› 7qbt

X-ray diffraction
1.9Å resolution

B12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, and S-methyl-5'-thioadenosine bound.

Released:
DOI: 10.2210/pdb7qbt/pdb
PDB entry 7qbt coloured by chain, front view.
PDB entry 7qbt coloured by chain, side view.
PDB entry 7qbt coloured by chain, top view.
Source organism: Methanosarcina acetivorans
Primary publication:
Crystallographic snapshots of a B12-dependent radical SAM methyltransferase.
Fyfe CD, Bernardo-García N, Fradale L, Grimaldi S, Guillot A, Brewee C, Chavas LMG, Legrand P, Benjdia A, Berteau O
Nature 602 336-342 (2022)
PMID: 35110733

Function and Biology Details

Reaction catalysed: 
2 S-adenosyl-L-methionine + a [methyl coenzyme-M reductase]-L-arginine + reduced acceptor = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + a [methyl coenzyme-M reductase]-(5S)-C-methyl-L-arginine + acceptor
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186276 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
[Methyl coenzyme M reductase]-L-arginine C-5-methyltransferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 436 amino acids
Theoretical weight: 47.96 KDa
Source organism: Methanosarcina acetivorans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8THG6 (Residues: 1-411; Coverage: 100%)
Gene name: MA_4551
Sequence domains: Radical SAM-like domain

Ligands and Environments

5 bound ligands:
Ligand SF4 4 x SF4
Ligand FE 4 x FE
Ligand MTA 4 x MTA
Ligand COB 4 x COB
Ligand NA 4 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21212
Unit cell:
a: 156.064Å b: 163.915Å c: 77.805Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.203 0.229
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Structural insights into auxiliary cofactor usage by radical S-adenosylmethionine enzymes.
Jeyachandran et al. (2022)
1 more

2 mentions without citation

Structure and Catalytic Mechanism of Radical SAM Methylases.
Nguyen et al. (2022)
1 more