6AFK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N1G37) Methyltransferase (TrmD) Inhibitors.

Zhong, W.Koay, A.Ngo, A.Li, Y.Nah, Q.Wong, Y.H.Chionh, Y.H.Ng, H.Q.Koh-Stenta, X.Poulsen, A.Foo, K.McBee, M.Choong, M.L.El Sahili, A.Kang, C.Matter, A.Lescar, J.Hill, J.Dedon, P.

(2019) ACS Infect Dis 5: 326-335

  • DOI: 10.1021/acsinfecdis.8b00275
  • Primary Citation of Related Structures:  
    6AFK

  • PubMed Abstract: 
  • Bacterial tRNA modification synthesis pathways are critical to cell survival under stress and thus represent ideal mechanism-based targets for antibiotic development. One such target is the tRNA-(N 1 G37) methyltransferase (TrmD), which is con ...

    Bacterial tRNA modification synthesis pathways are critical to cell survival under stress and thus represent ideal mechanism-based targets for antibiotic development. One such target is the tRNA-(N 1 G37) methyltransferase (TrmD), which is conserved and essential in many bacterial pathogens. Here we developed and applied a widely applicable, radioactivity-free, bioluminescence-based high-throughput screen (HTS) against 116350 compounds from structurally diverse small-molecule libraries to identify inhibitors of Pseudomonas aeruginosa TrmD ( PaTrmD). Of 285 compounds passing primary and secondary screens, a total of 61 TrmD inhibitors comprised of more than 12 different chemical scaffolds were identified, all showing submicromolar to low micromolar enzyme inhibitor constants, with binding affinity confirmed by thermal stability and surface plasmon resonance. S-Adenosyl-l-methionine (SAM) competition assays suggested that compounds in the pyridine-pyrazole-piperidine scaffold were substrate SAM-competitive inhibitors. This was confirmed in structural studies, with nuclear magnetic resonance analysis and crystal structures of PaTrmD showing pyridine-pyrazole-piperidine compounds bound in the SAM-binding pocket. Five hits showed cellular activities against Gram-positive bacteria, including mycobacteria, while one compound, a SAM-noncompetitive inhibitor, exhibited broad-spectrum antibacterial activity. The results of this HTS expand the repertoire of TrmD-inhibiting molecular scaffolds that show promise for antibiotic development.


    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)-)-methyltransferase AB269Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: trmDPA14_15990
EC: 2.1.1.228
Find proteins for Q02RL6 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02RL6 
Go to UniProtKB:  Q02RL6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
9WO
Query on 9WO

Download Ideal Coordinates CCD File 
B
N-{(3S)-1-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]piperidin-3-yl}-1H-indole-2-carboxamide
C22 H22 N6 O
ZFKKLBZXLNWYEO-KRWDZBQOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.02α = 90
b = 86.02β = 90
c = 149.191γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)SingaporeING137070-BIO
Ministry of Education (Singapore)SingaporeRG154/14
Ministry of Education (Singapore)SingaporeMOE2015-T2-2-075

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Database references