Glycosyltransferases (GTs) constitute an ubiquitous group of enzymes
that catalyse the synthesis of glycosidic linkages by the transfer
of a sugar residue from a donor to an acceptor. Acceptor substrates
are carbohydrates, proteins, lipids, DNA and numerous small molecules
such as antibiotics, flavonol, steroids... The majority of GTs utilize
nucleotide-sugards as donors, although lipid phosphate sugars and phosphate
sugars may be used. The transfer of saccharides by GTs is regiospecific
and stereospecific with two possible stereochemical outcomes resulting
in either inversion or retention of the anomeric configuration
of the transferred sugar. A classification system has been adopted
that groups GTs into families based on amino-acid sequence similarities
(CAZY database: http://www.cazy.org).
At the present time, more than 100 GTs crystal structures are available,
that have been grouped in 38 families.
A limited number of three-dimensional architectures, noted GT-A and GT-B,
have been observed for nucleotide-sugar dependent GTs.
As for the GTs that utilize lipid-phosphate donor substrates different folds have been observed.
Data Query
Upon reaching the search page, two buttons to query the data base appear
on the left hand panel: Simple search and Advanced Search.
Simple Search
The classification of the GTs proteins is made based on their origin:
animal
archea
bacteria
plant
virus
yeast & fungi
Upon selecting one family, a right click opens a new menu that prompts
the user to choose among a sub-classification based either on the function,
or the fold, i.e. GT-A, GT-B and GT-Alike. A further right click opens
a menu where the GTs are numbered according to the CAZY classification;
that allows the user to select the requested protein and being brought
to the “GT information” page.
Advanced Search
Under the name “Select Criteria”, a search box offers to select among the following items:
organism
family
PDB
authors
fold resulting linkage
enzyme nameAbbreviation.
A search box is provided in which appears a drop-down button enlisting all the entries
corresponding to the selected item. The result is prompt to guide the user in selecting
the “hits” found in the data base, by a simple search engine. More complex search can be
made by combining criteria which can be combined from up to four search boxes.
A preview of the results is displayed in an accordion fashion, whereby the classification,
the protein name, the GT type, and the structure fof the resulting carbohydrate are given.
The amount of information provided allows the user to make an informed choice prior going to “GT Information”.
Results
The detailed results are available under two tabs: “Lectin Information” and “Display and Download”.
GT information
Under the button: “GT Information” are given: origin, organism, CAZY family,
fold, enzyme name, abbreviation, PDB code, resolution and reference.
Links to PDB and Medline are also provided.
Display and Download
On this page, is represented one or more graphical representation of the glycosyltranferase,
that have been constructed from the reported atomic coordinates with
the help of PyMol software (www.pymol.org).
The three-dimensional structure can be displayed under Jmol applet windows
that enable basic viewing and measurements options.
The atomic coordinates at the PDB can be downloaded for further use.