5NRB

A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a-3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - alpha-3GalT in complex with Co2+, UDP-Gal and lactose - a3GalT-Co2+-UDP-Gal-LAT-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Snapshots of alpha-1,3-Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases.

Albesa-Jove, D.Sainz-Polo, M.A.Marina, A.Guerin, M.E.

(2017) Angew. Chem. Int. Ed. Engl. 56: 14853-14857

  • DOI: 10.1002/anie.201707922
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosyltransferases (GTs) are a key family of enzymes that catalyze the synthesis of glycosidic bonds in all living organisms. The reaction involves the transfer of a glycosyl moiety and can proceed with retention or inversion of the anomeric config ...

    Glycosyltransferases (GTs) are a key family of enzymes that catalyze the synthesis of glycosidic bonds in all living organisms. The reaction involves the transfer of a glycosyl moiety and can proceed with retention or inversion of the anomeric configuration. To date, the catalytic mechanism of retaining GTs is a topic of great controversy, particularly for those enzymes containing a putative nucleophilic residue in the active site, for which the occurrence of a double-displacement mechanism has been suggested. We report native ternary complexes of the retaining glycosyltransferase α-1,3-galactosyltransferase (α3GalT) from Bos taurus, which contains such a nucleophile in the active site, in a productive mode for catalysis in the presence of its sugar donor UDP-Gal, the acceptor substrate lactose, and the divalent cation cofactor. This new experimental evidence supports the occurrence of a front-side substrate-assisted SN i-type reaction for α3GalT, and suggests a conserved common catalytic mechanism among retaining GTs.


    Organizational Affiliation

    Structural Biology Unit-CIC bioGUNE, Technological Park of Bizkaia-Ed 800, 48160, Derio, Vizcaya, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetyllactosaminide alpha-1,3-galactosyltransferase
A, B
292Bos taurusMutation(s): 0 
Gene Names: GGTA1
EC: 2.4.1.87
Find proteins for P14769 (Bos taurus)
Go to UniProtKB:  P14769
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDU
Query on GDU

Download SDF File 
Download CCD File 
A, B
GALACTOSE-URIDINE-5'-DIPHOSPHATE
UDP-D-GALACTOPYRANOSE
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-ABVWGUQPSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
LAT
Query on LAT

Download SDF File 
Download CCD File 
A
BETA-LACTOSE
C12 H22 O11
GUBGYTABKSRVRQ-DCSYEGIMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.963α = 90.00
b = 65.646β = 102.92
c = 82.654γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references