UniProt release 12.2
Published September 11, 2007
Yeast PDR5: the first adopted protein in UniProtKB/Swiss-Prot
While progress in laboratory techniques allows the production of an ever-increasing flood of data, these data are still insufficiently exploited. One reason for this bottleneck is the lack of efficient integration into databases, making data more difficult, sometimes almost impossible, to access. The current information flow consists in two steps. First, scientists providing knowledge encode it in the format of a given journal. Then database curators have to decode and standardize it to make it computer-parsable and usable for the further research.
In order to reduce this time-consuming and error-prone process and to make the most of expert scientists, UniProtKB/Swiss-Prot proposes a new strategy called 'Adopt a Protein', where researchers can adopt one or more specific proteins. 'Foster parents' make sure that the information concerning their favourite protein(s) is up-to-date. UniProtKB/Swiss-Prot provides them with a draft with the correct sequence, up-to-date sequence analysis predictions and a description of the main topics that require annotation, such as protein names, bibliographic references, comments and protein features. The input of 'foster parents' is acknowledged in the entry.
The yeast Saccharomyces cerevisiae is a popular model organism used in hundreds of laboratories around the world and its genome has been fully sequenced and extensively studied over past a decade. Moreover, the yeast community has a long tradition of sharing information. Therefore, the yeast proteome has been chosen as a test platform to initiate the 'Adopt a Protein' scheme.
This release contains the first fully annotated adopted protein: PDR5. PDR5 is a 160-kDa yeast pleiotropic ABC efflux transporter of multiple drugs localized in the plasma membrane. It belongs to the ABC (ATP-binding cassette) transporter family, PDR subfamily. The PDR subfamily is specific to fungi and plants and exhibits distinctive structural features, such as extended extracellular loops and a degenerate ATP binding domain. Yeast strains lacking PDR5 are used for toxicity tests, whereas those overexpressing PDR5 are used for screening antifungal sensitizers.
PDR5 has been adopted by Professor André Goffeau from the Catholic University of Louvain (Belgium). We are grateful to him for committing precious time to help producing an annotation useful to the whole community. We hope that PDR5 is only the first member of a big adopted family! If you want to become a 'foster parent', please contact the UniProtKB/Swiss-Prot Fungal Proteome Annotation Program.
Changes concerning the section 'Web resources'
In the flat file, the 'Web resources' section is located in comment lines (CC). To be consistent with other comment lines, we have changed this topic from
CC -!- WEB RESOURCE: NAME=resource_name(; NOTE=free_text)?; URL="url".to
CC -!- WEB RESOURCE: Name=resource_name(; Note=free_text)?; URL="url";
Format change in the dbxref.txt and jourlist.txt document files
The dbxref.txt file lists the names and abbreviations and URLs of all databases cross-referenced in UniProtKB. The jourlist.txt file lists the titles and abbreviations of all journals cited in the UniProtKB/Swiss-Prot. We have added a new field, AC, to assign a stable identifier to each record in these files.
AC : DB-0022 Abbrev: EMBL Name : EMBL nucleotide sequence database Ref : Nucleic Acids Res. 35:D16-D20(2007); PubMed=17148479; DOI=10.1093/nar/gkl913; LinkTp: Explicit Server: http://www.ebi.ac.uk/embl/ Db_URL: www.ebi.ac.uk/htbin/expasyfetch?%s Cat : Sequence databases
AC : JN-1120 Abbrev: J. Mol. Biol. Title : Journal of Molecular Biology ISSN : 0022-2836 e-ISSN: 1089-8638 CODEN : JMOBAK Short : JMB Publis: Elsevier Science Server: http://www.elsevier.com/locate/issn/00222836