4KRV

Crystal structure of catalytic domain of bovine beta1,4-galactosyltransferase mutant M344H-GalT1 complex with 6-sulfo-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Investigations on beta 1,4-galactosyltransferase I using 6-sulfo-GlcNAc as an acceptor sugar substrate.

Ramakrishnan, B.Moncrief, A.J.Davis, T.A.Holland, L.A.Qasba, P.K.

(2013) Glycoconj J 30: 835-842

  • DOI: 10.1007/s10719-013-9488-4

  • PubMed Abstract: 
  • 6-sulfate modified N-acetylglucosamine (6-sulfo-GlcNAc) is often found as part of many biologically important carbohydrate epitopes such as 6-sulfo-Le(X). In these epitopes, the 6-sulfo-GlcNAc moiety is extended by a galactose sugar in a β1-4 linkage ...

    6-sulfate modified N-acetylglucosamine (6-sulfo-GlcNAc) is often found as part of many biologically important carbohydrate epitopes such as 6-sulfo-Le(X). In these epitopes, the 6-sulfo-GlcNAc moiety is extended by a galactose sugar in a β1-4 linkage. The β4GalT1 enzyme transfers galactose (Gal) from UDP-Gal to N-acetylglucosamine (GlcNAc) in the presence of manganese. Here we report that the β4GalT1 enzyme transfers Gal to the 6-sulfo-GlcNAc and 4-methylumbelliferyl-6-sulfo-N-acetyl-β-D-glucosaminide (6-sulfo-βGlcNAc-MU) acceptor substrates, although with very low efficiency. To understand the effect that the 6-sulfate group on the GlcNAc acceptor has on the catalytic activity of the β4GalT1 molecule, we have determined the crystal structure of the catalytic domain of bovine β4GalT1 mutant enzyme M344H-β4GalT1 complex with the 6-sulfo-GlcNAc molecule. In the crystal structure, the 6-sulfo-GlcNAc is bound to the protein in a way that is similar to the GlcNAc molecule. However, the 6-sulfate group engages in additional interactions with the hydrophobic region, residues 276-285, of the protein molecule, and this group is found wedged between the aromatic side chains of Phe-280 and Trp314 residues. Since the side chain of the Trp314 residue undergoes conformational changes during the catalytic cycle of the enzyme, molecular interaction between Trp314 and the 6-sulfate group might hinder this conformational change. Therefore, the lack of a favorable binding environment, together with hindrance to the conformational changes, might be responsible for the poor catalytic activity.


    Organizational Affiliation

    Structural Glycobiology Section, Basic Science Laboratory, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD, 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-1,4-galactosyltransferase 1
A, B
286Bos taurusMutation(s): 2 
Gene Names: B4GALT1 (GALT, GGTB2)
EC: 2.4.1.-
Find proteins for P08037 (Bos taurus)
Go to Gene View: B4GALT1
Go to UniProtKB:  P08037
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGS
Query on NGS

Download SDF File 
Download CCD File 
A, B
2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranose
N-ACETYL-D-GLUCOSAMINE-6-SULFATE
C8 H15 N O9 S
WJFVEEAIYIOATH-FMDGEEDCSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UDH
Query on UDH

Download SDF File 
Download CCD File 
A, B
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
C15 H27 N3 O12 P2
MLWJBKPFDKRHBM-FMKGYKFTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.282α = 90.00
b = 88.903β = 90.00
c = 139.734γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
REFMACphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references