5ZHN image
Entry Detail
PDB ID:
5ZHN
Keywords:
Title:
Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor
Biological Source:
PDB Version:
Deposition Date:
2018-03-13
Release Date:
2019-03-27
Method Details:
Experimental Method:
Resolution:
2.65 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 32 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:tRNA (guanine-N(1)-)-methyltransferase
Chain IDs:A, B
Chain Length:269
Number of Molecules:2
Biological Source:Pseudomonas aeruginosa UCBPP-PA14
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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