Structure of IDP91774

Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg

Edit deposit information
CSGID target
IDP91774 
PDB Id
4F78 (NCBI MMDB
Authors
P.J.Stogios,Z.Wawrzak,E.Evdokimova,G.Minasov,O.Egorova,R.Di Leo,M.Kudritska,V.Yim,D.Meziane-Cherif,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
May 15, 2012 
Release Date
May 23, 2012 

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-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. 
Functional assignment
antibiotic resistance 

Ligands

Ligand code Name Ligand type
EDO crystallization
SO4 crystallization
CL crystallization
ZN ZINC ION biological
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=38.91Å, b=43.96Å, c=80.20Å
α=90.00, β=99.19, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
39.58-1.95Å (2.00-1.95Å)  
Rall(%)
15.5 
Rwork(%)
15.4 (21.7) 
Rfree(%)
18.6 (27.8) 
Num. observed reflections
20683 (2747) 
Num. Rfree reflections
1032 (123) 
Completeness(%)
98.3 (98.0) 

Model parameters

Num Atoms
2055  
Num Waters
187  
Num Hetatoms
296  
Model mean isotropic B factor
26.700Å2  
RMSD bond length
0.016Å  
RMSD bond angle
1.494°  
RMSD dihedral angle
14.268°
 
Filename uploaded
4F78.pdb (uploaded on Apr 23, 2014 10:01 AM)  
Inserted
May 15, 2012