1HVB

CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.114 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A 1.2-A snapshot of the final step of bacterial cell wall biosynthesis.

Lee, W.McDonough, M.A.Kotra, L.Li, Z.H.Silvaggi, N.R.Takeda, Y.Kelly, J.A.Mobashery, S.

(2001) Proc Natl Acad Sci U S A 98: 1427-1431

  • DOI: https://doi.org/10.1073/pnas.98.4.1427
  • Primary Citation of Related Structures:  
    1HVB

  • PubMed Abstract: 

    The cell wall imparts structural strength and shape to bacteria. It is made up of polymeric glycan chains with peptide branches that are cross-linked to form the cell wall. The cross-linking reaction, catalyzed by transpeptidases, is the last step in cell wall biosynthesis. These enzymes are members of the family of penicillin-binding proteins, the targets of beta-lactam antibiotics. We report herein the structure of a penicillin-binding protein complexed with a cephalosporin designed to probe the mechanism of the cross-linking reaction catalyzed by transpeptidases. The 1.2-A resolution x-ray structure of this cephalosporin bound to the active site of the bifunctional serine type D-alanyl-D-alanine carboxypeptidase/transpeptidase (EC ) from Streptomyces sp. strain R61 reveals how the two peptide strands from the polymeric substrates are sequestered in the active site of a transpeptidase. The structure of this complex provides a snapshot of the enzyme and the bound cell wall components poised for the final and critical cross-linking step of cell wall biosynthesis.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE349Streptomyces sp. R61Mutation(s): 0 
EC: 3.4.16.4
UniProt
Find proteins for P15555 (Streptomyces sp. (strain R61))
Explore P15555 
Go to UniProtKB:  P15555
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15555
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CEH
Query on CEH

Download Ideal Coordinates CCD File 
B [auth A]5-{3-(S)-(4-(R)-ACETYLAMINO-4-CARBOXY-BUTYRYLAMINO)-3-[1-(R)-(1-(R)-CARBOXY-ETHYLCARBAMOYL)-ETHYLCARBAMOYL]-PROPYL}-2-( CARBOXY-PHENYLACETYLAMINO-METHYL)-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID
C32 H42 N6 O13 S
PEUIVMLYMKXUBF-PULJXETJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.114 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.778α = 90
b = 66.664β = 90
c = 100.928γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2024-10-30
    Changes: Structure summary