spacer
spacer

PDBsum entry 3eh5

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3eh5
Jmol
Contents
Protein chains
557 a.a. *
166 a.a. *
33 a.a. *
Ligands
HEM
HAS
CUA
BNG ×4
Metals
CU1
Waters ×83
* Residue conservation analysis
PDB id:
3eh5
Name: Oxidoreductase
Title: Structure of the reduced form of cytochrome ba3 oxidase from thermophilus
Structure: CytochromE C oxidase subunit 1. Chain: a. Fragment: unp residues 2-562. Synonym: cytochromE C oxidase polypeptide i, cytochromE C b subunit i, cytochrome cba3 subunit 1. Engineered: yes. Mutation: yes. CytochromE C oxidase subunit 2. Chain: b.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: cbaa, ttha1135. Expressed in: thermus thermophilus. Expression_system_taxid: 274. Gene: cbab, ctac, ttha1134. Gene: cbad, ttha1133.
Resolution:
2.80Å     R-factor:   0.200     R-free:   0.257
Authors: B Liu,Y.Chen,T.Doukov,S.M.Soltis,D.Stout,J.A.Fee
Key ref: B.Liu et al. (2009). Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Biochemistry, 48, 820-826. PubMed id: 19140675
Date:
11-Sep-08     Release date:   21-Apr-09    
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.
557 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.
33 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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)
+ 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    
 
 
Biochemistry 48:820-826 (2009)
PubMed id: 19140675  
 
 
Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme.
B.Liu, Y.Chen, T.Doukov, S.M.Soltis, C.D.Stout, J.A.Fee.
 
  ABSTRACT  
 
Three paths for obtaining crystals of reduced (II-E4Q/I-K258R) cytochrome ba(3) are described, and the structures of these are reported at approximately 2.8-3.0 A resolution. Microspectrophotometry of single crystals of Thermus ba(3) oxidase at 100 K was used to show that crystals of the oxidized enzyme are reduced in an intense X-ray (beam line 7-1 at the Stanford Synchrotron Radiation Laboratory), being nearly complete in 1 min. The previously reported structures of ba(3) (Protein Data Bank entries 1EHK and 1XME ), having a crystallographically detectable water between the Cu(B) and Fe(a3) metals of the dinuclear center, actually represent the X-ray radiation-reduced enzyme. Dithionite-reduced crystals or crystals formed from dithionite-reduced enzyme revealed the absence of the above-mentioned water and an increase in the Cu(B)-Fe(a3) distance of approximately 0.3 A. The new structures are discussed in terms of enzyme function. An unexpected optical absorption envelope at approximately 590 nm is also reported. This spectral feature is tentatively thought to arise from a five-coordinate, low-spin, ferrous heme a(3) that is trapped in the frozen crystals.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21419779 C.Coelho, P.J.González, J.G.Moura, I.Moura, J.Trincão, and M.João Romão (2011).
The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states.
  J Mol Biol, 408, 932-948.
PDB codes: 3ml1 3o5a
21205904 J.Liu, L.Qin, and S.Ferguson-Miller (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.
PDB codes: 3om3 3oma 3omi 3omn
20370613 A.V.Kalinovich, N.V.Azarkina, T.V.Vygodina, T.Soulimane, and A.A.Konstantinov (2010).
Peculiarities of cyanide binding to the ba3-type cytochrome oxidase from the thermophilic bacterium Thermus thermophilus.
  Biochemistry (Mosc), 75, 342-352.  
21097703 I.Szundi, C.Funatogawa, J.A.Fee, T.Soulimane, and O.Einarsdóttir (2010).
CO impedes superfast O2 binding in ba3 cytochrome oxidase from Thermus thermophilus.
  Proc Natl Acad Sci U S A, 107, 21010-21015.  
19397279 L.Qin, J.Liu, D.A.Mills, D.A.Proshlyakov, C.Hiser, and S.Ferguson-Miller (2009).
Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake.
  Biochemistry, 48, 5121-5130.
PDB codes: 3fye 3fyi
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 codes are shown on the right.