Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33602.54 
• Atom Count: 2349 
• Residue Count: 306 
• Unique protein chains: 1

1IOW

COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE

• DOI: 10.2210/pdb1IOW/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): 1 


• Deposited: 1996-09-20 Released: 1997-02-12 
• Deposition Author(s): Knox, J.R., Moews, P.C., Fan, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.234 
• R-Value Work: 0.158 

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

• PubMed: 9054558 
• DOI: 10.1021/bi962431t
• Primary Citation of Related Structures:  
  1IOV


• 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.

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Related Citations: 

• 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
• A Common Fold for Peptide Synthetases Cleaving ATP to Adp
  Fan, C.,Moews, P.C.,Shi, Y.,Walsh, C.T.,Knox, J.R.
  (1995) Proc.Natl.Acad.Sci.USA 92: 1172




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
D-ALA\:D-ALA LIGASE	A	306	Escherichia coli (strain K12)	Mutation(s): 1  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ADP	A	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
PHY	A	1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID C6 H15 N O7 P2 BAIYWTZQRMCJBV-DKDXWZAISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.234 
• R-Value Work: 0.158 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 99.800	α = 90.00
b = 51.700	β = 90.00
c = 51.700	γ = 90.00

Software Package:

Software Name	Purpose
XENGEN	data scaling
XENGEN	data reduction
X-PLOR	model building
X-PLOR	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-09-20 
• Released Date: 1997-02-12 
• Deposition Author(s): Knox, J.R., Moews, P.C., Fan, C.

Revision History 

• Version 1.0: 1997-02-12
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance