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› 6qox

X-ray diffraction
1.74Å resolution

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 27 (Methyl 2-(hydroxymethyl)-6H-thieno[2,3-b]pyrrole-5-carboxylate)

Released:
DOI: 10.2210/pdb6qox/pdb
Model geometry
Fit model/data
PDB entry 6qox coloured by chain, front view.
PDB entry 6qox coloured by chain, side view.
PDB entry 6qox coloured by chain, top view.
Source organism: Mycobacteroides abscessus
Primary publication:
Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification.
Thomas SE, Whitehouse AJ, Brown K, Burbaud S, Belardinelli JM, Sangen J, Lahiri R, Libardo MDJ, Gupta P, Malhotra S, Boshoff HIM, Jackson M, Abell C, Coyne AG, Blundell TL, Floto RA, Mendes V
OpenAccess logo Nucleic Acids Res 48 8099-8112 (2020)
PMID: 32602532

Function and Biology Details

Reaction catalysed: 
guanosine(37) in tRNA + S-adenosyl-L-methionine = N(1)-methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine + H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109342 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine-N(1)-)-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 244 amino acids
Theoretical weight: 26.43 KDa
Source organism: Mycobacteroides abscessus
Expression system: Escherichia coli
UniProt:
  • Canonical: B1MDI3 (Residues: 1-242; Coverage: 100%)
Gene names: MAB_3226c, trmD
Sequence domains: tRNA (Guanine-1)-methyltransferase

Ligands and Environments

1 bound ligand:
Ligand JA5 1 x JA5
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 74.963Å b: 78.46Å c: 88.483Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.214
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Fragment-to-Lead Medicinal Chemistry Publications in 2020.
de Esch et al. (2022)
5 more

1 mention without citation

Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification.
Thomas et al. (2020)