8P1X | pdb_00008p1x

TarM(Se)_G117R-UDP-glucose

PDB DOI: https://doi.org/10.2210/pdb8P1X/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus epidermidis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-05-13 Released: 2023-12-06
Deposition Author(s): Guo, Y., Stehle, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.238 (Depositor), 0.244 (DCC)
R-Value Work:
0.201 (Depositor), 0.206 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Invasive Staphylococcus epidermidis uses a unique processive wall teichoic acid glycosyltransferase to evade immune recognition.

Guo, Y., Du, X., Krusche, J., Beck, C., Ali, S., Walter, A., Winstel, V., Mayer, C., Codee, J.D.C., Peschel, A., Stehle, T.

(2023) Sci Adv 9: eadj2641-eadj2641

PubMed: 38000019 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adj2641
Primary Citation Related Structures:
7QD7, 7QH9, 7QNT, 8P1X, 8P20

PubMed Abstract:
Staphylococcus epidermidis expresses glycerol phosphate wall teichoic acid (WTA), but some health care-associated methicillin-resistant S. epidermidis (HA-MRSE) clones produce a second, ribitol phosphate (RboP) WTA, resembling that of the aggressive pathogen Staphylococcus aureus . RboP-WTA promotes HA-MRSE persistence and virulence in bloodstream infections. We report here that the TarM enzyme of HA-MRSE [TarM(Se)] glycosylates RboP-WTA with glucose, instead of N -acetylglucosamine (GlcNAc) by TarM(Sa) in S. aureus . Replacement of GlcNAc with glucose in RboP-WTA impairs HA-MRSE detection by human immunoglobulin G, which may contribute to the immune-evasion capacities of many invasive S. epidermidis . Crystal structures of complexes with uridine diphosphate glucose (UDP-glucose), and with UDP and glycosylated poly(RboP), reveal the binding mode and glycosylation mechanism of this enzyme and explain why TarM(Se) and TarM(Sa) link different sugars to poly(RboP). These structural data provide evidence that TarM(Se) is a processive WTA glycosyltransferase. Our study will support the targeted inhibition of TarM enzymes, and the development of RboP-WTA targeting vaccines and phage therapies.

Organizational Affiliation

Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.

Macromolecule Content

Total Structure Weight: 61.02 kDa
Atom Count: 4,218
Modeled Residue Count: 492
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TarM(Se)	A [auth AAA]	508	Staphylococcus epidermidis	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG (Subject of Investigation/LOI) Query on UPG Download:Ideal Coordinates CCD File SDF format, chain H [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain H [auth AAA]	H [auth AAA]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain H [auth AAA] Interactions & Density Focus chain H [auth AAA]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] MOL2 format, chain J [auth AAA] mmCIF format, chain J [auth AAA]	J [auth AAA]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth AAA] Interactions & Density Focus chain J [auth AAA]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain K [auth AAA] MOL2 format, chain K [auth AAA] mmCIF format, chain K [auth AAA]	K [auth AAA]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth AAA] Interactions & Density Focus chain K [auth AAA]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA], F [auth AAA], G [auth AAA]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain I [auth AAA]	I [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth AAA] Interactions & Density Focus chain I [auth AAA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] SDF format, chain B [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA], C [auth AAA], D [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA] Focus chain D [auth AAA]