3EE5

Crystal structure of human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in complex with GLCNAC-Beta1,3-Gal-Beta-Naphthalenemethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report



Literature

Deoxygenated Disaccharide Analogs as Specific Inhibitors of {beta}1-4-Galactosyltransferase 1 and Selectin-mediated Tumor Metastasis

Brown, J.R.Yang, F.Sinha, A.Ramakrishnan, B.Tor, Y.Qasba, P.K.Esko, J.D.

(2009) J Biol Chem 284: 4952-4959

  • DOI: 10.1074/jbc.M805782200
  • Primary Citation of Related Structures:  
    3EE5

  • PubMed Abstract: 
  • The disaccharide peracetylated GlcNAcbeta1-3Galbeta-O-naphthalenemethanol (disaccharide 1) diminishes the formation of the glycan sialyl Lewis X (Neu5Acalpha2-3Galbeta1-4(Fucalpha1-3) GlcNAc; sLe(X)) in tumor cells. Previous studies showed that the mecha ...

    The disaccharide peracetylated GlcNAcbeta1-3Galbeta-O-naphthalenemethanol (disaccharide 1) diminishes the formation of the glycan sialyl Lewis X (Neu5Acalpha2-3Galbeta1-4(Fucalpha1-3) GlcNAc; sLe(X)) in tumor cells. Previous studies showed that the mechanism of action of disaccharide 1 involves three steps: (i) deacetylation by carboxyesterases, (ii) action as a biosynthetic intermediate for downstream enzymes involved in sLe(X) assembly, and (iii) generation of several glycans related to sLe(X). In this report, we show that GlcNAcbeta1-3Galbeta-O-naphthalenemethanol binds to the acceptor site of human beta1-4-galactosyltransferase much like the acceptor trisaccharide, GlcNAcbeta1-2Manbeta1-6Man, which is present on N-linked glycans. The 4'-deoxy analog, in which the acceptor hydroxyl group was replaced by -H, did not act as a substrate but instead acted as a competitive inhibitor of the enzyme. The acetylated form of this compound inhibited sLe(X) formation in U937 monocytic leukemia cells, suggesting that it had inhibitory activity in vivo as well. A series of synthetic acetylated analogs of 1 containing -H, -F, -N(3), -NH(2), or -OCH(3) instead of the hydroxyl groups at C-3'- and C-4'-positions of the terminal N-acetylglucosamine residue also blocked sLe(X) formation in cells. The reduction of sLe(X) by the 4'-deoxy analog also diminished experimental tumor metastasis by Lewis lung carcinoma in vivo. These data suggest that nonsubstrate disaccharides have therapeutic potential through their ability to bind to glycosyltransferases in vivo and to alter glycan-dependent pathologic processes.


    Organizational Affiliation

    Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California 92093, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-1,4-galactosyltransferase 1 ABC287Homo sapiensMutation(s): 3 
Gene Names: B4GALT1GGTB2
EC: 2.4.1.38 (PDB Primary Data), 2.4.1 (UniProt), 2.4.1.22 (UniProt), 2.4.1.90 (UniProt), 2.4.1.275 (UniProt)
Find proteins for P15291 (Homo sapiens)
Explore P15291 
Go to UniProtKB:  P15291
NIH Common Fund Data Resources
PHAROS:  P15291
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose
D, E, F
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDH
Query on UDH

Download Ideal Coordinates CCD File 
A, B, C
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
C15 H27 N3 O12 P2
MLWJBKPFDKRHBM-FMKGYKFTSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
C
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
2NA
Query on 2NA

Download Ideal Coordinates CCD File 
A, B, C
naphthalen-2-ylmethanol
C11 H10 O
MFGWMAAZYZSWMY-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download Ideal Coordinates CCD File 
C
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.127α = 90
b = 195.742β = 90
c = 143.801γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MERLOTphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary