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 

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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
  • Primary Citation of Related Structures:  
    5EKE, 5EKP

  • 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 synthase (DPMS), which generates the mannose donor for glycosylation in the endoplasmic reticulum ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized glycosyltransferase sll0501B [auth A], C [auth B], A [auth C], D341Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: sll0501
EC: 2.4
Membrane Entity: Yes 
UniProt
Find proteins for Q55487 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q55487 
Go to UniProtKB:  Q55487
Protein Feature View
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  • Reference Sequence
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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