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› 5zhl

X-ray diffraction
2.25Å resolution

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor

Released:
DOI: 10.2210/pdb5zhl/pdb
Model geometry
Fit model/data
PDB entry 5zhl coloured by chain, front view.
PDB entry 5zhl coloured by chain, side view.
PDB entry 5zhl coloured by chain, top view.
Source organism: Mycobacterium tuberculosis CDC1551
Primary publication:
Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.
Zhong W, Pasunooti KK, Balamkundu S, Wong YH, Nah Q, Gadi V, Gnanakalai S, Chionh YH, McBee ME, Gopal P, Lim SH, Olivier N, Buurman ET, Dick T, Liu CF, Lescar J, Dedon PC
OpenAccess logo J Med Chem 62 7788-7805 (2019)
PMID: 31442049

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-161443 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine-N(1)-)-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 238 amino acids
Theoretical weight: 26.17 KDa
Source organism: Mycobacterium tuberculosis CDC1551
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WFY7 (Residues: 1-230; Coverage: 100%)
Gene names: MTCY274.37c, Rv2906c, trmD
Sequence domains: tRNA (Guanine-1)-methyltransferase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 9D0 1 x 9D0
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2
Unit cell:
a: 73.69Å b: 50.23Å c: 57.94Å
α: 90° β: 90.95° γ: 90°
R-values:
R R work R free
0.161 0.158 0.211
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity.
de Crécy-Lagard et al. (2021)
4 more

2 mentions without citation

An Outline of the Latest Crystallographic Studies on Inhibitor-Enzyme Complexes for the Design and Development of New Therapeutics against Tuberculosis.
Mori et al. (2021)
1 more