4WAD

Crystal Structure of TarM with UDP-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 

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Literature

Structural and Enzymatic Analysis of TarM Glycosyltransferase from Staphylococcus aureus Reveals an Oligomeric Protein Specific for the Glycosylation of Wall Teichoic Acid.

Koc, C.Gerlach, D.Beck, S.Peschel, A.Xia, G.Stehle, T.

(2015) J Biol Chem 290: 9874-9885

  • DOI: 10.1074/jbc.M114.619924
  • Primary Citation of Related Structures:  
    4WAC, 4WAD

  • PubMed Abstract: 
  • Anionic glycopolymers known as wall teichoic acids (WTAs) functionalize the peptidoglycan layers of many Gram-positive bacteria. WTAs play central roles in many fundamental aspects of bacterial physiology, and they are important determinants of pathogenesis and antibiotic resistance ...

    Anionic glycopolymers known as wall teichoic acids (WTAs) functionalize the peptidoglycan layers of many Gram-positive bacteria. WTAs play central roles in many fundamental aspects of bacterial physiology, and they are important determinants of pathogenesis and antibiotic resistance. A number of enzymes that glycosylate WTA in Staphylococcus aureus have recently been identified. Among these is the glycosyltransferase TarM, a component of the WTA de novo biosynthesis pathway. TarM performs the synthesis of α-O-N-acetylglycosylated poly-5'-phosphoribitol in the WTA structure. We have solved the crystal structure of TarM at 2.4 Å resolution, and we have also determined a structure of the enzyme in complex with its substrate UDP-GlcNAc at 2.8 Å resolution. The protein assembles into a propeller-like homotrimer in which each blade contains a GT-B-type glycosyltransferase domain with a typical Rossmann fold. The enzymatic reaction retains the stereochemistry of the anomeric center of the transferred GlcNAc-moiety on the polyribitol backbone. TarM assembles into a trimer using a novel trimerization domain, here termed the HUB domain. Structure-guided mutagenesis experiments of TarM identify residues critical for enzyme activity, assign a putative role for the HUB in TarM function, and allow us to propose a likely reaction mechanism.


    Organizational Affiliation

    From the Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany, German Center for Infection Research (DZIF), Partner site Tübingen, 72076 Tübingen, Germany, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennesse 37232 thilo.stehle@uni-tuebingen.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl transferase, group 1 family proteinA498Staphylococcus aureusMutation(s): 0 
Gene Names: 
EC: 2.4.1.5 (PDB Primary Data), 2.4.1.52 (PDB Primary Data)
UniProt
Find proteins for A0A0D6HUA0 (Staphylococcus aureus)
Explore A0A0D6HUA0 
Go to UniProtKB:  A0A0D6HUA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D6HUA0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UD1
Query on UD1

Download Ideal Coordinates CCD File 
B [auth A]URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.024α = 90
b = 124.024β = 90
c = 217.03γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 2.0: 2017-09-06
    Changes: Atomic model, Author supporting evidence, Derived calculations, Refinement description