› 3ehb

X-ray diffraction
2.32Å resolution

A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate

Released:
DOI: 10.2210/pdb3ehb/pdb
PDB entry 3ehb coloured by chain, front view.
PDB entry 3ehb coloured by chain, side view.
PDB entry 3ehb coloured by chain, top view.
Source organisms:
Primary publication:
A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate.
Dürr KL, Koepke J, Hellwig P, Müller H, Angerer H, Peng G, Olkhova E, Richter OM, Ludwig B, Michel H
J Mol Biol 384 865-77 (2008)
PMID: 18930738

Function and Biology Details

Reaction catalysed: 
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-134471 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Cytochrome c oxidase subunit 1-beta Chain: A
Molecule details ›
Chain: A
Length: 558 amino acids
Theoretical weight: 62.49 KDa
Source organism: Paracoccus denitrificans
Expression system: Escherichia coli
UniProt:
  • Canonical: P98002 (Residues: 1-558; Coverage: 100%)
Gene name: ctaDII
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Structure domains: Cytochrome c oxidase-like, subunit I domain
Cytochrome c oxidase subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 298 amino acids
Theoretical weight: 32.56 KDa
Source organism: Paracoccus denitrificans
Expression system: Escherichia coli
UniProt:
  • Canonical: P08306 (Residues: 1-298; Coverage: 100%)
Gene names: coiI, ctaB, ctaC
Sequence domains:
Structure domains:
Ig heavy chain V region 5-84 Chain: C
Molecule details ›
Chain: C
Length: 127 amino acids
Theoretical weight: 14.32 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P18525 (Residues: 20-117; Coverage: 100%)
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins
Ig kappa chain V-V region MOPC 149 Chain: D
Molecule details ›
Chain: D
Length: 120 amino acids
Theoretical weight: 13.26 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01636 (Residues: 1-95, 96-108; Coverage: 100%)
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

7 bound ligands:
Ligand HEA 2 x HEA
Ligand CU 3 x CU
Ligand MG 1 x MG
Ligand CA 1 x CA
Ligand LDA 9 x LDA
Ligand LMT 12 x LMT
Ligand PER 1 x PER
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 84.461Å b: 151.332Å c: 157.487Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.205 0.242
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Copper active sites in biology.
Solomon et al. (2014)
4 more

6 mentions without citation

Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport.
Sugitani et al. (2009)
5 more