› 6qqv

X-ray diffraction
1.71Å resolution

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

Released:
DOI: 10.2210/pdb6qqv/pdb
PDB entry 6qqv coloured by chain, front view.
PDB entry 6qqv coloured by chain, side view.
PDB entry 6qqv 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
OpenAccess logo 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-502149 (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

2 bound ligands:
Ligand JEW 2 x JEW
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 74.556Å b: 77.749Å c: 86.182Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.176 0.202
Expression system: Escherichia coli

Quick links

Citations

8 review citations

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

1 mention without citation

Development of Inhibitors against Mycobacterium abscessus tRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Whitehouse et al. (2019)