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 

Structure information

Unit cell parameters

Space Group

P 1 21 1  

Unit Cell

a=38.90Å, b=43.73Å, c=80.24Å
α=90.00, β=99.20, γ=90.00 

Solvent content

 

Matthews coefficient

 

Refinement

Data for the highest resolution shell is in parentheses.

Resolution range

38.40-1.36Å (1.38-1.36Å)  

R_all(%)

16.3 

R_work(%)

16.2 (30.6) 

R_free(%)

18.5 (33.7) 

Num. observed reflections

57560 (3231) 

Num. R_free reflections

2929 (134) 

Completeness(%)

96.5 (92.0) 

Model parameters

Num Atoms

2123  

Num Waters

285  

Num Hetatoms

366  

Model mean isotropic B factor

25.860Ų  

RMSD bond length

0.014Å  

RMSD bond angle

1.397°  

RMSD dihedral angle

14.795°

 

Filename uploaded

4MUQ.pdb (uploaded on Apr 23, 2014 10:04 AM)  

Inserted

Sep 26, 2013