4B4B

Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Allosteric competitive inhibitors of the glucose-1-phosphate thymidylyltransferase (RmlA) from Pseudomonas aeruginosa.

Alphey, M.S.Pirrie, L.Torrie, L.S.Boulkeroua, W.A.Gardiner, M.Sarkar, A.Maringer, M.Oehlmann, W.Brenk, R.Scherman, M.S.McNeil, M.Rejzek, M.Field, R.A.Singh, M.Gray, D.Westwood, N.J.Naismith, J.H.

(2013) ACS Chem. Biol. 8: 387-396

  • DOI: 10.1021/cb300426u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glucose-1-phosphate thymidylyltransferase (RmlA) catalyzes the condensation of glucose-1-phosphate (G1P) with deoxy-thymidine triphosphate (dTTP) to yield dTDP-d-glucose and pyrophosphate. This is the first step in the l-rhamnose biosynthetic pathway ...

    Glucose-1-phosphate thymidylyltransferase (RmlA) catalyzes the condensation of glucose-1-phosphate (G1P) with deoxy-thymidine triphosphate (dTTP) to yield dTDP-d-glucose and pyrophosphate. This is the first step in the l-rhamnose biosynthetic pathway. l-Rhamnose is an important component of the cell wall of many microorganisms, including Mycobacterium tuberculosis and Pseudomonas aeruginosa. Here we describe the first nanomolar inhibitors of P. aeruginosa RmlA. These thymine analogues were identified by high-throughput screening and subsequently optimized by a combination of protein crystallography, in silico screening, and synthetic chemistry. Some of the inhibitors show inhibitory activity against M. tuberculosis. The inhibitors do not bind at the active site of RmlA but bind at a second site remote from the active site. Despite this, the compounds act as competitive inhibitors of G1P but with high cooperativity. This novel behavior was probed by structural analysis, which suggests that the inhibitors work by preventing RmlA from undergoing the conformational change key to its ordered bi-bi mechanism.


    Organizational Affiliation

    Biomedical Sciences Research Complex, University of St. Andrews , St. Andrews KY16 9ST, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
A, B, C, D
303Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: rmlA
EC: 2.7.7.24
Find proteins for Q9HU22 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HU22
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GJB
Query on GJB

Download SDF File 
Download CCD File 
A, B, C, D
1-(2-phenylethyl)pyrimidine-2,4,6(1H,3H,5H)-trione
C12 H12 N2 O3
MHIKXQXNKSZIGX-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B, C
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 64.060α = 90.00
b = 154.240β = 92.78
c = 134.850γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-21
    Type: Database references, Structure summary
  • Version 1.2: 2013-03-06
    Type: Database references
  • Version 1.3: 2018-02-07
    Type: Database references