5NRD | pdb_00005nrd

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-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.249 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1002/anie.201707922
  • Primary Citation Related Structures: 
    5NR9, 5NRB, 5NRD, 5NRE

  • 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 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 S N 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.

Macromolecule Content 

  • Total Structure Weight: 70.42 kDa 
  • Atom Count: 4,873 
  • Modeled Residue Count: 561 
  • Deposited Residue Count: 584 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-acetyllactosaminide alpha-1,3-galactosyltransferase
A, B
292Bos taurusMutation(s): 0 
Gene Names: GGTA1
EC: 2.4.1.87
UniProt
Find proteins for P14769 (Bos taurus)
Explore P14769 
Go to UniProtKB:  P14769
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14769
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan: G84224TW
GlyCosmos: G84224TW
GlyGen: G84224TW

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.249 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.414α = 90
b = 65.694β = 102.89
c = 83.014γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary