5A5F

CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX WITH UMA AND ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited.

Sink, R.Kotnik, M.Zega, A.Barreteau, H.Gobec, S.Blanot, D.Dessen, A.Contreras-Martel, C.

(2016) PLoS ONE 11: e0152075-e0152075

  • DOI: 10.1371/journal.pone.0152075
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-h ...

    The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.


    Organizational Affiliation

    University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
A
438Escherichia 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MLI
Query on MLI

Download SDF File 
Download CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
UMA
Query on UMA

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
C23 H36 N4 O20 P2
NTMMCWJNQNKACG-KBKUWGQMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.440α = 90.00
b = 89.840β = 90.00
c = 108.540γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Database references, Source and taxonomy