6QRG

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report



Literature

Development of Inhibitors againstMycobacterium abscessustRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.

Whitehouse, A.J.Thomas, S.E.Brown, K.P.Fanourakis, A.Chan, D.S.Libardo, M.D.J.Mendes, V.Boshoff, H.I.M.Floto, R.A.Abell, C.Blundell, T.L.Coyne, A.G.

(2019) J Med Chem 62: 7210-7232

  • DOI: 10.1021/acs.jmedchem.9b00809
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mycobacterium abscessus ( Mab ) is a rapidly growing species of multidrug-resistant nontuberculous mycobacteria that has emerged as a growing threat to individuals with cystic fibrosis and other pre-existing chronic lung diseases.

    Mycobacterium abscessus ( Mab ) is a rapidly growing species of multidrug-resistant nontuberculous mycobacteria that has emerged as a growing threat to individuals with cystic fibrosis and other pre-existing chronic lung diseases. Mab pulmonary infections are difficult, or sometimes impossible, to treat and result in accelerated lung function decline and premature death. There is therefore an urgent need to develop novel antibiotics with improved efficacy. tRNA (m 1 G37) methyltransferase (TrmD) is a promising target for novel antibiotics. It is essential in Mab and other mycobacteria, improving reading frame maintenance on the ribosome to prevent frameshift errors. In this work, a fragment-based approach was employed with the merging of two fragments bound to the active site, followed by structure-guided elaboration to design potent nanomolar inhibitors against Mab TrmD. Several of these compounds exhibit promising activity against mycobacterial species, including Mycobacterium tuberculosis and Mycobacterium leprae in addition to Mab , supporting the use of TrmD as a target for the development of antimycobacterial compounds.


    Organizational Affiliation

    Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (guanine-N(1)-)-methyltransferase
A, B
244Mycobacteroides abscessusMutation(s): 0 
Gene Names: trmDMAB_3226c
EC: 2.1.1.228
Find proteins for B1MDI3 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543))
Go to UniProtKB:  B1MDI3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JET
Query on JET

Download CCD File 
A, B
[3-(2-methoxy-2-oxidanylidene-ethoxy)phenyl]methyl 1~{H}-pyrazole-4-carboxylate
C14 H14 N2 O5
HARZTHMZNXIIKQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.273α = 90
b = 77.867β = 90
c = 86.49γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited KingdomCystic Fibrosis Trust Registered Charity No. (England and Wales) 1079049, Registered Charity No. (Scotland) SC040196

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release