› 5zhj

X-ray diffraction
1.75Å resolution

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with S-adenosyl homocysteine (SAH)

Released:
DOI: 10.2210/pdb5zhj/pdb
PDB entry 5zhj coloured by chain, front view.
PDB entry 5zhj coloured by chain, side view.
PDB entry 5zhj coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
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
J Med Chem 62 7788-7805 (2019)
PMID: 31442049

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-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 H37Rv
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


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 72.96Å b: 50.761Å c: 53.309Å
α: 90° β: 95.1° γ: 90°
R-values:
R R work R free
0.178 0.177 0.202
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

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

1 mention without citation

Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.
Zhong et al. (2019)