ORENZA: a web resource for studying ORphan ENZyme activities

Olivier Lespinet,Bernard Labedan

doi:10.1186/1471-2105-7-436

Abstract

BackgroundDespite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) are not associated with any amino acid sequence in major public databases. This wide gap separating knowledge of biochemical function and sequence information is found for nearly all classes of enzymes. Thus, there is an urgent need to explore these sequence-less EC numbers, in order to progressively close this gap.DescriptionWe designed ORENZA, a PostgreSQL database of ORphan ENZyme Activities, to collate information about the EC numbers defined by the NC-IUBMB with specific emphasis on orphan enzyme activities. Complete lists of all EC numbers and of orphan EC numbers are available and will be periodically updated. ORENZA allows one to browse the complete list of EC numbers or the subset associated with orphan enzymes or to query a specific EC number, an enzyme name or a species name for those interested in particular organisms. It is possible to search ORENZA for the different biochemical properties of the defined enzymes, the metabolic pathways in which they participate, the taxonomic data of the organisms whose genomes encode them, and many other features. The association of an enzyme activity with an amino acid sequence is clearly underlined, making it easy to identify at once the orphan enzyme activities. Interactive publishing of suggestions by the community would provide expert evidence for re-annotation of orphan EC numbers in public databases.ConclusionORENZA is a Web resource designed to progressively bridge the unwanted gap between function (enzyme activities) and sequence (dataset present in public databases). ORENZA should increase interactions between communities of biochemists and of genomicists. This is expected to reduce the number of orphan enzyme activities by allocating gene sequences to the relevant enzymes.

Highlights

Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) are not associated with any amino acid sequence in major public databases
Description: We designed ORENZA, a PostgreSQL database of ORphan ENZyme Activities, to collate information about the EC numbers defined by the NC-IUBMB with specific emphasis on orphan enzyme activities
ORENZA allows one to browse the complete list of EC numbers or the subset associated with orphan enzymes or to query a specific EC number, an enzyme name or a species name for those interested in particular organisms

Summary

Conclusion

We consider ORENZA to be a useful resource for all categories of biologists. Let us take for instance the data summarized in Table 2 and more precisely the observation that human cells harbour six enzyme activities that are not found elsewhere and that are not associated with any amino acid sequence (Table 3). Any biologist would attempt to better understand the origin of such metabolic specificities. Any progress in this field could have positive consequences in terms of medical advances (see Table 3). The expert for either a specific enzyme or a physiological aspect related with these orphan enzyme activities would feel personally concerned and we hope that he/she will promptly answer such a challenge. ORENZA resource is freely available via the Internet at http://www.orenza.u-psud.fr. OL wrote the different programs necessary to collect all data from public sources and to build the relational database and the web server. Both authors participated in the data analysis and wrote the paper

Background

Discussion

Findings

Karp PD