2DLN

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

• PDB DOI: https://doi.org/10.2210/pdb2DLN/pdb

• Classification: LIGASE(PEPTIDOGLYCAN SYNTHESIS)
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1994-07-18 Released: 1995-11-01 
• Deposition Author(s): Knox, J.R., Moews, P.C., Fan, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

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: 7939684 
• DOI: https://doi.org/10.1126/science.7939684
• Primary Citation of Related Structures:  
  2DLN


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.62 kDa 
• Atom Count: 2,642 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ALANINE--D-ALANINE LIGASE	A	306	Escherichia coli	Mutation(s): 0  EC: 6.3.2.4
UniProt
Find proteins for P07862 (Escherichia coli (strain K12)) Explore P07862  Go to UniProtKB:  P07862

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PHY	E [auth A]	1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID C6 H15 N O7 P2 BAIYWTZQRMCJBV-DKDXWZAISA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.3	α = 90
b = 51.4	β = 90
c = 51.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-11-01 
Deposition Author(s): Knox, J.R., Moews, P.C., Fan, C.

Revision History  

• Version 1.0: 1995-11-01
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations