› 5guw

X-ray diffraction
3.2Å resolution

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa

Released:
DOI: 10.2210/pdb5guw/pdb
PDB entry 5guw coloured by chain, front view.
PDB entry 5guw coloured by chain, side view.
PDB entry 5guw coloured by chain, top view.
Source organism: Pseudomonas aeruginosa PAO1
Primary publication:
Dynamics of nitric oxide controlled by protein complex in bacterial system.
Terasaka E, Yamada K, Wang PH, Hosokawa K, Yamagiwa R, Matsumoto K, Ishii S, Mori T, Yagi K, Sawai H, Arai H, Sugimoto H, Sugita Y, Shiro Y, Tosha T
Proc Natl Acad Sci U S A 114 9888-9893 (2017)
PMID: 28847930

Function and Biology Details

Reactions catalysed: 
Nitrous oxide + 2 ferricytochrome c + H(2)O = 2 nitric oxide + 2 ferrocytochrome c + 2 H(+)
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
NH(3) + H(2)O + acceptor = hydroxylamine + reduced acceptor
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-176811 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Nitric oxide reductase subunit C Chains: A, C
Molecule details ›
Chains: A, C
Length: 146 amino acids
Theoretical weight: 16.37 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q59646 (Residues: 1-146; Coverage: 100%)
Gene names: PA0523, norC
Sequence domains: Cytochrome c
Structure domains: Cytochrome c-like domain
Nitric oxide reductase subunit B Chains: B, D
Molecule details ›
Chains: B, D
Length: 465 amino acids
Theoretical weight: 52.22 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q59647 (Residues: 1-466; Coverage: 100%)
Gene names: PA0524, norB
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Structure domains: Cytochrome c oxidase-like, subunit I domain
Nitrite reductase Chains: M, N
Molecule details ›
Chains: M, N
Length: 568 amino acids
Theoretical weight: 62.74 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: P24474 (Residues: 1-568; Coverage: 100%)
Gene names: PA0519, nirS
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM

Cofactor: Ligand DHE 2 x DHE

Cofactor: Ligand HEC 4 x HEC
5 bound ligands:
Ligand CA 2 x CA
Ligand 10M 3 x 10M
Ligand FE 2 x FE
Ligand O 2 x O
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 111.871Å b: 128.606Å c: 127.807Å
α: 90° β: 106.83° γ: 90°
R-values:
R R work R free
0.212 0.21 0.254

Quick links

Citations

3 review citations

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.
Muller et al. (2019)
2 more

2 mentions without citation

Dynamics of nitric oxide controlled by protein complex in bacterial system.
Terasaka et al. (2017)
1 more