4X7M

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

• PDB DOI:  https://doi.org/10.2210/pdb4X7M/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus 21178
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-12-09 Released: 2015-03-04 
• Deposition Author(s): Worrall, L.J., Sobhanifar, S., Strynadka, N.C.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Howard Hughes Medical Institute (HHMI)

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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 

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

• PubMed: 25624472 
• 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.

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Organizational Affiliation: 

Department of Biochemistry and Center for Blood Research, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 115.94 kDa 
• Atom Count: 8,181 
• Modelled Residue Count: 986 
• Deposited Residue Count: 986 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TarM	A, B	493	Staphylococcus aureus subsp. aureus 21178	Mutation(s): 1  Gene Names: SA21178_0837 EC: 2.4.1.70
UniProt
Find proteins for A0A0H2WWV6 (Staphylococcus aureus (strain COL)) Explore A0A0H2WWV6  Go to UniProtKB:  A0A0H2WWV6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD1	D [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N
UDP	C [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

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 = 44.072	α = 109.27
b = 90.944	β = 99.03
c = 94.441	γ = 101.53

Software Package:

Software Name	Purpose
xia2	data scaling
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Worrall, L.J., Sobhanifar, S., Strynadka, N.C.

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Funding Organization	Location	Grant 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