Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 167.41 kDa 
• Atom Count: 12319 
• Residue Count: 1480 
• Unique protein chains: 1

4ECL

Crystal structure of the cytoplasmic domain of vancomycin resistance serine racemase VanTg

• DOI: 10.2210/pdb4ECL/pdb

• Classification: ISOMERASE
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-26 Released: 2012-04-18 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., Minasov, G., Evdokimova, E., Egorova, O., Cosme, J., Di Leo, R., Krishnamoorthy, M., Meziane-Cherif, D., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.233 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Literature

Structural and Functional Adaptation of Vancomycin Resistance VanT Serine Racemases.

Meziane-Cherif, D., Stogios, P.J., Evdokimova, E., Egorova, O., Savchenko, A., Courvalin, P.

(2015) mBio 6: e00806-e00806

• PubMed: 26265719 
• DOI: 10.1128/mBio.00806-15
• Primary Citation of Related Structures:  
  4ECL


• PubMed Abstract: 
  

Vancomycin resistance in Gram-positive bacteria results from the replacement of the D-alanyl-D-alanine target of peptidoglycan precursors with D-alanyl-D-lactate or D-alanyl-D-serine (D-Ala-D-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of D-Ala-D-Ser-terminating precursors by converting L-Ser to D-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in L-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanTG from VanG-type resistant Enterococcus faecalis BM4518 was determined. The structure showed significant similarity to type III pyridoxal 5'-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanTG and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn696 which are responsible for the L-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanTG against L-Ser versus L-Ala implied that this enzyme relies on its membrane-bound domain for L-Ser transport to increase the overall rate of d-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria.

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Organizational Affiliation: 

Institut Pasteur, Unité des Agents Antibactériens, Paris, France [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine racemase	A, B, C, D	374	Enterococcus faecalis	Mutation(s): 0  Gene Names: vanTG EC: 5.1.1.1
Find proteins for Q6WRY3 (Enterococcus faecalis) Explore Q6WRY3  Go to UniProtKB:  Q6WRY3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A, B, C, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B,C,D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.233 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 10.18430/M34ECL Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.682	α = 90
b = 82.341	β = 90.14
c = 117.468	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-26 
• Released Date: 2012-04-18 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Minasov, G., Evdokimova, E., Egorova, O., Cosme, J., Di Leo, R., Krishnamoorthy, M., Meziane-Cherif, D., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History 

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references