3DWK | pdb_00003dwk

Identification of Dynamic Structural Motifs Involved in Peptidoglycan Glycosyltransfer

PDB DOI: https://doi.org/10.2210/pdb3DWK/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-07-22 Released: 2008-09-30
Deposition Author(s): Lovering, A.L., De Castro, L., Strynadka, N.C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.264 (Depositor), 0.243 (DCC)
R-Value Work:
0.218 (Depositor)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Identification of dynamic structural motifs involved in peptidoglycan glycosyltransfer.

Lovering, A.L., De Castro, L., Strynadka, N.C.

(2008) J Mol Biology 383: 167-177

PubMed: 18760285 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2008.08.020
Primary Citation Related Structures:
3DWK

PubMed Abstract:
We have determined the structure of a new form of the bifunctional peptidoglycan glycosyltransferase (GT)/transpeptidase penicillin-binding protein 2 from the pathogen Staphylococcus aureus. We observe several previously unstructured regions of the GT substrate-binding pockets, including a pi-bulge in the outer helix that may be responsible for the conformational flexibility of active-site motifs required for transfer of product to the donor binding site during processive rounds of peptidoglycan polymerization. The identification of a beta-hairpin in the usually unstructured region of the fold shares local structural homology to that of an exomuramidase, heightening comparisons between this biosynthetic enzyme and lytic peptidoglycan transglycosylases. This new form also shows remarkable interdomain flexibility, causing the linker region of the fold to project into the GT active site. This self-interaction may have significant consequences for the regulation of polymerization activity. The derived information is used to build a catalytic model of both donor and acceptor glycolipid substrates.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.

Macromolecule Content

Total Structure Weight: 283.16 kDa
Atom Count: 19,474
Modeled Residue Count: 2,444
Deposited Residue Count: 2,500
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 2	A, B, C, D	625	Staphylococcus aureus subsp. aureus COL	Mutation(s): 1 Gene Names: pbp2, SACOL1490
UniProt
Find proteins for Q8KHY3 (Staphylococcus aureus) Explore Q8KHY3 Go to UniProtKB: Q8KHY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KHY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain YA [auth D] MOL2 format, chain YA [auth D] mmCIF format, chain YA [auth D]	YA [auth D]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain YA [auth D] Interactions & Density Focus chain YA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain XA [auth D] SDF format, chain VA [auth D] SDF format, chain V [auth B] SDF format, chain UA [auth D] SDF format, chain TA [auth D] SDF format, chain SA [auth D] SDF format, chain S [auth A] SDF format, chain QA [auth D] SDF format, chain PA [auth D] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain DA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], S [auth A], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]