1E4E

D-alanyl-D-lacate ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA).

Roper, D.I.Huyton, T.Vagin, A.Dodson, G.

(2000) Proc. Natl. Acad. Sci. U.S.A. 97: 8921-8925

  • DOI: 10.1073/pnas.150116497

  • PubMed Abstract: 
  • d-alanine-d-lactate ligase from Enterococcus faecium BM4147 is directly responsible for the biosynthesis of alternate cell-wall precursors in bacteria, which are resistant to the glycopeptide antibiotic vancomycin. The crystal structure has been dete ...

    d-alanine-d-lactate ligase from Enterococcus faecium BM4147 is directly responsible for the biosynthesis of alternate cell-wall precursors in bacteria, which are resistant to the glycopeptide antibiotic vancomycin. The crystal structure has been determined with data extending to 2.5-A resolution. This structure shows that the active site has unexpected interactions and is distinct from previous models for d-alanyl-d-lactate ligase mechanistic studies. It appears that the preference of the enzyme for lactate as a ligand over d-alanine could be mediated by electrostatic effects and/or a hydrogen-bonding network, which principally involve His-244. The structure of d-alanyl-d-lactate ligase provides a revised interpretation of the molecular events that lead to vancomycin resistance.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, United Kingdom. roper@ysbl.york.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
A
343Enterococcus faeciumGene Names: vanA
EC: 6.1.2.1
Find proteins for P25051 (Enterococcus faecium)
Go to UniProtKB:  P25051
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
B
343Enterococcus faeciumGene Names: vanA
EC: 6.1.2.1
Find proteins for P25051 (Enterococcus faecium)
Go to UniProtKB:  P25051
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
A, B
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: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 123.204α = 90.00
b = 225.359β = 90.00
c = 72.439γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-07-03 
  • Released Date: 2001-06-28 
  • Deposition Author(s): Roper, D.I.

Revision History 

  • Version 1.0: 2001-06-28
    Type: Initial release
  • Version 1.1: 2011-09-21
    Type: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2017-09-13
    Type: Advisory, Database references