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› 5xm3

X-ray diffraction
1.7Å resolution

Crystal Structure of Methanol dehydrogenase from Methylophaga aminisulfidivorans

Released:
DOI: 10.2210/pdb5xm3/pdb
Model geometry
Fit model/data
PDB entry 5xm3 coloured by chain, front view.
PDB entry 5xm3 coloured by chain, side view.
PDB entry 5xm3 coloured by chain, top view.
Source organism: Methylophaga aminisulfidivorans MP
Primary publication:
The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT.
Cao TP, Choi JM, Kim SW, Lee SH
J Microbiol 56 246-254 (2018)
PMID: 29492864

Function and Biology Details

Reaction catalysed: 
2 Fe(III)-[cytochrome cL] + a primary alcohol = 2 Fe(II)-[cytochrome cL]+ an aldehyde + 2 H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107129 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Pyrrolo-quinoline quinone repeat domain-containing protein Chains: A, C
Molecule details ›
Chains: A, C
Length: 627 amino acids
Theoretical weight: 69.34 KDa
Source organism: Methylophaga aminisulfidivorans MP
Expression system: Methylophaga aminisulfidivorans MP
UniProt:
  • Canonical: A3FJ48 (Residues: 1-627; Coverage: 100%)
Gene name: MAMP_01209
Sequence domains: Outer membrane protein assembly factor BamB
Structure domains: Quinoprotein alcohol dehydrogenase-like superfamily
Methanol dehydrogenase [cytochrome c] subunit 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 90 amino acids
Theoretical weight: 9.98 KDa
Source organism: Methylophaga aminisulfidivorans MP
Expression system: Methylophaga aminisulfidivorans MP
UniProt:
  • Canonical: A3FJ51 (Residues: 1-90; Coverage: 100%)
Gene name: MAMP_01202
Sequence domains: Methanol dehydrogenase beta subunit
Structure domains: Methanol dehydrogenase, beta subunit

Ligands and Environments


Cofactor: Ligand PQQ 2 x PQQ
1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: P21
Unit cell:
a: 63.926Å b: 109.479Å c: 95.554Å
α: 90° β: 100.48° γ: 90°
R-values:
R R work R free
0.153 0.151 0.181
Expression system: Methylophaga aminisulfidivorans MP

Quick links

Citations

3 review citations

Methanol Dehydrogenases as a Key Biocatalysts for Synthetic Methylotrophy.
Le et al. (2021)
2 more

1 mention without citation

Crystal Structure of Cytochrome cL from the Aquatic Methylotrophic Bacterium Methylophaga aminisulfidivorans MPT.
Ghosh et al. (2020)