Structure of IDP91778

Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Ala-D-Ala phosphinate analog

Edit deposit information
CSGID target
IDP91778 
PDB Id
4MUS (NCBI MMDB
Authors
P.J.Stogios,E.Evdokimova,D.Meziane-Cherif,R.Di Leo,V.Yim,P.Courvalin,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Peter Stogios 
Responsible lab
University of Calgary 
Deposition Date
Sep 23, 2013 
Release Date
Oct 09, 2013 

Annotation

Description
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-γ-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 substrates. The molecular basis for the diverse specificity of Van D,D-peptidases remains unknown. Here we present the crystal structures of VanXYC and VanXYG in apo and transition state analog-bound forms and of VanXYC in complex with its substrate (D-Ala-D-Ala) and the product (D-Ala). Our structural and biochemical analysis identified the mobile cap formed by VanXYC residues 110 to 115 over the catalytic site as the key structural element involved in the switch between di- and penta-peptide hydrolysis. The structure of a VanY-like enzyme, BaLdcB, from Bacillus anthracis showed that the active site of VanY peptidases lacked this element featuring a molecular architecture in line with preference for larger substrates. Presented structural data also highlight the molecular basis for selection of D-Ala-terminating peptidoglycan precursors over the modified Van-resistant components. These results illustrate the remarkable adaptability of D,D-peptidase fold in response to antibiotic pressure via evolution of specific structural elements that confer bisubstrate hydrolytic activity. 
Functional assignment
antibiotic resistance 

Ligands

Ligand code Name Ligand type
2D8 crystallization
LY0 crystallization
SO4 crystallization
GOL crystallization
CL CHLORIDE ION crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=44.26Å, b=44.78Å, c=62.41Å
α=86.84, β=77.29, γ=64.15 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
37.20-1.68Å (1.69-1.67Å)  
Rall(%)
17.0 
Rwork(%)
16.8 (25.1) 
Rfree(%)
20.7 (27.4) 
Num. observed reflections
50650 (2936) 
Num. Rfree reflections
2183 (146) 
Completeness(%)
96.4 (90.0) 

Model parameters

Num Atoms
3182  
Num Waters
512  
Num Hetatoms
592  
Model mean isotropic B factor
30.530Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.289°  
RMSD dihedral angle
16.064°
 
Filename uploaded
4MUS.pdb (uploaded on Apr 23, 2014 10:08 AM)  
Inserted
Oct 09, 2013