4X7R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 2.2 of the entry. See complete history

Literature

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.USA 112: E576-E585

  • DOI: 10.1073/pnas.1418084112
  • Primary Citation of Related Structures:  

  • 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 ...

    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;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TarM
A, B
493Staphylococcus aureus (strain COL)Mutation(s): 1 
Gene Names: tarM
EC: 2.4.1.70
Find proteins for A0A0H2WWV6 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  A0A0H2WWV6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3YW
Query on 3YW

Download SDF File 
Download CCD File 
A, B
(2S)-2,3-dihydroxypropyl 2-(acetylamino)-2-deoxy-alpha-D-glucopyranoside
C11 H21 N O8
BURZSZGRQNCGQJ-KEWAQLPFSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, B
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
NTO
Query on NTO

Download SDF File 
Download CCD File 
A, B
TRISULFOAMINO HEPARIN PENTASACCHARIDE
Fondaparinux
C31 H53 N3 O49 S8
KANJSNBRCNMZMV-ABRZTLGGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.470α = 65.89
b = 92.140β = 83.66
c = 96.110γ = 84.12
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XSCALEdata scaling
xia2data scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanada--
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 2.0: 2017-07-12
    Type: Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2017-09-13
    Type: Author supporting evidence
  • Version 2.2: 2017-11-22
    Type: Refinement description