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PDBsum entry 4gp4

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
4gp4
Jmol
Contents
Protein chains
554 a.a.
166 a.a.
31 a.a.
Ligands
HEM
HAS-PER
OLC ×16
CUA
Metals
_CU
Waters ×115
PDB id:
4gp4
Name: Oxidoreductase
Title: Structure of recombinant cytochrome ba3 oxidase mutant y133f thermus thermophilus
Structure: CytochromE C oxidase subunit 1. Chain: a. Synonym: cytochromE C ba(3) subunit i, cytochromE C oxidase polypeptide i, cytochrome cba3 subunit 1. Engineered: yes. Mutation: yes. CytochromE C oxidase subunit 2. Chain: b. Synonym: cytochromE C ba(3) subunit ii, cytochromE C oxidas
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Gene: cbaa, ttha1135. Expressed in: thermus thermophilus. Expression_system_taxid: 274. Gene: cbab, ctac, ttha1134. Gene: cbad, ttha1133.
Resolution:
2.80Å     R-factor:   0.182     R-free:   0.227
Authors: Y.Li,Y.Chen,C.D.Stout
Key ref: W.McDonald et al. (2013). Ligand access to the active site in Thermus thermophilus ba(3) and bovine heart aa(3) cytochrome oxidases. Biochemistry, 52, 640-652. PubMed id: 23282175 DOI: 10.1021/bi301358a
Date:
20-Aug-12     Release date:   16-Jan-13    
Supersedes: 4f05
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SJ79  (COX1_THET8) -  Cytochrome c oxidase subunit 1
Seq:
Struc:
 
Seq:
Struc:
562 a.a.
554 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SJ80  (COX2_THET8) -  Cytochrome c oxidase subunit 2
Seq:
Struc:
168 a.a.
166 a.a.
Protein chain
Pfam   ArchSchema ?
P82543  (COXA_THET8) -  Cytochrome c oxidase polypeptide 2A
Seq:
Struc:
34 a.a.
31 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: 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 = HEM)
matches with 63.64% similarity
+
O(2)
Bound ligand (Het Group name = PER)
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   7 terms 
  Biochemical function     electron carrier activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi301358a Biochemistry 52:640-652 (2013)
PubMed id: 23282175  
 
 
Ligand access to the active site in Thermus thermophilus ba(3) and bovine heart aa(3) cytochrome oxidases.
W.McDonald, C.Funatogawa, Y.Li, I.Szundi, Y.Chen, J.A.Fee, C.D.Stout, ..Einarsdóttir.
 
  ABSTRACT  
 
Knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates the functions of these enzymes. Using photolabile NO and O(2) carriers, we recently found that NO and O(2) binding in Thermus thermophilus (Tt ) ba(3) is ∼10 times faster than in the bovine enzyme, indicating that inherent structural differences affect ligand access in these enzymes. Using X-ray crystallography, time-resolved optical absorption measurements, and theoretical calculations, we investigated ligand access in wild-type Tt ba(3) and the mutants, Y133W, T231F, and Y133W/T231F, in which tyrosine and threonine in the O(2) channel of Tt ba(3) are replaced by the corresponding bulkier tryptophan and phenylalanine, respectively, present in the aa(3) enzymes. NO binding in Y133W and Y133W/T231F was found to be 5 times slower than in wild-type ba(3) and the T231F mutant. The results show that the Tt ba(3) Y133W mutation and the bovine W126 residue physically impede NO access to the binuclear center. In the bovine enzyme, there is a hydrophobic "way station", which may further slow ligand access to the active site. Classical simulations of diffusion of Xe to the active sites in ba(3) and bovine aa(3) show conformational freedom of the bovine F238 and the F231 side chain of the Tt ba(3) Y133W/T231F mutant, with both residues rotating out of the ligand channel, resulting in no effect on ligand access in either enzyme.