› 3pot

X-ray diffraction
1.2Å resolution

Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis

Released:
DOI: 10.2210/pdb3pot/pdb
PDB entry 3pot coloured by chain, front view.
PDB entry 3pot coloured by chain, side view.
PDB entry 3pot coloured by chain, top view.
Source organism: Methanothermobacter marburgensis
Primary publication:
Structural analysis of a Ni-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis.
Cedervall PE, Dey M, Li X, Sarangi R, Hedman B, Ragsdale SW, Wilmot CM
J Am Chem Soc 133 5626-8 (2011)
PMID: 21438550

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 COM 2 x COM

Cofactor: Ligand TXZ 2 x TXZ

Cofactor: Ligand TP7 2 x TP7

Cofactor: Ligand F43 2 x F43
4 bound ligands:
Ligand MG 12 x MG
Ligand 06C 2 x 06C
Ligand K 1 x K
Ligand EDO 1 x EDO
5 modified residues:
Ligand MHS 2 x MHS
Ligand AGM 2 x AGM
Ligand MGN 2 x MGN
Ligand GL3 2 x GL3
Ligand SMC 2 x SMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 81.886Å b: 118.165Å c: 122.388Å
α: 90° β: 91.94° γ: 90°
R-values:
R R work R free
0.133 0.132 0.156

Quick links

Citations

3 review citations

Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes.
Thauer RK. (2019)
2 more

4 mentions without citation

Structure, function, and biosynthesis of nickel-dependent enzymes.
Alfano et al. (2020)
3 more