5E9U

Crystal structure of GtfA/B complex bound to UDP and GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of a cytosolic O-glycosyltransferase essential for the synthesis of a bacterial adhesion protein.

Chen, Y.Seepersaud, R.Bensing, B.A.Sullam, P.M.Rapoport, T.A.

(2016) Proc.Natl.Acad.Sci.USA 113: E1190-E1199

  • DOI: 10.1073/pnas.1600494113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • O-glycosylation of Ser and Thr residues is an important process in all organisms, which is only poorly understood. Such modification is required for the export and function of adhesin proteins that mediate the attachment of pathogenic Gram-positive b ...

    O-glycosylation of Ser and Thr residues is an important process in all organisms, which is only poorly understood. Such modification is required for the export and function of adhesin proteins that mediate the attachment of pathogenic Gram-positive bacteria to host cells. Here, we have analyzed the mechanism by which the cytosolic O-glycosyltransferase GtfA/B of Streptococcus gordonii modifies the Ser/Thr-rich repeats of adhesin. The enzyme is a tetramer containing two molecules each of GtfA and GtfB. The two subunits have the same fold, but only GtfA contains an active site, whereas GtfB provides the primary binding site for adhesin. During a first phase of glycosylation, the conformation of GtfB is restrained by GtfA to bind substrate with unmodified Ser/Thr residues. In a slow second phase, GtfB recognizes residues that are already modified with N-acetylglucosamine, likely by converting into a relaxed conformation in which one interface with GtfA is broken. These results explain how the glycosyltransferase modifies a progressively changing substrate molecule.


    Organizational Affiliation

    Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115; Department of Cell Biology, Harvard Medical School, Boston, MA 02115;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycosyltransferase Gtf1
A, C, E, G
503Streptococcus gordoniiMutation(s): 0 
Gene Names: gtf1 (gtfA)
EC: 2.4.1.-
Find proteins for Q9AET5 (Streptococcus gordonii)
Go to UniProtKB:  Q9AET5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glycosyltransferase-stabilizing protein Gtf2
B, D, F, H
446Streptococcus gordoniiMutation(s): 0 
Gene Names: gtf2 (gtfB)
Find proteins for Q79T00 (Streptococcus gordonii)
Go to UniProtKB:  Q79T00
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, D, E, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

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

Download SDF File 
Download CCD File 
A, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.269 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 148.975α = 90.00
b = 196.005β = 90.00
c = 215.673γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM052586
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations