1IOV

COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.156 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

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: 2531-2538

  • DOI: https://doi.org/10.1021/bi962431t
  • Primary Citation of Related Structures:  
    1IOV, 1IOW

  • PubMed Abstract: 

    The crystallographic structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli complexed with a D-Ala-D-alpha-hydroxybutyrate phosphonate and the structure of the Y216F mutant ligase complexed with a D-Ala-D-Ala phosphinate have been determined to 2.2 and 1.9 A resolution, respectively, and refined to R factors of 0.156 and 0.158. In each complex the inhibitor has reacted with ATP to produce ADP and a tight-binding phosphorylated transition state intermediate. Comparison of these two structures with the known crystal structure of the phosphinate intermediate of the wild-type ligase shows no major conformational changes, but B factors indicate differences in mobility of loops covering the binding site. The weaker inhibition of the Y216F mutant by both inhibitors is thought to be due in part to the loss of an interloop hydrogen bond. A similar mechanism may account for poor inhibition of VanA, the homologous D-Ala:D-lactate ligase produced by vancomycin-resistant enterococci.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-ALA\:D-ALA LIGASE306Escherichia coliMutation(s): 0 
EC: 6.3.2.4
UniProt
Find proteins for P07862 (Escherichia coli (strain K12))
Explore P07862 
Go to UniProtKB:  P07862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07862
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.6α = 90
b = 51β = 90
c = 51.2γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection