› 6qrb

X-ray diffraction
1.66Å resolution

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor

Released:
DOI: 10.2210/pdb6qrb/pdb
PDB entry 6qrb coloured by chain, front view.
PDB entry 6qrb coloured by chain, side view.
PDB entry 6qrb coloured by chain, top view.
Source organism: Mycobacteroides abscessus
Primary publication:
Development of Inhibitors against Mycobacterium abscessus tRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Whitehouse AJ, Thomas SE, Brown KP, Fanourakis A, Chan DS, Libardo MDJ, Mendes V, Boshoff HIM, Floto RA, Abell C, Blundell TL, Coyne AG
J Med Chem 62 7210-7232 (2019)
PMID: 31282680

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
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 JEQ 2 x JEQ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P212121
Unit cell:
a: 75.461Å b: 77.752Å c: 86.78Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.191 0.21
Expression system: Escherichia coli

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Citations

8 review citations

In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery.
de Souza Neto et al. (2020)
7 more