PDBsum entry 3omn

Oxidoreductase

PDB id: 3omn

Contents

Protein chains

535 a.a. *

256 a.a. *

Ligands

_OH ×2

DMU ×11

TRD ×9

HEA ×4

HTH

Metals

_CL ×2

_CD ×4

CU1 ×6

_MG ×2

_CA ×2

Waters ×461

* Residue conservation analysis

PDB id:

3omn

Name:

Oxidoreductase

Title:

Catalytic core subunits (i and ii) of cytochromE C oxidase from rhodobacter sphaeroides with d132a mutation in the reduced state

Structure:

CytochromE C oxidase, aa3 type, subunit i. Chain: a, c. Fragment: unp residues 17-551. Engineered: yes. Mutation: yes. CytochromE C oxidase subunit 2. Chain: b, d. Fragment: unp residues 30-281. Engineered: yes

Source:

Rhodobacter sphaeroides 2.4.1. Organism_taxid: 272943. Strain: atcc 17023/2.4.1/ncib 8253/dsm 158. Gene: coxi, ctad, rhos4_04590, rsp_1877. Expressed in: rhodobacter sphaeroides. Expression_system_taxid: 1063. Gene: coxii, ctab, ctac, rhos4_04060, rsp_1826.

Resolution:

2.15Å R-factor: 0.199 R-free: 0.219

Authors:

J.Liu,L.Qin,S.Ferguson-Miller

Key ref:

J.Liu et al. (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. PubMed id: 21205904

Date:

27-Aug-10 Release date: 02-Feb-11

Protein chains

Q3J5A7  (Q3J5A7_RHOS4) -  Cytochrome c oxidase subunit 1 from Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)

Seq: 566 a.a.

Struc: 535 a.a.*

Protein chains

Q3J5G0  (Q3J5G0_RHOS4) -  Cytochrome c oxidase subunit 2 from Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)

Seq: 303 a.a.

Struc: 256 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: 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

Proc Natl Acad Sci U S A 108:1284-1289 (2011)

PubMed id: 21205904

Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.

J.Liu, L.Qin, S.Ferguson-Miller.

ABSTRACT

Crystal structures in both oxidized and reduced forms are reported for two bacterial cytochrome c oxidase mutants that define the D and K proton paths, showing conformational change in response to reduction and the loss of strategic waters that can account for inhibition of proton transfer. In the oxidized state both mutants of the Rhodobacter sphaeroides enzyme, D132A and K362M, show overall structures similar to wild type, indicating no long-range effects of mutation. In the reduced state, the mutants show an altered conformation similar to that seen in reduced wild type, confirming this reproducible, reversible response to reduction. In the strongly inhibited D132A mutant, positions of residues and waters in the D pathway are unaffected except in the entry region close to the mutation, where a chloride ion replaces the missing carboxyl and a 2-Å shift in N207 results in loss of its associated water. In K362M, the methionine occupies the same position as the original lysine, but K362- and T359-associated waters in the wild-type structure are missing, likely accounting for the severe inhibition. Spectra of oxidized frozen crystals taken during X-ray radiation show metal center reduction, but indicate development of a strained configuration that only relaxes to a native form upon annealing. Resistance of the frozen crystal to structural change clarifies why the oxidized conformation is observable and supports the conclusion that the reduced conformation has functional significance. A mechanism is described that explains the conformational change and the incomplete response of the D-path mutant.