ligand. In the D-pathway a hydrogen bonded chain of six water molecules connects Asn131 and Glu278, but the access for protons to this water chain is blocked by Asn113, Asn131 and Asn199. The K-pathway contains two firmly bound water molecules, an additional water chain seems to form its entrance. Above the hemes a cluster of 13 water molecules is observed which potentially form multiple exit pathways for pumped protons. The hydrogen bond pattern excludes that the Cu(B) ligand His326 is present in the imidazolate form.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21368144 I.von der Hocht, J.H.van Wonderen, F.Hilbers, H.Angerer, F.MacMillan, and H.Michel (2011).
Interconversions of P and F intermediates of cytochrome c oxidase from Paracoccus denitrificans.
  Proc Natl Acad Sci U S A, 108, 3964-3969.  
20798065 L.N.Ojemyr, H.J.Lee, R.B.Gennis, and P.Brzezinski (2010).
Functional interactions between membrane-bound transporters and membranes.
  Proc Natl Acad Sci U S A, 107, 15763-15767.  
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