The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Short‐chain dehydrogenases/reductases (SDRs): Coenzyme‐based functional assignments in completed genomes
Open accessAbstract
Short‐chain dehydrogenases/reductases (SDRs) are enzymes of great functional diversity. Even at sequence identities of typically only 15–30%, specific sequence motifs are detectable, reflecting common folding patterns. We have developed a functional assignment scheme based on these motifs and we find five families. Two of these families were known previously and are called ‘classical’ and ‘extended’ families, but they are now distinguished at a further level based on coenzyme specificities. This analysis gives seven subfamilies of classical SDRs and three subfamilies of extended SDRs. We find that NADP(H) is the preferred coenzyme among most classical SDRs, while NAD(H) is that preferred among most extended SDRs. Three families are novel entities, denoted ‘intermediate’, ‘divergent’ and ‘complex’, encompassing short‐chain alcohol dehydrogenases, enoyl reductases and multifunctional enzymes, respectively. The assignment scheme was applied to the genomes of human, mouse, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae. In the animal genomes, the extended SDRs amount to around one quarter or less of the total number of SDRs, while in the A. thaliana and S. cerevisiae genomes, the extended members constitute about 40% of the SDR forms. The numbers of NAD(H)‐dependent and NADP(H)‐dependent SDRs aresimilar in human, mouse and plant, while the proportions of NAD(H)‐dependent enzymes are much lower in fruit fly, worm and yeast. We show that, in spite of the great diversity of the SDR superfamily, the primary structure alone can be used for functional assignments and for predictions of coenzyme preference.
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Cites
The sequence of the human genome
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The Genome Sequence of Drosophila melanogaster
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Bairoch, A. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.38 · Cited by 3,280
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
Bairoch, A. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.45 · Cited by 3,093
Short-chain dehydrogenases/reductases (SDR)
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Cited by
Kavanagh, K. L., Jörnvall, H., Persson, B., & Oppermann, U. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-8588-y · Cited by 908
Self-citationKusaba, M., Ito, H., Morita, R., Iida, S., Sato, Y., Fujimoto, M., Kawasaki, S., Tanaka, R., Hirochika, H., Nishimura, M., et al. (2007) · The Plant Cell · doi:10.1105/tpc.106.042911 · Cited by 554
The Aldo-Keto Reductase Superfamily and its Role in Drug Metabolism and Detoxification
Barski, O. A., Tipparaju, S. M., & Bhatnagar, A. (2008) · Drug Metabolism Reviews · doi:10.1080/03602530802431439 · Cited by 542
The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative
Persson, B., Kallberg, Y., Bray, J. E., Bruford, E., Dellaporta, S. L., Favia, A. D., Duarte, R. G., Jörnvall, H., Kavanagh, K. L., Kedishvili, N., et al. (2009) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2008.10.040 · Cited by 396
Self-citationBlanc, G., Agarkova, I., Grimwood, J., Kuo, A., Brueggeman, A., Dunigan, D. D., Gurnon, J., Ladunga, I., Lindquist, E., Lucas, S., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-5-r39 · Cited by 317
Metadata
- Authors
- Kallberg, Y., Oppermann, U., Jörnvall, H., & Persson, B.
- Venue
- European Journal of Biochemistry
- Publisher
- Wiley
- Published
- 2002-09
- Volume
- 269
- Issue
- 18
- Pages
- 4409-4417
- ISSN
- 0014-2956 (ISSN-L)
- 1432-1033
- OpenAlex
- W1848490583
- Cited by
- 430
- References
- 39
- FWCI
- 11.23
- Type
- journal article
- Language
- en
- Open access
- bronze
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