PDBsum entry 6joe

Transferase

PDB id: 6joe

Contents

Protein chains

242 a.a.

Ligands

BWR

PO4

SAM

Waters ×191

PDB id:

6joe

Name:

Transferase

Title:

Crystal structure of trmd from pseudomonas aeruginosa in complex with active-site inhibitor

Structure:

tRNA (guanine-n(1)-)-methyltransferase. Chain: a, b. Synonym: m1g-methyltransferase,tRNA [gm37] methyltransferase. Engineered: yes

Source:

Pseudomonas aeruginosa ucbpp-pa14. Organism_taxid: 208963. Strain: ucbpp-pa14. Gene: trmd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.21Å R-factor: 0.211 R-free: 0.245

Authors:

W.Zhong,K.K.Pasunooti,S.Balamkundu,Y.W.Wong,Q.Nah,C.F.Liu,J.Lescar, P.C.Dedon

Key ref:

W.Zhong et al. (2019). 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. PubMed id: 31442049 DOI: 10.1021/acs.jmedchem.9b00582

Date:

20-Mar-19 Release date: 04-Sep-19

Protein chains

Q02RL6  (TRMD_PSEAB) -  tRNA (guanine-N(1)-)-methyltransferase from Pseudomonas aeruginosa (strain UCBPP-PA14)

Seq: 252 a.a.

Struc: 242 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1.228 - tRNA (guanine(37)-N(1))-methyltransferase.
• Reaction: guanosine₃₇ in tRNA + S-adenosyl-L-methionine = N₁- methylguanosine₃₇ in tRNA + S-adenosyl-L-homocysteine + H⁺

guanosine(37) in tRNA + S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) = N(1)- methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/acs.jmedchem.9b00582

J Med Chem 62:7788-7805 (2019)

PubMed id: 31442049

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

W.Zhong, K.K.Pasunooti, S.Balamkundu, Y.H.Wong, Q.Nah, V.Gadi, S.Gnanakalai, Y.H.Chionh, M.E.McBee, P.Gopal, S.H.Lim, N.Olivier, E.T.Buurman, T.Dick, C.F.Liu, J.Lescar, P.C.Dedon.

ABSTRACT

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.