5EKE

Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB (F215A mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.001 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis.

Ardiccioni, C.Clarke, O.B.Tomasek, D.Issa, H.A.von Alpen, D.C.Pond, H.L.Banerjee, S.Rajashankar, K.R.Liu, Q.Guan, Z.Li, C.Kloss, B.Bruni, R.Kloppmann, E.Rost, B.Manzini, M.C.Shapiro, L.Mancia, F.

(2016) Nat Commun 7: 10175-10175

  • DOI: 10.1038/ncomms10175
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The attachment of a sugar to a hydrophobic polyisoprenyl carrier is the first step for all extracellular glycosylation processes. The enzymes that perform these reactions, polyisoprenyl-glycosyltransferases (PI-GTs) include dolichol phosphate mannose ...

    The attachment of a sugar to a hydrophobic polyisoprenyl carrier is the first step for all extracellular glycosylation processes. The enzymes that perform these reactions, polyisoprenyl-glycosyltransferases (PI-GTs) include dolichol phosphate mannose synthase (DPMS), which generates the mannose donor for glycosylation in the endoplasmic reticulum. Here we report the 3.0 Å resolution crystal structure of GtrB, a glucose-specific PI-GT from Synechocystis, showing a tetramer in which each protomer contributes two helices to a membrane-spanning bundle. The active site is 15 Å from the membrane, raising the question of how water-soluble and membrane-embedded substrates are brought into apposition for catalysis. A conserved juxtamembrane domain harbours disease mutations, which compromised activity in GtrB in vitro and in human DPM1 tested in zebrafish. We hypothesize a role of this domain in shielding the polyisoprenyl-phosphate for transport to the active site. Our results reveal the basis of PI-GT function, and provide a potential molecular explanation for DPM1-related disease.


    Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized glycosyltransferase sll0501
A, B, C, D
341Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 1 
EC: 2.4.-.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Glycosyltransfereases
Protein: 
GtrB polyisoprenyl-glycosyltransferase (PI-GT)
Find proteins for Q55487 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  Q55487
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.001 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.135α = 90.00
b = 142.243β = 97.16
c = 102.010γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
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 StatesGM111980
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM095315

Revision History 

  • Version 1.0: 2016-01-06
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations