3POT image
Deposition Date 2010-11-23
Release Date 2011-04-13
Last Version Date 2023-09-06
Entry Detail
PDB ID:
3POT
Keywords:
TRANSFERASE
Title:
Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis
Biological Source:
Source Organism:
Methanothermobacter marburgensis (Taxon ID: 145263)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.20 Å
R-Value Free:
0.15
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
P 1 21 1
3POT validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Methyl-coenzyme M reductase I subunit alpha
Gene (Uniprot):mcrA
Chain IDs:A, D
Chain Length:550
Number of Molecules:2
Biological Source:Methanothermobacter marburgensis
UniProt ID:P11558 Pfam ID:PF02745, PF02249 EC:2.8.4.1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Methyl-coenzyme M reductase I subunit beta
Gene (Uniprot):mcrB
Chain IDs:B, E
Chain Length:443
Number of Molecules:2
Biological Source:Methanothermobacter marburgensis
UniProt ID:P11560 Pfam ID:PF02783, PF02241 EC:2.8.4.1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Methyl-coenzyme M reductase I subunit gamma
Gene (Uniprot):mcrG
Chain IDs:C, F
Chain Length:249
Number of Molecules:2
Biological Source:Methanothermobacter marburgensis
UniProt ID:P11562 Pfam ID:PF02240 EC:2.8.4.1
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
AGM A ARG 5-METHYL-ARGININE
GL3 A GLY THIOGLYCIN
MGN A GLN 2-METHYL-GLUTAMINE
MHS A HIS N1-METHYLATED HISTIDINE
SMC A CYS S-METHYLCYSTEINE
Ligand Molecules
06C
COM
EDO
F43
K
MG
TP7
TXZ
Primary Citation
Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis.
J.Am.Chem.Soc. 133 5626 5628 (2011)
PMID: 21438550 DOI: 10.1021/ja110492p

Abstact

We present the 1.2 Å resolution X-ray crystal structure of a Ni-methyl species that is a proposed catalytic intermediate in methyl-coenzyme M reductase (MCR), the enzyme that catalyzes the biological formation of methane. The methyl group is situated 2.1 Å proximal of the Ni atom of the MCR coenzyme F(430). A rearrangement of the substrate channel has been posited to bring together substrate species, but Ni(III)-methyl formation alone does not lead to any observable structural changes in the channel.

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Primary Citation of related structures
3POT