Database accession: MF7000726
Name: TrmD (apo form) (Mycobacterium abscessus)
PDB ID: 5zhi
Experimental method: X-ray (2.20 Å)
Assembly: Homodimer
Source organism: Mycobacterium tuberculosis
Primary publication of the structure:
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
Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.
(2019) J. Med. Chem. 62: 7788-7805
PMID: 31442049
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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
tRNA (guanine(37)-N1)-methyltransferase activity tRNA (guanine(37)-N1)-methyltransferase activity
Biological process:
tRNA N1-guanine methylation tRNA N1-guanine methylation
Cellular component:
cytosol cytosol
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: tRNA (guanine-N(1)-)-methyltransferase
Source organism: Mycobacterium tuberculosis
Length: 230 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRIDIVTIFPACLDPLRQSLPGKAIESGLVDLNVHDLRRWTHDVHHSVDDAPYGGGPGMVMKAPVWGEALDEICSSETLLIVPTPAGVLFTQATAQRWTTESHLVFACGRYEGIDQRVVQDAARRMRVEEVSIGDYVLPGGESAAVVMVEAVLRLLAGVLGNPASHQDDSHSTGLDGLLEGPSYTRPASWRGLDVPEVLLSGDHARIAAWRREVSLQRTRERRPDLSHPD
UniProtKB AC: P9WFY7 (positions: 1-226)
Coverage: 98%
Name: tRNA (guanine-N(1)-)-methyltransferase
Source organism: Mycobacterium tuberculosis
Length: 230 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRIDIVTIFPACLDPLRQSLPGKAIESGLVDLNVHDLRRWTHDVHHSVDDAPYGGGPGMVMKAPVWGEALDEICSSETLLIVPTPAGVLFTQATAQRWTTESHLVFACGRYEGIDQRVVQDAARRMRVEEVSIGDYVLPGGESAAVVMVEAVLRLLAGVLGNPASHQDDSHSTGLDGLLEGPSYTRPASWRGLDVPEVLLSGDHARIAAWRREVSLQRTRERRPDLSHPD
UniProtKB AC: P9WFY7 (positions: 1-226)
Coverage: 98%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: tRNA (Guanine-1)-methyltransferase
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
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 A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
