7QH9

TarM(Se)_G117R-4RboP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.1 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

  • DOI: https://doi.org/10.1126/sciadv.adj2641
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TarM(Se)_G117R-4RboPA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
508Staphylococcus epidermidisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CWI (Subject of Investigation/LOI)
Query on CWI

Download Ideal Coordinates CCD File 
E [auth AAA],
G [auth BBB],
H [auth CCC],
K [auth DDD]
[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl] [(2~{S},3~{R},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl] hydrogen phosphate
C10 H25 O18 P3
WSKFFGXJZASWLI-UXAOAXNSSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth BBB],
L [auth DDD]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth CCC],
J [auth CCC],
M [auth DDD]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.243 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.87α = 89.971
b = 70.57β = 90.013
c = 137.38γ = 90.02
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyCRC-TR261

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Data collection, Database references