5ZHM

Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

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

(2019) J Med Chem 62: 7788-7805

  • DOI: 10.1021/acs.jmedchem.9b00582
  • Primary Citation of Related Structures:  
    5ZHL, 5ZHK, 5ZHN, 5ZHM, 5ZHJ, 5ZHI, 6JOF, 6JOE

  • PubMed 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 1 G37) methyltransferase, TrmD, which is an essential enzyme in many bacterial pathogens ...

    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 1 G37) 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.


    Organizational Affiliation

    Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (guanine-N(1)-)-methyltransferaseA, B269Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: trmDPA14_15990
EC: 2.1.1.228
UniProt
Find proteins for Q02RL6 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02RL6 
Go to UniProtKB:  Q02RL6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
D [auth B]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
9D3 (Subject of Investigation/LOI)
Query on 9D3

Download Ideal Coordinates CCD File 
C [auth A]N-({4-[(diethylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
C19 H22 N4 O2 S
SNPTXDKRQKLKGA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9D3 BindingDB:  5ZHM IC50: 730 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.5α = 90
b = 84.5β = 90
c = 147.271γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Singapore SMART Innovation CentreSingaporeING137070-BIO

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-25
    Changes: Data collection, Database references