{"entry": {"accession": "MF7000727", "general": {"name": "TrmD with SAH (Mycobacterium tuberculosis)", "pdb_id": "5zhj", "exp_method": "X-ray", "resolution": "1.75", "assembly": "Homodimer", "source_organism": "Mycobacterium tuberculosis", "publication": {"pmid": "31442049", "authors": "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", "title": {"i": "N", "sub": "1", "#text": "Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism."}, "journal": "J. Med. Chem.", "year": "2019", "issue": "17", "volume": "62", "pages": "7788-7805", "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-(N<sub>1</sub>G37) methyltransferase, TrmD, which is an essential enzyme in many bacterial pathogens. On the basis of crystal structures of TrmDs from <i>Pseudomonas aeruginosa</i> and <i>Mycobacterium tuberculosis</i>, 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 <i>P. aeruginosa</i> TrmD and renders the enzyme inaccessible to the cofactor <i>S</i>-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."}}, "function": {"molecular_function": {"go": {"accession": "GO:0052906", "name": "tRNA (guanine(37)-N1)-methyltransferase activity"}}, "cellular_component": {"go": {"accession": "GO:0005829", "name": "cytosol"}}, "biological_process": {"go": {"accession": "GO:0002939", "name": "tRNA N1-guanine methylation"}}}, "macromolecules": {"general": {"nr_of_chains": "2", "nr_of_unique_protein_segments": "1", "class": "Homooligomeric enzymes", "subclass": "Homodimeric enzymes", "note": "All chains according to the most probable oligomerization state stored in PDBe were considered."}, "chain": [{"id": "A", "name": "tRNA (guanine-N(1)-)-methyltransferase", "source_organism": "Mycobacterium tuberculosis", "uniprot": {"id": "P9WFY7", "start": "1", "end": "226", "coverage": "98%", "sequence": "MRIDIVTIFPACLDPLRQSLPGKAIESGLVDLNVHDLRRWTHDVHHSVDDAPYGGGPGMVMKAPVWGEALDEICSSETLLIVPTPAGVLFTQATAQRWTTESHLVFACGRYEGIDQRVVQDAARRMRVEEVSIGDYVLPGGESAAVVMVEAVLRLLAGVLGNPASHQDDSHSTGLDGLLEGPSYTRPASWRGLDVPEVLLSGDHARIAAWRREVSLQRTRERRPDLSHPD", "length": "230"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "9", "region_end": "17"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "18", "region_end": "27"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "38", "region_end": "41"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "62", "region_end": "74"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "91", "region_end": "99"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "116", "region_end": "123"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "141", "region_end": "160"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "196", "region_end": "201"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "203", "region_end": "223"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "2", "region_end": "7"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "31", "region_end": "36"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "49", "region_end": "50"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "60", "region_end": "61"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "79", "region_end": "83"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "88", "region_end": "89"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "103", "region_end": "107"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "127", "region_end": "132"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "189", "region_end": "190"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "193", "region_end": "194"}, {"region_type": "pfam", "region_id": "PF01746", "region_name": "tRNA (Guanine-1)-methyltransferase", "region_start": "22", "region_end": "224"}]}}, {"id": "A-2", "name": "tRNA (guanine-N(1)-)-methyltransferase", "source_organism": "Mycobacterium tuberculosis", "uniprot": {"id": "P9WFY7", "start": "1", "end": "226", "coverage": "98%", "sequence": "MRIDIVTIFPACLDPLRQSLPGKAIESGLVDLNVHDLRRWTHDVHHSVDDAPYGGGPGMVMKAPVWGEALDEICSSETLLIVPTPAGVLFTQATAQRWTTESHLVFACGRYEGIDQRVVQDAARRMRVEEVSIGDYVLPGGESAAVVMVEAVLRLLAGVLGNPASHQDDSHSTGLDGLLEGPSYTRPASWRGLDVPEVLLSGDHARIAAWRREVSLQRTRERRPDLSHPD", "length": "230"}, "regions": {"region": {"region_type": "pfam", "region_id": "PF01746", "region_name": "tRNA (Guanine-1)-methyltransferase", "region_start": "22", "region_end": "224"}}}]}, "evidence": {"evidence_level": "Indirect evidence", "evidence_coverage": "The full structure participates in mutual synergistic folding.", "sequence_domain": "tRNA (Guanine-1)-methyltransferase", "complex_evidence": "Multisubdomain structure, where both subdomains participate in dimerization. The C-terminal domain is TRP repressor-like. The structure suggests that the dimer is the functional form of the protein since it has an extensive and tight hydrophobic interface and a large buried surface area. DLS data of the protein solution suggest that the A. aeolicus tRNA (m1G37) methyltransferase is oligomeric (dimer or trimer) in solution (PMID:12773376). The active site is also located at the subunit interface (PMID:14517984).", "chain_evidence": [{"chain_id": "A", "support": "N/A"}, {"chain_id": "A-2", "support": "N/A"}]}, "related_structures": {"id": ["MF7000723", "MF7000724", "MF7000725", "MF7000726", "MF7000727", "MF7000728", "MF7000729", "MF7000730", "MF7000731", "MF7000732", "MF7000733", "MF7000734", "MF7000735", "MF7000736", "MF7000737", "MF7000738"]}}}