2OLU

Structural Insight Into the Transglycosylation Step Of Bacterial Cell Wall Biosynthesis : Apoenzyme

PDB DOI: https://doi.org/10.2210/pdb2OLU/pdb

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

Deposited: 2007-01-19 Released: 2007-03-20
Deposition Author(s): Lovering, A.L., De Castro, L.H., Lim, D., Strynadka, N.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.246
R-Value Work: 0.191
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 17347437 Search on PubMed
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.

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: 74.7 kDa
Atom Count: 4,803
Modelled Residue Count: 608
Deposited Residue Count: 669
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 2	A	669	Staphylococcus aureus	Mutation(s): 12 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9R744
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.246
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.495	α = 90
b = 249.891	β = 90
c = 103.164	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-03-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-03-20
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