8P20 | pdb_00008p20

TarM(Se)_G117R-UDP-4RboP-glucose

PDB DOI: https://doi.org/10.2210/pdb8P20/pdb

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

Deposited: 2023-05-14 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: 2.85 Å
R-Value Free:
0.266 (Depositor), 0.264 (DCC)
R-Value Work:
0.228 (Depositor), 0.229 (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: 245.68 kDa
Atom Count: 15,161
Modeled Residue Count: 1,967
Deposited Residue Count: 2,032
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TarM(Se)_G117R	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	508	Staphylococcus epidermidis	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BJT (Subject of Investigation/LOI) Query on BJT Download:Ideal Coordinates CCD File SDF format, chain Y [auth DDD] SDF format, chain Q [auth CCC] SDF format, chain K [auth BBB] SDF format, chain E [auth AAA] MOL2 format, chain Y [auth DDD] MOL2 format, chain Q [auth CCC] MOL2 format, chain K [auth BBB] MOL2 format, chain E [auth AAA] mmCIF format, chain Y [auth DDD] mmCIF format, chain Q [auth CCC] mmCIF format, chain K [auth BBB] mmCIF format, chain E [auth AAA]	E [auth AAA], K [auth BBB], Q [auth CCC], Y [auth DDD]	[(2~{R},3~{S},4~{S})-2-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentoxy]phosphoryl]oxy-pentoxy]phosphoryl]oxy-pentyl] [(2~{S},3~{R},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl] hydrogen phosphate C₂₆ H₅₆ O₃₄ P₄ DYIPZANUDJDCKR-AXBQPTFUSA-N		Interactions Focus chain E [auth AAA] Focus chain K [auth BBB] Focus chain Q [auth CCC] Focus chain Y [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain K [auth BBB] Focus chain Q [auth CCC] Focus chain Y [auth DDD]
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain X [auth CCC] SDF format, chain P [auth BBB] SDF format, chain J [auth AAA] SDF format, chain DA [auth DDD] MOL2 format, chain X [auth CCC] MOL2 format, chain P [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain DA [auth DDD] mmCIF format, chain X [auth CCC] mmCIF format, chain P [auth BBB] mmCIF format, chain J [auth AAA] mmCIF format, chain DA [auth DDD]	DA [auth DDD], J [auth AAA], P [auth BBB], X [auth CCC]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain DA [auth DDD] Focus chain J [auth AAA] Focus chain P [auth BBB] Focus chain X [auth CCC] Interactions & Density Focus chain DA [auth DDD] Focus chain J [auth AAA] Focus chain P [auth BBB] Focus chain X [auth CCC]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth BBB] SDF format, chain N [auth BBB] MOL2 format, chain O [auth BBB] MOL2 format, chain N [auth BBB] mmCIF format, chain O [auth BBB] mmCIF format, chain N [auth BBB]	N [auth BBB], O [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth BBB] Focus chain O [auth BBB] Interactions & Density Focus chain N [auth BBB] Focus chain O [auth BBB]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain AA [auth DDD] SDF format, chain BA [auth DDD] SDF format, chain CA [auth DDD] SDF format, chain G [auth AAA] SDF format, chain I [auth AAA] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain S [auth CCC] SDF format, chain T [auth CCC] SDF format, chain U [auth CCC] SDF format, chain V [auth CCC] SDF format, chain W [auth CCC] SDF format, chain H [auth AAA] MOL2 format, chain AA [auth DDD] MOL2 format, chain BA [auth DDD] MOL2 format, chain CA [auth DDD] MOL2 format, chain G [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain S [auth CCC] MOL2 format, chain T [auth CCC] MOL2 format, chain U [auth CCC] MOL2 format, chain V [auth CCC] MOL2 format, chain W [auth CCC] MOL2 format, chain H [auth AAA] mmCIF format, chain AA [auth DDD] mmCIF format, chain BA [auth DDD] mmCIF format, chain CA [auth DDD] mmCIF format, chain G [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB] mmCIF format, chain S [auth CCC] mmCIF format, chain T [auth CCC] mmCIF format, chain U [auth CCC] mmCIF format, chain V [auth CCC] mmCIF format, chain W [auth CCC] mmCIF format, chain H [auth AAA]	AA [auth DDD] BA [auth DDD] CA [auth DDD] G [auth AAA] H [auth AAA] AA [auth DDD], BA [auth DDD], CA [auth DDD], G [auth AAA], H [auth AAA], I [auth AAA], L [auth BBB], M [auth BBB], S [auth CCC], T [auth CCC], U [auth CCC], V [auth CCC], W [auth CCC]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain AA [auth DDD] Focus chain BA [auth DDD] Focus chain CA [auth DDD] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain V [auth CCC] Focus chain W [auth CCC] Interactions & Density Focus chain AA [auth DDD] Focus chain BA [auth DDD] Focus chain CA [auth DDD] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Focus chain U [auth CCC] Focus chain V [auth CCC] Focus chain W [auth CCC]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth DDD] SDF format, chain R [auth CCC] SDF format, chain F [auth AAA] MOL2 format, chain Z [auth DDD] MOL2 format, chain R [auth CCC] MOL2 format, chain F [auth AAA] mmCIF format, chain Z [auth DDD] mmCIF format, chain R [auth CCC] mmCIF format, chain F [auth AAA]	F [auth AAA], R [auth CCC], Z [auth DDD]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth AAA] Focus chain R [auth CCC] Focus chain Z [auth DDD] Interactions & Density Focus chain F [auth AAA] Focus chain R [auth CCC] Focus chain Z [auth DDD]