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Roles of Individual Residues of Alpha-1,3 Galactosyltransferases in Substrate Binding and Catalysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Roles of individual enzyme-substrate interactions by alpha-1,3-galactosyltransferase in catalysis and specificity.

Zhang, Y.Swaminathan, G.J.Deshpande, A.Boix, E.Natesh, R.Xie, Z.Acharya, K.R.Brew, K.

(2003) Biochemistry 42: 13512-13521

  • DOI: 10.1021/bi035430r
  • Primary Citation of Related Structures:  
  • Also Cited By: 1VZX, 1VZU

  • PubMed Abstract: 
  • The retaining glycosyltransferase, alpha-1,3-galactosyltransferase (alpha3GT), is mutationally inactivated in humans, leading to the presence of circulating antibodies against its product, the alpha-Gal epitope. alpha3GT catalyzes galactose transfer ...

    The retaining glycosyltransferase, alpha-1,3-galactosyltransferase (alpha3GT), is mutationally inactivated in humans, leading to the presence of circulating antibodies against its product, the alpha-Gal epitope. alpha3GT catalyzes galactose transfer from UDP-Gal to beta-linked galactosides, such as lactose, and in the absence of an acceptor substrate, to water at a lower rate. We have used site-directed mutagenesis to investigate the roles in catalysis and specificity of residues in alpha3GT that form H-bonds as well as other interactions with substrates. Mutation of the conserved Glu(317) to Gln weakens lactose binding and reduces the k(cat) for galactosyltransfer to lactose and water by 2400 and 120, respectively. The structure is not perturbed by this substitution, but the orientation of the bound lactose molecule is changed. The magnitude of these changes does not support a previous proposal that Glu(317) is the catalytic nucleophile in a double displacement mechanism and suggests it acts in acceptor substrate binding and in stabilizing a cationic transition state for cleavage of the bond between UDP and C1 of the galactose. Cleavage of this bond also linked to a conformational change in the C-terminal region of alpha3GT that is coupled with UDP binding. Mutagenesis indicates that His(280), which is projected to interact with the 2-OH of the galactose moiety of UDP-Gal, is a key residue in the stringent donor substrate specificity through its role in stabilizing the bound UDP-Gal in a suitable conformation for catalysis. Mutation of Gln(247), which forms multiple interactions with acceptor substrates, to Glu reduces the catalytic rate of galactose transfer to lactose but not to water. This mutation is predicted to perturb the orientation or environment of the bound acceptor substrate. The results highlight the importance of H-bonds between enzyme and substrates in this glycosyltransferase, in arranging substrates in appropriate conformations and orientation for efficient catalysis. These factors are manifested in increases in catalytic rate rather than substrate affinity.


    Related Citations: 
    • Bovine Alpha1,3-Galactosyltransferase Catalytic Domain Structure and its Relationship with Abo Histo-Blood Group and Glycophingolipid Glycosyltransferases
      Gastinel, L.N.,Bignon, C.,Misra, A.K.,Hindsgaul, O.,Shaper, J.H.,Joziasse, D.H.
      (2001) Embo J. 20: 638
    • Structure of Udp Complex of Udp-Galactose:Beta-Galactoside-Alpha-1,3-Galactosyltransferase at 1.53-A Resolution Reveals a Conformational Change in the Catalytically Important C Terminus
      Boix, E.,Swaminathan, G.J.,Zhang, Y.,Natesh, R.,Brew, K.,Acharya, K.R.
      (2001) J.Biol.Chem. 276: 48608


    Organizational Affiliation

    Department of Biomedical Sciences, Florida Atlantic University, Boca Raton, Florida 33341, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
A, B
289Bos taurusMutation(s): 1 
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
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

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

Download SDF File 
Download CCD File 
A, B
BETA-LACTOSE
C12 H22 O11
GUBGYTABKSRVRQ-DCSYEGIMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LATKd: 2690000 nM BINDINGMOAD
UDPKd: 32000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.202α = 90.00
b = 94.288β = 99.10
c = 94.675γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-06
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2018-02-28
    Type: Database references, Source and taxonomy, Structure summary