1EHI

D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCONOSTOC MESENTEROIDES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides.

Kuzin, A.P.Sun, T.Jorczak-Baillass, J.Healy, V.L.Walsh, C.T.Knox, J.R.

(2000) Structure Fold.Des. 8: 463-470


  • PubMed Abstract: 
  • The bacterial cell wall and the enzymes that synthesize it are targets of glycopeptide antibiotics (vancomycins and teicoplanins) and beta-lactams (penicillins and cephalosporins). Biosynthesis of cell wall peptidoglycan requires a crosslinking of pe ...

    The bacterial cell wall and the enzymes that synthesize it are targets of glycopeptide antibiotics (vancomycins and teicoplanins) and beta-lactams (penicillins and cephalosporins). Biosynthesis of cell wall peptidoglycan requires a crosslinking of peptidyl moieties on adjacent glycan strands. The D-alanine-D-alanine transpeptidase, which catalyzes this crosslinking, is the target of beta-lactam antibiotics. Glycopeptides, in contrast, do not inhibit an enzyme, but bind directly to D-alanine-D-alanine and prevent subsequent crosslinking by the transpeptidase. Clinical resistance to vancomycin in enterococcal pathogens has been traced to altered ligases producing D-alanine-D-lactate rather than D-alanine-D-alanine.


    Related Citations: 
    • D-alanine:D-alanine ligase: Phosphonate and Phosphinate Intermediates with Wild-type and the Y216F Mutant
      Fan, C.,Park, I.-S.,Walsh, C.T.,Knox, J.R.
      (1997) Biochemistry 36: 2531
    • Vancomycin Resistance: Structure of D-alanine:D-alanine Ligase at 2.3 A Resolution
      Fan, C.,Moews, P.C.,Walsh, C.T.,Knox, J.R.
      (1994) Science 266: 439


    Organizational Affiliation

    Department of Molecular and Cell Biology, The University of Connecticut, Storrs, CT 06269-3125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-ALANINE:D-LACTATE LIGASE
A, B
377Leuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 / NCDO 523)Gene Names: ddl
EC: 6.3.2.4
Find proteins for Q03ZI1 (Leuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 / NCDO 523))
Go to UniProtKB:  Q03ZI1
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
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PHY
Query on PHY

Download SDF File 
Download CCD File 
A
1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
C6 H15 N O7 P2
BAIYWTZQRMCJBV-DKDXWZAISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.200α = 90.00
b = 90.800β = 92.10
c = 82.100γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description