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...) |
|||
| Line 1: | Line 1: | ||
'''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]]. | '''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 structure is represented by several | + | The structure is represented by several links; access to the molecule's crystal structure in the RCSB Protein Data Bank through its PDB ID, links 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. |
| − | |||
| − | |||
==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, 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) | + | We thank to Gyorgy Fenyofalvi, Gabor Zachuczky, Istvan Andrejkovics 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)] |
Revision as of 12:19, 24 July 2007
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 structure is represented by several links; access to the molecule's crystal structure in the RCSB Protein Data Bank through its PDB ID, links 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.
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 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)
