6JOF image
Deposition Date 2019-03-20
Release Date 2019-09-04
Last Version Date 2023-11-22
Entry Detail
PDB ID:
6JOF
Title:
Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:tRNA (guanine-N(1)-)-methyltransferase
Gene (Uniprot):trmD
Chain IDs:A
Chain Length:238
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis H37Rv
Ligand Molecules
Primary Citation
Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.
J.Med.Chem. 62 7788 7805 (2019)
PMID: 31442049 DOI: 10.1021/acs.jmedchem.9b00582

Abstact

Among the >120 modified ribonucleosides in the prokaryotic epitranscriptome, many tRNA modifications are critical to bacterial survival, which makes their synthetic enzymes ideal targets for antibiotic development. Here we performed a structure-based design of inhibitors of tRNA-(N1G37) methyltransferase, TrmD, which is an essential enzyme in many bacterial pathogens. On the basis of crystal structures of TrmDs from Pseudomonas aeruginosa and Mycobacterium tuberculosis, we synthesized a series of thienopyrimidinone derivatives with nanomolar potency against TrmD in vitro and discovered a novel active site conformational change triggered by inhibitor binding. This tyrosine-flipping mechanism is uniquely found in P. aeruginosa TrmD and renders the enzyme inaccessible to the cofactor S-adenosyl-l-methionine (SAM) and probably to the substrate tRNA. Biophysical and biochemical structure-activity relationship studies provided insights into the mechanisms underlying the potency of thienopyrimidinones as TrmD inhibitors, with several derivatives found to be active against Gram-positive and mycobacterial pathogens. These results lay a foundation for further development of TrmD inhibitors as antimicrobial agents.

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