Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

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This is version 1.5 of the entry. See complete history


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: https://doi.org/10.1021/cb300426u
  • Primary Citation of Related Structures:  
    3ZLK, 3ZLL, 4ARW, 4ASJ, 4ASY, 4B2W, 4B2X, 4B3U, 4B42, 4B4B, 4B4G, 4B4M, 4B5B

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
303Pseudomonas aeruginosa PAO1Mutation(s): 0 
Find proteins for Q9HU22 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HU22 
Go to UniProtKB:  Q9HU22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HU22
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on KKT

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
M [auth D]
C16 H22 N4 O4 S
Query on MES

Download Ideal Coordinates CCD File 
I [auth B],
K [auth C]
C6 H13 N O4 S
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
L [auth C],
N [auth D]
Binding Affinity Annotations 
IDSourceBinding Affinity
KKT Binding MOAD:  4B4G IC50: 175 (nM) from 1 assay(s)
PDBBind:  4B4G IC50: 175 (nM) from 1 assay(s)
BindingDB:  4B4G IC50: 175 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.11α = 90
b = 153.07β = 92.57
c = 134.84γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references, Structure summary
  • Version 1.2: 2013-03-06
    Changes: Database references
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2018-02-07
    Changes: Database references
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description