Difference between revisions of "Transdab"
(New page: '''TranSDAB''' is a transglutaminase substrate database containing {{NUMBEROFARTICLES}} entries, the substrates for several transglutaminase types such as FXIIIa, [[:C...) |
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| − | ''' | + | '''TRANSDAB''' is a transglutaminase substrate database containing {{NUMBEROFARTICLES}} entries, the substrates for several transglutaminase types such as [[:Category:FXIIIa|FXIIIa]], [[:Category:Keratinocyte transglutaminase|TG1]], [[:Category:Tissue transglutaminase|TG2]], [[:Category:Epidermal transglutaminase|TG3]], [[:Category:TG5|TG5]] and [[:Category:Microbial transglutaminase|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 | + | 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 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 | + | Also there are specified the reactive residues and for literature reference there is a PubMed identification code given with a link 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 italic, to ease the database searches. |
| − | The | + | The structural information are represented by a picture gallery of reactive glutamine and lysine residues and video image of the rotating molecule, all drawn with [http://www.ks.uiuc.edu/Research/vmd/ VMD] using the structural information from crystal structure files deposited in protein databank [http://www.rcsb.org/pdb/home/home.do RCSB PDB]. For color codes, please click [[Color codes|here]]. |
| + | The crystal structure is also accessible via link to the RCSB PDB through the PDBID. The surface accessibility data obtained with [http://www.netasa.org/asaview/ ASAView] web server for those substrate proteins where the modification site is known and the crystal structure contains these residues is available in .pdf and text format. | ||
| + | For intrinsic disorder prediction there is a link to one of most widely used predictor [http://iupred.enzim.hu/ IUPred]. | ||
| − | + | Beside the substrates of the transglutaminase activity, TRANSDAB contains the substrates of the [http://genomics.dote.hu/wiki/index.php/Category:Kinase kinase] and [http://genomics.dote.hu/wiki/index.php/Category:Deamidase deamidase] activities as well. | |
==Transglutaminase review articles== | ==Transglutaminase review articles== | ||
| − | Lorand,L. and Graham,R.M. (2003) Nat Rev Mol Cell Biol. 4, 140-56 | + | [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12563291 Lorand,L. and Graham,R.M. (2003) Nat Rev Mol Cell Biol. 4, 140-56]<br> |
| − | Fesus,L. and Piacentini,M. (2002) Trends. Biochem. Sci. 27, 534-539 | + | [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12368090 Fesus,L. and Piacentini,M. (2002) Trends. Biochem. Sci. 27, 534-539]<br> |
| − | Griffin,M., Casadio,R. and Bergamini,C. (2002) Biochem. J. 368, 377-396 | + | [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12366374 Griffin,M., Casadio,R. and Bergamini,C. (2002) Biochem. J. 368, 377-396] |
==Transglutaminase sites of interests:== | ==Transglutaminase sites of interests:== | ||
| − | TRANSIT | + | [http://bioinformatica.isa.cnr.it/TRANSIT TRANSIT]<br> |
| − | W.H.A.T. | + | [http://crisceb.unina2.it/what/ W.H.A.T.] |
==Acknowledgements== | ==Acknowledgements== | ||
| − | We thank to Gyorgy Fenyofalvi, Gabor Zachuczky | + | We thank to [http://scienceroll.com/about/ Meskó, Bertalan], Istvan Andrejkovics, Gyorgy Fenyofalvi, Gabor Zachuczky and Peter Bagossi for their help. This work was supported by grant from the [http://www.esf.org/esf_article.php?language=0&article=94&domain=3&activity=1 ESF Protein Cross-Linking - The ESF Transglutaminases Programme (PCL)] |
Latest revision as of 08:16, 22 April 2008
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 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 link 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 italic, to ease the database searches.
The structural information are represented by a picture gallery of reactive glutamine and lysine residues and video image of the rotating molecule, all drawn with VMD using the structural information from crystal structure files deposited in protein databank RCSB PDB. For color codes, please click here. The crystal structure is also accessible via link to the RCSB PDB through the PDBID. The surface accessibility data obtained with ASAView web server for those substrate proteins where the modification site is known and the crystal structure contains these residues is available in .pdf and text format. For intrinsic disorder prediction there is a link to one of most widely used predictor IUPred.
Beside the substrates of the transglutaminase activity, TRANSDAB contains the substrates of the kinase and deamidase activities as well.
Transglutaminase review articles
Lorand,L. and Graham,R.M. (2003) Nat Rev Mol Cell Biol. 4, 140-56
Fesus,L. and Piacentini,M. (2002) Trends. Biochem. Sci. 27, 534-539
Griffin,M., Casadio,R. and Bergamini,C. (2002) Biochem. J. 368, 377-396
Transglutaminase sites of interests:
Acknowledgements
We thank to Meskó, Bertalan, Istvan Andrejkovics, Gyorgy Fenyofalvi, Gabor Zachuczky and Peter Bagossi for their help. This work was supported by grant from the ESF Protein Cross-Linking - The ESF Transglutaminases Programme (PCL)
