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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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.

    Related Citations: 
    • Binding of Cephalothin and Cefotaxime to D-Ala-D-Ala-Peptidase Reveals A Functional Basis of a Natural Mutation in a Low-Affinity Penicillin-Binding Protein and in Extended-Spectrum Beta-Lactamases
      Kuzin, A.P., Liu, H., Kelly, J.A., Knox, J.R.
      (1995) Biochemistry 34: 9532
    • The Refined Crystallographic Structure of a DD-Peptidase Penicillin-target Enzyme at 1.6 Angstrom Resolution
      Kelly, J.A., Kuzin, A.P.
      (1995) J Mol Biol 254: 223
    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
MoleculeChainsSequence LengthOrganismDetailsImage
D-ALANYL-D-ALANINE CARBOXYPEPTIDASEA349Streptomyces 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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		 Ligand Interaction
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

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View more in-depth experimental data

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