4F78 | pdb_00004f78

Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg

• PDB DOI: https://doi.org/10.2210/pdb4F78/pdb

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


• Deposited: 2012-05-15 Released: 2012-05-23 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., Evdokimova, E., Minasov, G., Egorova, O., Di Leo, R., Kudritska, M., Yim, V., 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: 1.95 Å
• R-Value Free: 
  0.186 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Structural basis for the evolution of vancomycin resistance D,D-peptidases.

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

(2014) Proc Natl Acad Sci U S A 111: 5872-5877

• PubMed: 24711382 
• DOI: https://doi.org/10.1073/pnas.1402259111
• Primary Citation Related Structures: 
  4F78, 4MUQ, 4MUR, 4MUS, 4MUT, 4OAK


• PubMed Abstract: 
  

  Vancomycin resistance in Gram-positive bacteria is due to production of cell-wall precursors ending in D-Ala-D-Lac or D-Ala-D-Ser, to which vancomycin exhibits low binding affinities, and to the elimination of the high-affinity precursors ending in D-Ala-D-Ala. Depletion of the susceptible high-affinity precursors is catalyzed by the zinc-dependent D,D-peptidases VanX and VanY acting on dipeptide (D-Ala-D-Ala) or pentapeptide (UDP-MurNac-L-Ala-D-Glu-L-Lys-D-Ala-D-Ala), respectively. Some of the vancomycin resistance operons encode VanXY D,D-carboxypeptidase, which hydrolyzes both di- and pentapeptide. The molecular basis for the diverse specificity of Van D,D-peptidases remains unknown. We present the crystal structures of VanXYC and VanXYG in apo and transition state analog-bound forms and of VanXYC in complex with the D-Ala-D-Ala substrate and D-Ala product. Structural and biochemical analysis identified the molecular determinants of VanXY dual specificity. VanXY residues 110-115 form a mobile cap over the catalytic site, whose flexibility is involved in the switch between di- and pentapeptide hydrolysis. Structure-based alignment of the Van D,D-peptidases showed that VanY enzymes lack this element, which promotes binding of the penta- rather than that of the dipeptide. The structures also highlight the molecular basis for selection of D-Ala-ending precursors over the modified resistance targets. These results illustrate the remarkable adaptability of the D,D-peptidase fold in response to antibiotic pressure via evolution of specific structural elements that confer hydrolytic activity against vancomycin-susceptible peptidoglycan precursors.

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Organizational Affiliation: 
• Unité des Agents Antibactériens, Institut Pasteur, 75724 Paris Cedex 15, France.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 30.87 kDa 
• Atom Count: 2,351 
• Modeled Residue Count: 251 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D,D-dipeptidase/D,D-carboxypeptidase	A	255	Enterococcus faecalis	Mutation(s): 0  Gene Names: vanXYG, vanYG2
UniProt
Find proteins for Q9KHL8 (Enterococcus faecalis) Explore Q9KHL8  Go to UniProtKB:  Q9KHL8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	O [auth A], P [auth A], Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.186 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34f78

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.912	α = 90
b = 43.96	β = 99.19
c = 80.199	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Evdokimova, E., Minasov, G., Egorova, O., Di Leo, R., Kudritska, M., Yim, V., Meziane-Cherif, D., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Structure summary
• Version 1.2: 2013-10-16
  Changes: Structure summary
• Version 1.3: 2014-01-22
  Changes: Other
• Version 1.4: 2014-04-23
  Changes: Database references
• Version 1.5: 2014-05-14
  Changes: Database references
• Version 1.6: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary