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PDBsum entry 3bvd

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3bvd
Jmol
Contents
Protein chains
550 a.a. *
166 a.a. *
33 a.a. *
Ligands
HEM
HAS
CUA
Metals
_XE ×7
_CU
* Residue conservation analysis
PDB id:
3bvd
Name: Oxidoreductase
Title: Structure of surface-engineered cytochrome ba3 oxidase from thermus thermophilus under xenon pressure, 100psi 5min
Structure: CytochromE C oxidase subunit 1. Chain: a. Synonym: cytochromE C oxidase polypeptide i, cytochromE C ba3, subunit i, cytochrome cba3 subunit 1. Engineered: yes. Mutation: yes. CytochromE C oxidase subunit 2. Chain: b. Synonym: cytochromE C oxidase polypeptide ii, cytochromE C
Source: Thermus thermophilus. Strain: hb8. Atcc: 27634. Gene: cbaa. Expressed in: thermus thermophilus. Gene: cbab, ctac. Gene: cbad.
Resolution:
3.37Å     R-factor:   0.292     R-free:   0.336
Authors: V.M.Luna,Y.Chen,J.A.Fee,C.D.Stout
Key ref: V.M.Luna et al. (2008). Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus: structural analysis and role of oxygen transport channels in the heme-Cu oxidases. Biochemistry, 47, 4657-4665. PubMed id: 18376849
Date:
07-Jan-08     Release date:   20-May-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SJ79  (COX1_THET8) -  Cytochrome c oxidase subunit 1
Seq:
Struc:
 
Seq:
Struc:
562 a.a.
550 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 63.00% 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 47:4657-4665 (2008)
PubMed id: 18376849  
 
 
Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus: structural analysis and role of oxygen transport channels in the heme-Cu oxidases.
V.M.Luna, Y.Chen, J.A.Fee, C.D.Stout.
 
  ABSTRACT  
 
Cytochrome ba3 is a cytochrome c oxidase from the plasma membrane of Thermus thermophilus and is the preferred terminal enzyme of cellular respiration at low dioxygen tensions. Using cytochrome ba 3 crystals pressurized at varying conditions under Xe or Kr gas, and X-ray data for six crystals, we identify the relative affinities of Xe and Kr atoms for as many as seven distinct binding sites. These sites track a continuous, Y-shaped channel, 18-20 A in length, lined by hydrophobic residues, which leads from the surface of the protein where two entrance holes, representing the top of the Y, connect the bilayer to the a3-CuB center at the base of the Y. Considering the increased affinity of O2 for hydrophobic environments, the hydrophobic nature of the channel, its orientation within the bilayer, its connection to the active site, its uniform diameter, its virtually complete occupation by Xe, and its isomorphous presence in the native enzyme, we infer that the channel is a diffusion pathway for O2 into the dinuclear center of cytochrome ba3. These observations provide a basis for analyzing similar channels in other oxidases of known structure, and these structures are discussed in terms of mechanisms of O2 transport in biological systems, details of CO binding to and egress from the dinuclear center, the bifurcation of the oxygen-in and water-out pathways, and the possible role of the oxygen channel in aerobic thermophily.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20352642 A.Guskov, A.Gabdulkhakov, M.Broser, C.Glöckner, J.Hellmich, J.Kern, J.Frank, F.Müh, W.Saenger, and A.Zouni (2010).
Recent progress in the crystallographic studies of photosystem II.
  Chemphyschem, 11, 1160-1171.  
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.  
21164002 P.Moënne-Loccoz, and J.A.Fee (2010).
Biochemistry. Catalyzing NO to N2O in the nitrogen cycle.
  Science, 330, 1632-1633.  
19140675 B.Liu, Y.Chen, T.Doukov, S.M.Soltis, C.D.Stout, and J.A.Fee (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.
PDB codes: 3eh3 3eh4 3eh5
19805275 H.Y.Chang, J.Hemp, Y.Chen, J.A.Fee, and R.B.Gennis (2009).
The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping.
  Proc Natl Acad Sci U S A, 106, 16169-16173.  
19705820 S.Satagopan, S.S.Scott, T.G.Smith, and F.R.Tabita (2009).
A Rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration.
  Biochemistry, 48, 9076-9083.  
19815515 Y.Tu, P.Xiu, R.Wan, J.Hu, R.Zhou, and H.Fang (2009).
Water-mediated signal multiplication with Y-shaped carbon nanotubes.
  Proc Natl Acad Sci U S A, 106, 18120-18124.  
18830685 G.Renger, and T.Renger (2008).
Photosystem II: The machinery of photosynthetic water splitting.
  Photosynth Res, 98, 53-80.  
18928258 J.A.Fee, D.A.Case, and L.Noodleman (2008).
Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus.
  J Am Chem Soc, 130, 15002-15021.  
18975062 P.Brzezinski, and R.B.Gennis (2008).
Cytochrome c oxidase: exciting progress and remaining mysteries.
  J Bioenerg Biomembr, 40, 521-531.  
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.