2OLV

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

• PDB DOI: https://doi.org/10.2210/pdb2OLV/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2007-01-19 Released: 2007-03-13 
• Deposition Author(s): Lovering, A.L., De Castro, L., Lim, D., Strynadka, N.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.280 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 

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

• PubMed: 17347437 
• DOI: https://doi.org/10.1126/science.1136611
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 2	A, B	669	Staphylococcus aureus	Mutation(s): 14  Gene Names: pbp2 EC: 2.3.2 (PDB Primary Data), 2.4.99.28 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q9R744 (Staphylococcus aureus) Explore Q9R744  Go to UniProtKB:  Q9R744

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M0E	C [auth A], D [auth B]	MOENOMYCIN C69 H106 N5 O34 P NXPRJQIAIORCGO-ZLPAOQQDSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.280 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.565	α = 90
b = 212.211	β = 90
c = 91.635	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Lovering, A.L., De Castro, L., Lim, D., Strynadka, N.C.J.

Revision History  

• 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