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RNRdb


NAR Molecular Biology Database Collection entry number 901
Lundin D., Torrents E., Furrer E., Larsson Birgander P., Sahlin M., Poole A.M. and Sjöberg B.-M.
Department of Molecular Biology & Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden

Database Description

RNRdb - the Ribonucleotide Reductase Database - is a tool developed for ribonucleotide reductase (RNR) research. RNR is an enzyme that uses radical chemistry to reduce ribonucleotides to deoxyribonucleotides. Since this is the only pathway for the de novo synthesis of DNA building blocks, the activity of RNR is essential in all dividing cells, and RNR genes are found in virtually every organism including numerous viruses. RNRs are classified into three main groups (class I, class II and class III) according to reaction mechanism, cofactor requirements (tyrosyl radical, dexoyadenosylcobalamin, or S-adenosylmethionine/glycyl radical) and quaternary structure (Α, Α2 or Α2Β2). In addition substrate specificity (ribonucleoside diphosphates or ribonucleoside triphosphates) and amino acid sequences differ between the classes. Despite these extensive differences the common three-dimensional structure of the Α-components of all three classes clearly points to a common evolutionary origin for all RNRs. RNRdb contains curated RNR sequence data including genomic and species data, a compilation of all published 3D structures of different RNR proteins, and a compilation of all mutant proteins constructed including links to the relevant publication(s). Users can easily retrieve RNR protein sequences that have been either experimentally characterised or predicted from genome sequence data for any given organism, or search the database for occurrence of RNR classes in taxonomic groups. A BLAST server allows sequences to be BLASTed against all sequences in RNRdb and results can be retreived in FASTA format. The current version of RNRdb also includes a brief introduction to RNRs, a glossary and links to recent review articles.

Recent Developments

Upcoming extensions of the RNRdb will include operon structure and nucleotide sequences.

Acknowledgements

Work on the RNRdb was supported by grants from the Swedish Research Council to AP and BMS.

References

1. Lundin, D., Torrents, E., Furrer, E., Larsson Birgander, P., Sahlin, M., Poole, A.M. and Sjöberg, B.-M. (2005) RNRdb: The ribonucleotide reductase database. Dept. of Molecular Biology & Functional Genetics, Stockholm University, Stockholm, Sweden. version 1.0 http://rnrdb.molbio.su.se


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