2DLN

VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 439-443


  • PubMed Abstract: 
  • The molecular structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli, co-crystallized with an S,R-methylphosphinate and adenosine triphosphate, was determined by x-ray diffraction to a resolution of 2.3 angstroms. A catalyti ...

    The molecular structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli, co-crystallized with an S,R-methylphosphinate and adenosine triphosphate, was determined by x-ray diffraction to a resolution of 2.3 angstroms. A catalytic mechanism for the ligation of two D-alanine substrates is proposed in which a helix dipole and a hydrogen-bonded triad of tyrosine, serine, and glutamic acid assist binding and deprotonation steps. From sequence comparison, it is proposed that a different triad exists in a recently discovered D-alanine:D-lactate ligase (VanA) present in vancomycin-resistant enterococci. A molecular mechanism for the altered specificity of VanA is suggested.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-ALANINE--D-ALANINE LIGASE
A
306Escherichia coli (strain K12)Gene Names: ddlB (ddl)
EC: 6.3.2.4
Find proteins for P07862 (Escherichia coli (strain K12))
Go to UniProtKB:  P07862
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: 2.3 Å
  • R-Value Work: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.300α = 90.00
b = 51.400β = 90.00
c = 51.200γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-11-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance