1VZX

Roles of active site tryptophans in substrate binding and catalysis by ALPHA-1,3 GALACTOSYLTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report



Literature

Roles of active site tryptophans in substrate binding and catalysis by alpha-1,3 galactosyltransferase.

Zhang, Y.Deshpande, A.Xie, Z.Natesh, R.Acharya, K.R.Brew, K.

(2004) Glycobiology 14: 1295-1302

  • DOI: 10.1093/glycob/cwh119
  • Primary Citation of Related Structures:  
    1VZX, 1VZU

  • PubMed Abstract: 
  • Aromatic amino acids are frequent components of the carbohydrate binding sites of lectins and enzymes. Previous structural studies have shown that in alpha-1,3 galactosyltransferase, the binding site for disaccharide acceptor substrates is encircled ...

    Aromatic amino acids are frequent components of the carbohydrate binding sites of lectins and enzymes. Previous structural studies have shown that in alpha-1,3 galactosyltransferase, the binding site for disaccharide acceptor substrates is encircled by four tryptophans, residues 249, 250, 314, and 356. To investigate their roles in enzyme specificity and catalysis, we expressed and characterized variants of the catalytic domain of alpha-1,3 galactosyltransferase with substitutions for each tryptophan. Substitution of glycine for tryptophan 249, whose indole ring interacts with the nonpolar B face of glucose or GlcNAc, greatly increases the K(m) for the acceptor substrate. In contrast, the substitution of tyrosine for tryptophan 314, which interacts with the beta-galactosyl moiety of the acceptor and UDP-galactose, decreases k(cat) for the galactosyltransferase reaction but does not affect the low UDP-galactose hydrolase activity. Thus, this highly conserved residue stabilizes the transition state for the galactose transfer to disaccharide but not to water. High-resolution crystallographic structures of the Trp(249)Gly mutant and the Trp(314)Tyr mutant indicate that the mutations do not affect the overall structure of the enzyme or its interactions with ligands. Substitutions for tryptophan 250 have only small effects on catalytic activity, but mutation of tryptophan 356 to threonine reduces catalytic activity for both transferase and hydrolase activities and reduces affinity for the acceptor substrate. This residue is adjacent to the flexible C-terminus that becomes ordered on binding UDP to assemble the acceptor binding site and influence catalysis. The results highlight the diverse roles of these tryptophans in enzyme action and the importance of k(cat) changes in modulating glycosyltransferase specificity.


    Related Citations: 
    • 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
    • Bovine Alpha1,3-Galactosyltransferase Catalytic Domain Structure and its Relationship with Abo Hhisto-Blood Group and Glycophingolipid Glycosyltransferases
      Gastinal, 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, FL 33341, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASEAB289Bos taurusMutation(s): 1 
Gene Names: GGTA1
EC: 2.4.1.151 (PDB Primary Data), 2.4.1.87 (UniProt)
Find proteins for P14769 (Bos taurus)
Explore P14769 
Go to UniProtKB:  P14769
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

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

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.22α = 90
b = 94.48β = 99
c = 94.447γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary