5EKP

Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB (WT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Structures With Same Primary Citation

  • 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. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: sll0501
EC: 2.4
Membrane protein
Mpstruc
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
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download CCD File 
A, B, C, D
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.331α = 90
b = 137.518β = 98.5
c = 101.448γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-06
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references