Transdab
TranSDAB is a transglutaminase substrate database containing 506 entries, the substrates for several transglutaminase types such as FXIIIa, TG1, TG2, TG3, TG5 and TGM.
Our aim was to generate a structural database of translgutaminase substrate proteins which provides information about the microenvironment of reactive and non-reactive glutamine and lysine residues. There is an entry for each substrate protein which includes the substrate protein's name, the determination type (in vitro/in situ), the source organism from where it was studied and its intracellular/extracellular localization.
Also there are specified the reactive residues and for literature reference there is a PubMed identification code given with a hyperlink to the relevant PubMed Abstract. The Expasy/TrEMBL entry is also accessible and there is a small part of the sequence given, with reactive residues in bold, to ease the database searches.
The structure is represented by several hyperlinks; access to the molecule's crystal structure in the RCSB Protein Data Bank through its PDB ID, hyperlinks to a table which gives the amino acids surrounding the glutamine and lysine residues in a 10.0 A radius sphere around them and also to the molecule's structure drawn with VMD using data from PDB files. The images are attached as Power Point Presentations and .avi files also and it may take several seconds to start rotating the molecule. For colour codes, please click here.
The distance measurement and the estimation of solvent exposed residues was done with Protein Explorer.
Transglutaminase review articles
Lorand,L. and Graham,R.M. (2003) Nat Rev Mol Cell Biol. 4, 140-56 PMID:12563291 Fesus,L. and Piacentini,M. (2002) Trends. Biochem. Sci. 27, 534-539 PMID:12368090 Griffin,M., Casadio,R. and Bergamini,C. (2002) Biochem. J. 368, 377-396 PMID:12366374
Transglutaminase sites of interests:
TRANSIT W.H.A.T.
Acknowledgements
We thank to Gyorgy Fenyofalvi, Gabor Zachuczky, Istvan Andrejkovics and Peter Bagossi for their help. This work was supported by grant from the ESF Protein Cross-Linking - The ESF Transglutaminases Programme (PCL)
