ArticleBMC evolutionary biology2018
Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.
Article in BMC evolutionary biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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20 citing papers in PubMed.
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- Structural flexibility of the nicotinamide group of NADH in butanol dehydrogenase YqdH from Fusobacterium nucleatum.PloS one · 2025Article
- Designing Cyclic-Constrained Peptides to Inhibit Human Phosphoglycerate Dehydrogenase.Molecules (Basel, Switzerland) · 2023Article
- A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells.ACS synthetic biology · 2023Review
- Electrochemically mediated bioconversion and integrated purification greatly enhanced co-production of 1,3-propanediol and organic acids from glycerol in an industrial bioprocess.Bioprocess and biosystems engineering · 2023Article
- Directed Evolution of (ACS synthetic biology · 2022Article
- Valinophos Reveals a New Route in Microbial Phosphonate Biosynthesis That Is Broadly Conserved in Nature.Journal of the American Chemical Society · 2022Article
- Production of Hydroxycarboxylic Acid Receptor 3 (HCAMicroorganisms · 2021Article
- Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages.The ISME journal · 2021Article
- The diversity and evolution of microbial dissimilatory phosphite oxidation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.The FEBS journal · 2020Article
- Molstack: A platform for interactive presentations of electron density and cryo-EM maps and their interpretations.Protein science : a publication of the Protein Society · 2020Article
- Correction to: Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.BMC psychiatry · 2019Article
- Dimerization of PHGDH via the catalytic unit is essential for its enzymatic function.The Journal of biological chemistryArticle
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
backgroundThe family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members.
resultsWe report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase.
conclusionsThe knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.
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