Crystal structure of S. aureus TarM G117R mutant in complex with Fondaparinux, alpha-GlcNAc-glycerol and UDP

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Structure and mechanism of Staphylococcus aureus TarM, the wall teichoic acid alpha-glycosyltransferase.

Sobhanifar, S.Worrall, L.J.Gruninger, R.J.Wasney, G.A.Blaukopf, M.Baumann, L.Lameignere, E.Solomonson, M.Brown, E.D.Withers, S.G.Strynadka, N.C.

(2015) Proc Natl Acad Sci U S A 112: E576-E585

  • DOI: https://doi.org/10.1073/pnas.1418084112
  • Primary Citation of Related Structures:  
    4X6L, 4X7M, 4X7P, 4X7R

  • PubMed Abstract: 

    Unique to Gram-positive bacteria, wall teichoic acids are anionic glycopolymers cross-stitched to a thick layer of peptidoglycan. The polyol phosphate subunits of these glycopolymers are decorated with GlcNAc sugars that are involved in phage binding, genetic exchange, host antibody response, resistance, and virulence. The search for the enzymes responsible for GlcNAcylation in Staphylococcus aureus has recently identified TarM and TarS with respective α- and β-(1-4) glycosyltransferase activities. The stereochemistry of the GlcNAc attachment is important in balancing biological processes, such that the interplay of TarM and TarS is likely important for bacterial pathogenicity and survival. Here we present the crystal structure of TarM in an unusual ternary-like complex consisting of a polymeric acceptor substrate analog, UDP from a hydrolyzed donor, and an α-glyceryl-GlcNAc product formed in situ. These structures support an internal nucleophilic substitution-like mechanism, lend new mechanistic insight into the glycosylation of glycopolymers, and reveal a trimerization domain with a likely role in acceptor substrate scaffolding.

  • Organizational Affiliation

    Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, BC, Canada V6T 1Z3;

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
493Staphylococcus aureus subsp. aureus 21178Mutation(s): 1 
Gene Names: SA21178_0837
Find proteins for A0A0H2WWV6 (Staphylococcus aureus (strain COL))
Explore A0A0H2WWV6 
Go to UniProtKB:  A0A0H2WWV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2WWV6
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside
C, D
Glycosylation Resources
GlyTouCan:  G25282IW
GlyCosmos:  G25282IW
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.47α = 65.89
b = 92.14β = 83.66
c = 96.11γ = 84.12
Software Package:
Software NamePurpose
xia2data scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 2.0: 2017-07-12
    Changes: Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 2.2: 2017-11-22
    Changes: Refinement description
  • Version 2.3: 2019-11-20
    Changes: Author supporting evidence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2024-02-28
    Changes: Data collection, Database references, Structure summary