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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 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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:  

  • 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: 
    • 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
    • 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
    • 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


    Organizational Affiliation

    Department of Biomedical Sciences, Florida Atlantic University, Boca Raton, FL 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 5 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
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
UDP
Query on UDP

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

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.220α = 90.00
b = 94.480β = 99.00
c = 94.447γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-28
    Type: Database references, Source and taxonomy