4X7M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 U S A 112: E576-E585

  • DOI: 10.1073/pnas.1418084112
  • Structures With Same Primary Citation

  • 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; ncjs@mail.ubc.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TarM
A, B
493Staphylococcus aureus subsp. aureus 21178Mutation(s): 1 
Gene Names: SA21178_0837
EC: 2.4.1.70
Find proteins for A0A0H2WWV6 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  A0A0H2WWV6
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UD1
Query on UD1

Download CCD File 
B
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N
 Ligand Interaction
UDP
Query on UDP

Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.072α = 109.27
b = 90.944β = 99.03
c = 94.441γ = 101.53
Software Package:
Software NamePurpose
xia2data scaling
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



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 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.2: 2017-11-22
    Changes: Refinement description, Structure summary
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence