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SRPDB

http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html

Alm Rosenblad, M.1, Gorodkin, J.2, Knudsen, B.3, Zwieb, C.4, Samuelsson, T.1

1Department of Medical Biochemistry, University of Gšteborg, Box 440, SE-405 30 Gšteborg, Sweden
2Division of Genetics, The Royal Veterinary and Agricultural University, Institute of Animal Science and Animal Health, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark
3Bioinformatics Research Center, University of Aarhus, H¿egh Guldbergsgade 10, DK-8000 Aarhus C, Denmark
4Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, U.S.A.

Contact   zwieb@uthct.edu


Database Description

Signal recognition particle (SRP) is an ribonucleoprotein particle designed to recognize secretory signal sequences as they emerge from the ribosome. SRP associates with the SRP-receptor in the ER membrane, is released from the ribosome, and recycled (for review, see [1]). To help in understanding the molecular details of this essential cellular function, the SRP database (SRPDB) provides sequences of SRP RNA, SRP proteins, and the SRP receptor ordered alphabetically and phylogenetically with links to the primary sources, as well as a manually-checked alignments. The SRP RNA alignment serves to derive phylogenetically-supported secondary structures and to evaluate potential tertiary interactions. The SRPDB is maintained at the University of Texas Health Science Center at Tyler, Texas, accessible on the World Wide Web at the URL http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and at the European mirror at the University of Göteborg, Sweden (http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html). SRPDB is updated regularly at least once a year.

Recent Developments

The SRPDB is in the process of being updated to include a total of 181 SRP RNA sequences, 7 protein SRP9, 11 SRP14, 31 SRP19, 113 SRP54 (Ffh), 9 SRP68, and 12 SRP72 sequences. There are 44 new sequences of the SRP receptor alpha subunit and its FtsY homolog (a total of 99 entries). A web interface where a nucleotide sequence can be submitted to predict SRP RNA genes has been added.

Acknowledgements

We thank Florian Mueller for ERNA-3D, and Ingolf Sommer for VCMD software. J.G. was supported by the Danish Technical Research Council and the Ministry of Food, Agriculture and Fisheries. This work was supported by NIH grant GM-49034 to C.Z.

REFERENCES

Keenan, R.J., Freymann, D.M., Stroud, R.M. and Walter, P. (2001). The Signal Recognition Particle. Annu. Rev. Biochem., 70, 755-775.

Category   RNA Sequences

Go to the abstract in the NAR 2003 Database Issue.

 

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