Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 158.69 kDa 
• Atom Count: 9240 
• Residue Count: 1190 
• Unique protein chains: 1

5EKE

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

• DOI: 10.2210/pdb5EKE/pdb

• Classification: TRANSFERASE
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-11-03 Released: 2016-01-06 
• Deposition Author(s): Ardiccioni, C., Clarke, O.B., Tomasek, D., Banerjee, S., Rajashankar, K.R., Liu, Q., Shapiro, L., Mancia, F., New York Consortium on Membrane Protein Structure (NYCOMPS)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.277 
• R-Value Work: 0.249 
• R-Value Observed: 0.250 

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

• PubMed: 26729507 
• DOI: 10.1038/ncomms10175
• Primary Citation of Related Structures:  
  5EKP, 5EKE


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized glycosyltransferase sll0501	A, B, C, D	341	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 1  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)) Explore Q55487  Go to UniProtKB:  Q55487

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	A, B, C, D	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.277 
• R-Value Work: 0.249 
• R-Value Observed: 0.250 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.135	α = 90
b = 142.243	β = 97.16
c = 102.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-03 
• Released Date: 2016-01-06 
Deposition Author(s): Ardiccioni, C., Clarke, O.B., Tomasek, D., Banerjee, S., Rajashankar, K.R., Liu, Q., Shapiro, L., Mancia, F., New York Consortium on Membrane Protein Structure (NYCOMPS)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111980
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM095315

Revision History 

• Version 1.0: 2016-01-06
  Type: Initial release
  
• Version 1.1: 2016-02-03
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence