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Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs)
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, The Institute of Technology.
Karolinska Institute, Sweden .
2013 (English)In: Chemico-Biological Interactions, ISSN 0009-2797, E-ISSN 1872-7786, Vol. 202, no 1-3, 111-115 p.Article in journal (Refereed) Published
Abstract [en]

The short-chain dehydrogenases/reductases (SDRs) constitute one of the largest protein superfamilies known today. The members are distantly related with typically 20-30% residue identity in pair-wise comparisons. Still, all hitherto structurally known SDRs present a common three-dimensional structure consisting of a Rossmann fold with a parallel beta sheet flanked by three helices on each side. Using hidden Markov models (HMMs), we have developed a semi-automated subclassification system for this huge family. Currently, 75% of all SDR forms have been assigned to one of the 464 families totalling 122,940 proteins. There are 47 human SDR families, corresponding to 75 genes. Most human SDR families (35 families) have only one gene, while 12 have between 2 and 8 genes. For more than half of the human SDR families, the three-dimensional fold is known. The number of SDR members increases considerably every year, but the number of SDR families now starts to converge. The classification method has paved the ground for a sustainable and expandable nomenclature system. Information on the SDR superfamily is continuously updated at http://sdr-enzymes.org/.

Place, publisher, year, edition, pages
ELSEVIER IRELAND LTD, ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO, CLARE, 00000, IRELAND , 2013. Vol. 202, no 1-3, 111-115 p.
Keyword [en]
Short-chain dehydrogenases/reductases, Hidden Markov models, Functional assignment, Nomenclature, Classification, Bioinformatics
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:liu:diva-93268DOI: 10.1016/j.cbi.2012.11.009ISI: 000317539500015OAI: oai:DiVA.org:liu-93268DiVA: diva2:623743
Available from: 2013-05-28 Created: 2013-05-28 Last updated: 2017-12-06

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Persson, Bengt

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