PDBsum entry 3abk

Oxidoreductase

PDB id: 3abk

Contents

Protein chains

514 a.a. *

227 a.a. *

259 a.a. *

144 a.a. *

105 a.a. *

98 a.a. *

84 a.a. *

79 a.a. *

73 a.a. *

58 a.a. *

49 a.a. *

46 a.a. *

43 a.a. *

Ligands

HEA ×3

_NO

PGV ×8

CUA ×2

TGL ×6

PSC ×2

CHD ×8

UNX ×2

PEK ×6

CDL ×4

DMU

HEA-_NO

Metals

_ZN ×2

_CU ×2

_MG ×2

_NA ×2

Waters ×1580

* Residue conservation analysis

PDB id:

3abk

Name:

Oxidoreductase

Title:

Bovine heart cytochromE C oxidase at the no-bound fully reduced state (50k)

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:

2.00Å R-factor: 0.183 R-free: 0.219

Authors:

K.Ohta,K.Muramoto,K.Shinzawa-Itoh,E.Yamashita,S.Yoshikawa,T.Tsukihara

Key ref:

K.Ohta et al. (2010). X-ray structure of the NO-bound Cu(B) in bovine cytochrome c oxidase. Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 251-253. PubMed id: 20208153

Date:

16-Dec-09 Release date: 09-Mar-10

Protein chains

P00396  (COX1_BOVIN) -  Cytochrome c oxidase subunit 1 from Bos taurus

Seq: 514 a.a.

Struc: 514 a.a.*

Protein chains

P68530  (COX2_BOVIN) -  Cytochrome c oxidase subunit 2 from Bos taurus

Seq: 227 a.a.

Struc: 227 a.a.*

Protein chains

P00415  (COX3_BOVIN) -  Cytochrome c oxidase subunit 3 from Bos taurus

Seq: 261 a.a.

Struc: 259 a.a.

Protein chains

P00423  (COX41_BOVIN) -  Cytochrome c oxidase subunit 4 isoform 1, mitochondrial from Bos taurus

Seq: 169 a.a.

Struc: 144 a.a.

Protein chains

P00426  (COX5A_BOVIN) -  Cytochrome c oxidase subunit 5A, mitochondrial from Bos taurus

Seq: 152 a.a.

Struc: 105 a.a.

Protein chains

P00428  (COX5B_BOVIN) -  Cytochrome c oxidase subunit 5B, mitochondrial from Bos taurus

Seq: 129 a.a.

Struc: 98 a.a.

Protein chains

P07471  (CX6A2_BOVIN) -  Cytochrome c oxidase subunit 6A2, mitochondrial from Bos taurus

Seq: 97 a.a.

Struc: 84 a.a.*

Protein chains

P00429  (CX6B1_BOVIN) -  Cytochrome c oxidase subunit 6B1 from Bos taurus

Seq: 86 a.a.

Struc: 79 a.a.

Protein chains

P04038  (COX6C_BOVIN) -  Cytochrome c oxidase subunit 6C from Bos taurus

Seq: 74 a.a.

Struc: 73 a.a.*

Protein chains

P07470  (CX7A1_BOVIN) -  Cytochrome c oxidase subunit 7A1, mitochondrial from Bos taurus

Seq: 80 a.a.

Struc: 58 a.a.

Protein chains

P13183  (COX7B_BOVIN) -  Cytochrome c oxidase subunit 7B, mitochondrial from Bos taurus

Seq: 80 a.a.

Struc: 49 a.a.

Protein chains

P00430  (COX7C_BOVIN) -  Cytochrome c oxidase subunit 7C, mitochondrial from Bos taurus

Seq: 63 a.a.

Struc: 46 a.a.

Protein chains

P10175  (COX8B_BOVIN) -  Cytochrome c oxidase subunit 8B, mitochondrial from Bos taurus

Seq: 70 a.a.

Struc: 43 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, N, O, P: E.C.7.1.1.9 - cytochrome-c oxidase.
• Reaction: 4 Fe(II)-[cytochrome c] + O2 + 8 H⁺(in) = 4 Fe(III)-[cytochrome c] + 2 H2O + 4 H⁺(out)
• Cofactor: Cu cation

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

Acta Crystallogr Sect F Struct Biol Cryst Commun 66:251-253 (2010)

PubMed id: 20208153

X-ray structure of the NO-bound Cu(B) in bovine cytochrome c oxidase.

K.Ohta, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara.

ABSTRACT

The X-ray crystallographic structure of nitric oxide-treated bovine heart cytochrome c oxidase (CcO) in the fully reduced state has been determined at 50 K under light illumination. In this structure, nitric oxide (NO) is bound to the CcO oxygen-reduction site, which consists of haem and a Cu atom (the haem a(3)-Cu(B) site). Electron density for the NO molecule was observed close to Cu(B). The refined structure indicates that NO is bound to Cu(B) in a side-on manner.