2OLV | pdb_00002olv

Structural Insight Into the Transglycosylation Step Of Bacterial Cell Wall Biosynthesis : Donor Ligand Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.280 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

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This is version 1.4 of the entry. See complete history. 

Literature

Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis.

Lovering, A.L., de Castro, L.H., Lim, D., Strynadka, N.C.

(2007) Science 315: 1402-1405

  • DOI: https://doi.org/10.1126/science.1136611
  • Primary Citation Related Structures: 
    2OLU, 2OLV

  • PubMed Abstract: 

    Peptidoglycan glycosyltransferases (GTs) catalyze the polymerization step of cell-wall biosynthesis, are membrane-bound, and are highly conserved across all bacteria. Long considered the "holy grail" of antibiotic research, they represent an essential and easily accessible drug target for antibiotic-resistant bacteria, including methicillin-resistant Staphylococcus aureus. We have determined the 2.8 angstrom structure of a bifunctional cell-wall cross-linking enzyme, including its transpeptidase and GT domains, both unliganded and complexed with the substrate analog moenomycin. The peptidoglycan GTs adopt a fold distinct from those of other GT classes. The structures give insight into critical features of the catalytic mechanism and key interactions required for enzyme inhibition.

    • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada.

Macromolecule Content 

  • Total Structure Weight: 152.44 kDa 
  • Atom Count: 9,878 
  • Modeled Residue Count: 1,235 
  • Deposited Residue Count: 1,338 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Penicillin-binding protein 2
A, B
669Staphylococcus aureusMutation(s): 14 
Gene Names: pbp2
EC: 2.3.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9R744 (Staphylococcus aureus)
Explore Q9R744 
Go to UniProtKB:  Q9R744
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R744
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.280 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.565α = 90
b = 212.211β = 90
c = 91.635γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary