1E4E

D-alanyl-D-lacate ligase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1073/pnas.150116497
  • Primary Citation of Related Structures:  
    1E4E

  • 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 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA343Enterococcus faeciumMutation(s): 0 
Gene Names: VANA
EC: 6.1.2.1
UniProt
Find proteins for P25051 (Enterococcus faecium)
Explore P25051 
Go to UniProtKB:  P25051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25051
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA343Enterococcus faeciumMutation(s): 0 
Gene Names: VANA
EC: 6.1.2.1
UniProt
Find proteins for P25051 (Enterococcus faecium)
Explore P25051 
Go to UniProtKB:  P25051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25051
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
C [auth A],
Q [auth B]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PHY
Query on PHY
Download Ideal Coordinates CCD File 
D [auth A],
R [auth B]		1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
C6 H15 N O7 P2
BAIYWTZQRMCJBV-DKDXWZAISA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
U [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth B]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
AA [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
S [auth B],
T [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 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
b = 225.359β = 90
c = 72.439γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-28
    Type: Initial release
  • Version 1.1: 2011-09-21
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2017-09-13
    Changes: Advisory, Database references
  • Version 1.3: 2019-10-09
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description