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PDBsum entry 3abl

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3abl
Jmol
Contents
Protein chains
514 a.a. *
227 a.a. *
259 a.a. *
144 a.a. *
104 a.a. *
93 a.a. *
84 a.a. *
75 a.a. *
71 a.a. *
57 a.a. *
49 a.a. *
46 a.a. *
43 a.a. *
Ligands
PER ×2
HEA ×4
TGL ×6
PGV ×8
CUA ×2
PSC ×2
CHD ×8
DMU ×4
UNX ×2
CDL ×4
PEK
Metals
_ZN
_CU ×2
_MG ×2
_NA ×2
Waters ×1708
* Residue conservation analysis
PDB id:
3abl
Name: Oxidoreductase
Title: Bovine heart cytochromE C oxidase at the fully oxidized state (15-s x-ray exposure dataset)
Structure: CytochromE C oxidase subunit 1. Chain: a, n. Synonym: cytochromE C oxidase polypeptide i. CytochromE C oxidase subunit 2. Chain: b, o. Synonym: cytochromE C oxidase polypeptide ii. CytochromE C oxidase subunit 3. Chain: c, p. Synonym: cytochromE C oxidase polypeptide iii.
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organism_taxid: 9913
Resolution:
2.10Å     R-factor:   0.176     R-free:   0.210
Authors: H.Aoyama,K.Muramoto,K.Shinzawa-Itoh,E.Yamashita,T.Tsukihara, T.Ogura,S.Yoshikawa
Key ref:
H.Aoyama et al. (2009). A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump. Proc Natl Acad Sci U S A, 106, 2165-2169. PubMed id: 19164527 DOI: 10.1073/pnas.0806391106
Date:
16-Dec-09     Release date:   19-Jan-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00396  (COX1_BOVIN) -  Cytochrome c oxidase subunit 1
Seq:
Struc:
514 a.a.
514 a.a.*
Protein chains
Pfam   ArchSchema ?
P68530  (COX2_BOVIN) -  Cytochrome c oxidase subunit 2
Seq:
Struc:
227 a.a.
227 a.a.*
Protein chains
Pfam   ArchSchema ?
P00415  (COX3_BOVIN) -  Cytochrome c oxidase subunit 3
Seq:
Struc:
261 a.a.
259 a.a.
Protein chains
Pfam   ArchSchema ?
P00423  (COX41_BOVIN) -  Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Seq:
Struc:
169 a.a.
144 a.a.
Protein chains
Pfam   ArchSchema ?
P00426  (COX5A_BOVIN) -  Cytochrome c oxidase subunit 5A, mitochondrial
Seq:
Struc:
152 a.a.
104 a.a.
Protein chains
Pfam   ArchSchema ?
P00428  (COX5B_BOVIN) -  Cytochrome c oxidase subunit 5B, mitochondrial
Seq:
Struc:
129 a.a.
93 a.a.
Protein chains
Pfam   ArchSchema ?
P07471  (CX6A2_BOVIN) -  Cytochrome c oxidase subunit 6A2, mitochondrial
Seq:
Struc:
97 a.a.
84 a.a.*
Protein chains
Pfam   ArchSchema ?
P00429  (CX6B1_BOVIN) -  Cytochrome c oxidase subunit 6B1
Seq:
Struc:
86 a.a.
75 a.a.
Protein chains
Pfam   ArchSchema ?
P04038  (COX6C_BOVIN) -  Cytochrome c oxidase subunit 6C
Seq:
Struc:
74 a.a.
71 a.a.
Protein chains
Pfam   ArchSchema ?
P07470  (CX7A1_BOVIN) -  Cytochrome c oxidase subunit 7A1, mitochondrial
Seq:
Struc:
80 a.a.
57 a.a.
Protein chains
Pfam   ArchSchema ?
P13183  (COX7B_BOVIN) -  Cytochrome c oxidase subunit 7B, mitochondrial
Seq:
Struc:
80 a.a.
49 a.a.
Protein chains
Pfam   ArchSchema ?
P00430  (COX7C_BOVIN) -  Cytochrome c oxidase subunit 7C, mitochondrial
Seq:
Struc:
63 a.a.
46 a.a.
Protein chains
Pfam   ArchSchema ?
P10175  (COX8B_BOVIN) -  Cytochrome c oxidase subunit 8B, mitochondrial
Seq:
Struc:
70 a.a.
43 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, N: 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 = 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   11 terms 
  Biological process     oxidation-reduction process   8 terms 
  Biochemical function     electron carrier activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0806391106 Proc Natl Acad Sci U S A 106:2165-2169 (2009)
PubMed id: 19164527  
 
 
A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump.
H.Aoyama, K.Muramoto, K.Shinzawa-Itoh, K.Hirata, E.Yamashita, T.Tsukihara, T.Ogura, S.Yoshikawa.
 
  ABSTRACT  
 
The fully oxidized form of cytochrome c oxidase, immediately after complete oxidation of the fully reduced form, pumps protons upon each of the initial 2 single-electron reduction steps, whereas protons are not pumped during single-electron reduction of the fully oxidized "as-isolated" form (the fully oxidized form without any reduction/oxidation treatment) [Bloch D, et al. (2004) The catalytic cycle of cytochrome c oxidase is not the sum of its two halves. Proc Natl Acad Sci USA 101:529-533]. For identification of structural differences causing the remarkable functional difference between these 2 distinct fully oxidized forms, the X-ray structure of the fully oxidized as-isolated bovine heart cytochrome c oxidase was determined at 1.95-A resolution by limiting the X-ray dose for each shot and by using many (approximately 400) single crystals. This minimizes the effects of hydrated electrons induced by the X-ray irradiation. The X-ray structure showed a peroxide group bridging the 2 metal sites in the O(2) reduction site (Fe(3+)-O(-)-O(-)-Cu(2+)), in contrast to a ferric hydroxide (Fe(3+)-OH(-)) in the fully oxidized form immediately after complete oxidation from the fully reduced form, as has been revealed by resonance Raman analyses. The peroxide-bridged structure is consistent with the reductive titration results showing that 6 electron equivalents are required for complete reduction of the fully oxidized as-isolated form. The structural difference between the 2 fully oxidized forms suggests that the bound peroxide in the O(2) reduction site suppresses the proton pumping function.
 
  Selected figure(s)  
 
Figure 2.
(Fo-Fc) difference electron density maps for the 1- s and 15-s datasets, calculated at 2.5-Å resolution. The datasets are depicted together with the structural model of heme a[3], Cu[B], and 3 water molecules. Heme a[3], Cu[B], and the oxygen atom of each of the water molecules are colored in red, green, and light blue, respectively. Three water molecules, 2,007, 2,014 and 2,039, were not included in the structural refinements performed to compare their electron densities with the electron density between Fe[a3] and Cu[B]. (A) The cages of the difference map for the 1-s data are drawn at the 4.5σ level. (B) The cages for the 15-s data are drawn at the 5σ level.
Figure 4.
Coordination geometries of the peroxide anion obtained from structural refinement of the 15-s dataset calculated at 2.1-Å resolution. The interatomic distances are given in angstroms. Other distances and angles are Fe[a3]-Cu[B], 4.87 Å; N[ε2](H376)- Fe[a3]-O[1], 168.5°; Fe[a3]-O[1]-O[2], 144.1° and O[1]-O[2]-Cu[B], 90.5°. These geometries are fully consistent with those of the X-ray structure determined from the 103.5-s exposures at 1.95-Å resolution.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21286652 A.V.Dyuba, A.M.Arutyunyan, T.V.Vygodina, N.V.Azarkina, A.V.Kalinovich, Y.A.Sharonov, and A.A.Konstantinov (2011).
Circular dichroism spectra of cytochrome c oxidase.
  Metallomics, 3, 417-432.  
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
21545285 S.Yoshikawa, K.Muramoto, and K.Shinzawa-Itoh (2011).
Proton-pumping mechanism of cytochrome C oxidase.
  Annu Rev Biophys, 40, 205-223.  
20385840 K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, and S.Yoshikawa (2010).
Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate.
  Proc Natl Acad Sci U S A, 107, 7740-7745.
PDB codes: 3ag1 3ag2 3ag3 3ag4
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20029110 L.Giachini, G.Veronesi, F.Francia, G.Venturoli, and F.Boscherini (2010).
Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins.
  J Synchrotron Radiat, 17, 41-52.  
20354773 M.Sakaguchi, K.Shinzawa-Itoh, S.Yoshikawa, and T.Ogura (2010).
A resonance Raman band assignable to the O-O stretching mode in the resting oxidized state of bovine heart cytochrome c oxidase.
  J Bioenerg Biomembr, 42, 241-243.  
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.