2JFH

Crystal structure of MurD ligase in complex with L-Glu containing sulfonamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Functional Characterization of Enantiomeric Glutamic Acid Derivatives as Potential Transition State Analogue Inhibitors of Murd Ligase.

Kotnik, M.Humljan, J.Contreras-Martel, C.Oblak, M.Kristan, K.Herve, M.Blanot, D.Urleb, U.Gobec, S.Dessen, A.Solmajer, T.

(2007) J.Mol.Biol. 370: 107

  • DOI: 10.1016/j.jmb.2007.04.048
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mur ligases play an essential role in the intracellular biosynthesis of bacterial peptidoglycan, the main component of the bacterial cell wall, and represent attractive targets for the design of novel antibacterials. UDP-N-acetylmuramoyl-L-alanine:D- ...

    Mur ligases play an essential role in the intracellular biosynthesis of bacterial peptidoglycan, the main component of the bacterial cell wall, and represent attractive targets for the design of novel antibacterials. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) catalyses the addition of D-glutamic acid to the cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine (UMA) and is the second in the series of Mur ligases. MurD ligase is highly stereospecific for its substrate, D-glutamic acid (D-Glu). Here, we report the high resolution crystal structures of MurD in complexes with two novel inhibitors designed to mimic the transition state of the reaction, which contain either the D-Glu or the L-Glu moiety. The binding modes of N-sulfonyl-D-Glu and N-sulfonyl-L-Glu derivatives were also characterised kinetically. The results of this study represent an excellent starting point for further development of novel inhibitors of this enzyme.


    Organizational Affiliation

    Lek Pharmaceuticals d. d., Drug Discovery, Verovskova 57, 1526 Ljubljana, Slovenia. miha.kotnik@sandoz.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-ACETYLMURAMOYL-ALANINE-D-GLUTAMATE LIGASE
A
445Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: murD
EC: 6.3.2.9
Find proteins for P14900 (Escherichia coli (strain K12))
Go to UniProtKB:  P14900
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LK1
Query on LK1

Download SDF File 
Download CCD File 
A
N-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-L-GLUTAMIC ACID
C19 H23 N O7 S
UAGYXJBYAFGRFR-KRWDZBQOSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LK1IC50: 710000 nM (100) BINDINGDB
LK1Ki: 240000 nM BINDINGMOAD
LK1Ki: 870000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 65.593α = 90.00
b = 65.593β = 90.00
c = 135.485γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Source and taxonomy