4ARW

Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 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:  
    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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASEA, B, C, D302Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: rmlAPA5163
EC: 2.7.7.74 (PDB Primary Data), 2.7.7.24 (UniProt)
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HNR
Query on HNR

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
P [auth D]
N-(6-AMINO-1-BUTYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-N-METHYL-BENZENESULFONAMIDE
C15 H20 N4 O4 S
BDLSZMGNNJOQJF-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
Q [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
S [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C],
O [auth C],
R [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HNR PDBBind:  4ARW Kd: 74 (nM) from 1 assay(s)
Binding MOAD:  4ARW Kd: 74 (nM) from 1 assay(s)
BindingDB:  4ARW IC50: 210 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.99α = 90
b = 153.76β = 92.32
c = 134.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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: 2012-12-19
    Changes: Atomic model, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2013-03-06
    Changes: Database references
  • Version 1.4: 2017-07-05
    Changes: Data collection
  • Version 1.5: 2018-02-07
    Changes: Database references
  • Version 1.6: 2020-03-04
    Changes: Derived calculations, Other