3V0N

Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-GalNAc derived inhibitor (3GW and 4GW)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Base-modified donor analogues reveal novel dynamic features of a glycosyltransferase.

Jrgensen, R.Pesnot, T.Lee, H.J.Palcic, M.M.Wagner, G.K.

(2013) J.Biol.Chem. 288: 26201-26208

  • DOI: 10.1074/jbc.M113.465963
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosyltransferases (GTs) are enzymes that are involved, as Nature's "glycosylation reagents," in many fundamental biological processes including cell adhesion and blood group biosynthesis. Although of similar importance to that of other large enzym ...

    Glycosyltransferases (GTs) are enzymes that are involved, as Nature's "glycosylation reagents," in many fundamental biological processes including cell adhesion and blood group biosynthesis. Although of similar importance to that of other large enzyme families such as protein kinases and proteases, the undisputed potential of GTs for chemical biology and drug discovery has remained largely unrealized to date. This is due, at least in part, to a relative lack of GT inhibitors and tool compounds for structural, mechanistic, and cellular studies. In this study, we have used a novel class of GT donor analogues to obtain new structural and enzymological information for a representative blood group GT. These analogues interfere with the folding of an internal loop and the C terminus, which are essential for catalysis. Our experiments have led to the discovery of an entirely new active site folding mode for this enzyme family, which can be targeted in inhibitor development, similar to the DFG motif in protein kinases. Taken together, our results provide new insights into substrate binding, dynamics, and utilization in this important enzyme family, which can very likely be harnessed for the rational development of new GT inhibitors and probes.


    Organizational Affiliation

    Department of Microbiology and Infection Control, Statens Serum Institut, DK-2300 Copenhagen S, Denmark. renj@ssi.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histo-blood group ABO system transferase
A, B
298Homo sapiensMutation(s): 2 
Gene Names: ABO
Find proteins for P16442 (Homo sapiens)
Go to Gene View: ABO
Go to UniProtKB:  P16442
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
3GW
Query on 3GW

Download SDF File 
Download CCD File 
B
5-(5-formylthiophen-2-yl)uridine-5'(2-(acetylamino)-2-deoxy-alpha-D-galactosyl)-diphosphate
C22 H29 N3 O18 P2 S
PRYRELLFERSIJT-DVUHHYPWSA-N
 Ligand Interaction
4GW
Query on 4GW

Download SDF File 
Download CCD File 
A, B
5-(5-formylthiophen-2-yl)uridine 5'-(trihydrogen diphosphate)
C14 H16 N2 O13 P2 S
JAVHWQPALRUGBE-UORFTKCHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.200α = 90.00
b = 153.830β = 90.00
c = 52.400γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
MAR345data collection
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Structure summary
  • Version 1.2: 2015-02-18
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Data collection, Refinement description