PDBsum entry 2eim

Oxidoreductase

PDB id: 2eim

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 ×4

PGV ×8

CHD ×8

CUA ×2

TGL ×6

PSC ×2

DMU ×4

PEK ×6

CDL ×4

Metals

_ZN ×6

_CU ×2

_MG ×2

_NA ×2

Waters ×1227

* Residue conservation analysis

PDB id:

2eim

Name:

Oxidoreductase

Title:

Zinc ion binding structure of bovine heart cytochromE C oxidase in the fully reduced state

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. Cattle. Organism_taxid: 9913. Tissue: heart. Tissue: heart

Resolution:

2.60Å R-factor: 0.204 R-free: 0.256

Authors:

K.Muramoto,K.Hirata,K.Shinzawa-Itoh,S.Yoko-O,E.Yamashita,H.Aoyama, T.Tsukihara,S.Yoshikawa

Key ref:

K.Muramoto et al. (2007). A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase. Proc Natl Acad Sci U S A, 104, 7881-7886. PubMed id: 17470809 DOI: 10.1073/pnas.0610031104

Date:

13-Mar-07 Release date: 29-May-07

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

DOI no: 10.1073/pnas.0610031104

Proc Natl Acad Sci U S A 104:7881-7886 (2007)

PubMed id: 17470809

A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase.

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-o, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa.

ABSTRACT

Cytochrome c oxidase transfers electrons and protons for dioxygen reduction coupled with proton pumping. These electron and proton transfers are tightly coupled with each other for the effective energy transduction by various unknown mechanisms. Here, we report a coupling mechanism by a histidine (His-503) at the entrance of a proton transfer pathway to the dioxygen reduction site (D-pathway) of bovine heart cytochrome c oxidase. In the reduced state, a water molecule is fixed by hydrogen bonds between His-503 and Asp-91 of the D-pathway and is linked via two water arrays extending to the molecular surface. The microenvironment of Asp-91 appears in the x-ray structure to have a proton affinity as high as that of His-503. Thus, Asp-91 and His-503 cooperatively trap, on the fixed water molecule, the proton that is transferred through the water arrays from the molecular surface. On oxidation, the His-503 imidazole plane rotates by 180 degrees to break the hydrogen bond to the protonated water and releases the proton to Asp-91. On reduction, Asp-91 donates the proton to the dioxygen reduction site through the D-pathway. The proton collection controlled by His-503 was confirmed by partial electron transfer inhibition by binding of Zn2+ and Cd2+ to His-503 in the x-ray structures. The estimated Kd for Zn2+ binding to His-503 in the x-ray structure is consistent with the reported Kd for complete proton-pumping inhibition by Zn2+ [Kannt A, Ostermann T, Muller H, Ruitenberg M (2001) FEBS Lett 503:142-146]. These results suggest that His-503 couples the proton transfer for dioxygen reduction with the proton pumping.

Selected figure(s)

Figure 1.
Fig. 1. Redox-coupled conformational changes in the His-503–Asp-91 region near the entrance of the D-pathway deduced from the x-ray structures of bovine heart CcO from the 1.8-Å oxidized and 1.9-Å reduced x-ray structures of bovine heart CcO. (a and b) The structures of the D-pathway entrance regions in the reduced and oxidized states shown in stereoviews. The red dotted lines indicate hydrogen bonds that are independent of oxidation state. The blue dotted lines indicate hydrogen bonds that are dependent on the oxidation state. The blue, green, and orange sticks represent the C^ backbones of subunits I, III, and VIIc, respectively. The red spheres represent fixed water molecules. (c and d) Schematic representations of the redox-coupled conformational changes of His-503 in the Cd^2+-free and bound CcO, respectively. The blue and red drawings represent the structures in the reduced and oxidized states, respectively. The black dotted lines represent hydrogen bonds uninfluenced by the oxidation state change. The blue and red dotted lines depict hydrogen bonds appearing in the reduced and oxidized states, respectively. The blue and red thick dotted lines in d represent the coordination bonds that appear in the reduced and oxidized states, respectively.

Figure 5.
Fig. 5. Redox-controlled proton collection and supply by His-503. Only one of the water arrays connecting W207 and W4 and two other possible hydrogen-bonding groups to W207 is shown for the sake of simplicity. The red and blue structures represent the oxidized and reduced (or electron-released and electron-accepted) states of the redox site (or sites) controlling the conformation of the imidazole of His-503. The structures before the oxidation state change are the stable oxidized and reduced states. The circles with arrowheads indicate the rotation of the imidazole group during the transition.

Figures were selected by an automated process.