1HVB | pdb_00001hvb

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

• PDB DOI: https://doi.org/10.2210/pdb1HVB/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp. R61
• Mutation(s): No 


• Deposited: 2001-01-08 Released: 2001-02-07 
• Deposition Author(s): McDonough, M.A., Lee, W., Silvaggi, N.R., Mobashery, S., Kelly, J.A.

---

Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 11171967 
• DOI: https://doi.org/10.1073/pnas.98.4.1427
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.17 kDa 
• Atom Count: 3,318 
• Modeled Residue Count: 346 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE	A	349	Streptomyces sp. R61	Mutation(s): 0  EC: 3.4.16.4
UniProt
Find proteins for P15555 (Streptomyces sp. (strain R61)) Explore P15555  Go to UniProtKB:  P15555

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CEH	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 (Depositor) 
• R-Value Work:  0.113 (Depositor) 
• R-Value Observed: 0.114 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.778	α = 90
b = 66.664	β = 90
c = 100.928	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-07 
Deposition Author(s): McDonough, M.A., Lee, W., Silvaggi, N.R., Mobashery, S., Kelly, J.A.

Revision History  

• 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