› 5g0r

X-ray diffraction
1.25Å resolution

METHYL-COENZYME M REDUCTASE I FROM METHANOTHERMOBACTER MARBURGENSIS EXPOSED TO 3-NITROOXYPROPANOL

Released:
DOI: 10.2210/pdb5g0r/pdb
PDB entry 5g0r coloured by chain, front view.
PDB entry 5g0r coloured by chain, side view.
PDB entry 5g0r coloured by chain, top view.
Source organism: Methanothermobacter marburgensis
Primary publication:
Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol.
Duin EC, Wagner T, Shima S, Prakash D, Cronin B, Yáñez-Ruiz DR, Duval S, Rümbeli R, Stemmler RT, Thauer RK, Kindermann M
Proc Natl Acad Sci U S A 113 6172-7 (2016)
PMID: 27140643

Function and Biology Details

Reaction catalysed: 
Methyl-CoM + CoB = CoM-S-S-CoB + methane
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145876 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Methyl-coenzyme M reductase I subunit alpha Chains: A, D
Molecule details ›
Chains: A, D
Length: 550 amino acids
Theoretical weight: 60.64 KDa
Source organism: Methanothermobacter marburgensis
UniProt:
  • Canonical: P11558 (Residues: 1-550; Coverage: 100%)
Gene names: MTBMA_c15480, mcrA
Sequence domains:
Structure domains:
Methyl-coenzyme M reductase I subunit beta Chains: B, E
Molecule details ›
Chains: B, E
Length: 443 amino acids
Theoretical weight: 47.28 KDa
Source organism: Methanothermobacter marburgensis
UniProt:
  • Canonical: P11560 (Residues: 1-443; Coverage: 100%)
Gene names: MTBMA_c15520, mcrB
Sequence domains:
Structure domains:
Methyl-coenzyme M reductase I subunit gamma Chains: C, F
Molecule details ›
Chains: C, F
Length: 249 amino acids
Theoretical weight: 28.8 KDa
Source organism: Methanothermobacter marburgensis
UniProt:
  • Canonical: P11562 (Residues: 1-249; Coverage: 100%)
Gene names: MTBMA_c15490, mcrG
Sequence domains: Methyl-coenzyme M reductase gamma subunit
Structure domains: Methyl-coenzyme M reductase, gamma subunit

Ligands and Environments


Cofactor: Ligand TP7 2 x TP7

Cofactor: Ligand F43 2 x F43
4 bound ligands:
Ligand MG 18 x MG
Ligand NA 3 x NA
Ligand K 1 x K
Ligand CL 3 x CL
6 modified residues:
Ligand MHS 2 x MHS
Ligand AGM 2 x AGM
Ligand MGN 2 x MGN
Ligand GL3 2 x GL3
Ligand DYA 2 x DYA
Ligand SMC 2 x SMC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 82.2Å b: 118.101Å c: 122.64Å
α: 90° β: 92.03° γ: 90°
R-values:
R R work R free
0.106 0.105 0.124

Quick links

Citations

13 review citations

Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future.
Huws et al. (2018)
12 more

2 mentions without citation

Metadata Analysis Approaches for Understanding and Improving the Functional Involvement of Rumen Microbial Consortium in Digestion and Metabolism of Plant Biomass.
Kameshwar et al. (2019)
1 more