2OQO

Crystal structure of a peptidoglycan glycosyltransferase from a class A PBP: insight into bacterial cell wall synthesis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis.

Yuan, Y., Barrett, D., Zhang, Y., Kahne, D., Sliz, P., Walker, S.

(2007) Proc.Natl.Acad.Sci.Usa 104: 5348-5353

  • DOI: 10.1073/pnas.0701160104

  • PubMed Abstract: 

    • Peptidoglycan is an essential polymer that forms a protective shell around bacterial cell membranes. Peptidoglycan biosynthesis is the target of many clinically used antibiotics, including the beta-lactams, imipenems, cephalosporins, and glycopeptide ...

    Peptidoglycan is an essential polymer that forms a protective shell around bacterial cell membranes. Peptidoglycan biosynthesis is the target of many clinically used antibiotics, including the beta-lactams, imipenems, cephalosporins, and glycopeptides. Resistance to these and other antibiotics has prompted interest in an atomic-level understanding of the enzymes that make peptidoglycan. Representative structures have been reported for most of the enzymes in the pathway. Until now, however, there have been no structures of any peptidoglycan glycosyltransferases (also known as transglycosylases), which catalyze formation of the carbohydrate chains of peptidoglycan from disaccharide subunits on the bacterial cell surface. We report here the 2.1-A crystal structure of the peptidoglycan glycosyltransferase (PGT) domain of Aquifex aeolicus PBP1A. The structure has a different fold from all other glycosyltransferase structures reported to date, but it bears some resemblance to lambda-lysozyme, an enzyme that degrades the carbohydrate chains of peptidoglycan. An analysis of the structure, combined with biochemical information showing that these enzymes are processive, suggests a model for glycan chain polymerization.

    Organizational Affiliation: 

    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Penicillin-binding protein 1A (PBP-1a) (PBP1a)
A
200Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: mrcA (ponA)
EC: 2.4.1.129, 3.4.16.4
Membrane protein
mpstruct		Group: 
MONOTOPIC MEMBRANE PROTEINS		Sub Group: 
Glycosyltransferases		Protein: 
Peptidoglycan Glycosyltransferase penicillin-binding protein 1a (PBP1a)
Find proteins for O66874 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66874
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CPS
Query on CPS
Download SDF File 
Download CCD File 
A
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
CHAPS
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.817α = 90.00
b = 100.305β = 90.00
c = 104.012γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
SnBphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description