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Author: Grafiati
Published: 14 March 2023

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1

Gallego, Oriol, Olga V. Belyaeva, Sergio Porté, F. Xavier Ruiz, Anton V. Stetsenko, Elena V. Shabrova, Natalia V. Kostereva, Jaume Farrés, Xavier Parés, and Natalia Y. Kedishvili. "Comparative functional analysis of human medium-chain dehydrogenases, short-chain dehydrogenases/reductases and aldo-keto reductases with retinoids." Biochemical Journal 399, no. 1 (September 13, 2006): 101–9. http://dx.doi.org/10.1042/bj20051988.

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Retinoic acid biosynthesis in vertebrates occurs in two consecutive steps: the oxidation of retinol to retinaldehyde followed by the oxidation of retinaldehyde to retinoic acid. Enzymes of the MDR (medium-chain dehydrogenase/reductase), SDR (short-chain dehydrogenase/reductase) and AKR (aldo-keto reductase) superfamilies have been reported to catalyse the conversion between retinol and retinaldehyde. Estimation of the relative contribution of enzymes of each type was difficult since kinetics were performed with different methodologies, but SDRs would supposedly play a major role because of their low Km values, and because they were found to be active with retinol bound to CRBPI (cellular retinol binding protein type I). In the present study we employed detergent-free assays and HPLC-based methodology to characterize side-by-side the retinoid-converting activities of human MDR [ADH (alcohol dehydrogenase) 1B2 and ADH4), SDR (RoDH (retinol dehydrogenase)-4 and RDH11] and AKR (AKR1B1 and AKR1B10) enzymes. Our results demonstrate that none of the enzymes, including the SDR members, are active with CRBPI-bound retinoids, which questions the previously suggested role of CRBPI as a retinol supplier in the retinoic acid synthesis pathway. The members of all three superfamilies exhibit similar and low Km values for retinoids (0.12–1.1 μM), whilst they strongly differ in their kcat values, which range from 0.35 min−1 for AKR1B1 to 302 min−1 for ADH4. ADHs appear to be more effective retinol dehydrogenases than SDRs because of their higher kcat values, whereas RDH11 and AKR1B10 are efficient retinaldehyde reductases. Cell culture studies support a role for RoDH-4 as a retinol dehydrogenase and for AKR1B1 as a retinaldehyde reductase in vivo.
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2

Gabrielli, Franco, Marco Antinucci, and Sergio Tofanelli. "Gene Structure Evolution of the Short-Chain Dehydrogenase/Reductase (SDR) Family." Genes 14, no. 1 (December 30, 2022): 110. http://dx.doi.org/10.3390/genes14010110.

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SDR (Short-chain Dehydrogenases/Reductases) are one of the oldest and heterogeneous superfamily of proteins, whose classification is problematic because of the low percent identity, even within families. To get clearer insights into SDR molecular evolution, we explored the splicing site organization of the 75 human SDR genes across their vertebrate and invertebrate orthologs. We found anomalous gene structures in members of the human SDR7C and SDR42E families that provide clues of retrogene properties and independent evolutionary trajectories from a common invertebrate ancestor. The same analyses revealed that the identity value between human and invertebrate non-allelic variants is not necessarily associated with the homologous gene structure. Accordingly, a revision of the SDR nomenclature is proposed by including the human SDR40C1 and SDR7C gene in the same family.
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3

Li, Aipeng, Lidan Ye, Xiaohong Yang, Chengcheng Yang, Jiali Gu, and Hongwei Yu. "Structure-guided stereoselectivity inversion of a short-chain dehydrogenase/reductase towards halogenated acetophenones." Chemical Communications 52, no. 37 (2016): 6284–87. http://dx.doi.org/10.1039/c6cc00051g.

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4

Joles, Jaap, Nel Willekes-Koolschijn, Hein Koomans, Arie van Tol, Tini Geelhoed-Mieras, Daan Crommelin, Louis van Bloois, et al. "Subcutaneous administration of HMG-CoA reductase inhibitors in hyperlipidaemic and normal rats." Laboratory Animals 26, no. 4 (October 1, 1992): 269–80. http://dx.doi.org/10.1258/002367792780745689.

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Recent reports demonstrate a hypocholesterolaemic effect of daily subcutaneous injections of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors in different rat models of hyperlipidaemia. However, this effect is not seen after oral administration of HMG-CoA reductase inhibitors in rats. We found that oral administration of the HMG-CoA reductase inhibitor Simvastatin also had no effect on plasma cholesterol in severely hyperlipidaemic Nagase analbuminaemic rats (NAR). Simvastatin (an apolar compound dissolved in propylene glycol) was infused continuously for 28 days into the subcutis of control Sprague-Dawley rats (SDR) and NAR using an implanted osmotic pump. All doses which were effective in reducing cholesterol in the NAR (reductions up to -60%), reduced apolipoprotein AI but not apolipoprotein B and caused a severe inflammatory reaction in the dermis. Similar toxicity was observed in the SDR. Subcutaneous administration of the vehicle (propylene glycol) did not cause this reaction and did not affect plasma lipids. Administration of Lovastatin in osmotic pumps resulted in a similar inflammatory reaction. Incorporation of Simvastatin into liposomes did not diminish the toxic effect. On the other hand, infusion of Pravastatin (a polar HMG-CoA reductase inhibitor dissolved in isotonic saline) caused no changes in the dermis and had no effect on plasma lipids in NAR or SDR. Liver microsomes prepared from the Pravastatin-treated rats demonstrated a 3- to 4-fold increase in HMG-CoA reductase activity as compared to untreated rats, confirming uptake of the drug. We conclude that continuous subcutaneous administration of the HMG-CoA reductase inhibitors Simvastatin, Lovastatin and Pravastatin for 28 days may not reduce plasma cholesterol in rats by a mechanism which is related to inhibition of HMG-CoA reductase activity in the liver. The decrease of plasma cholesterol effected by subcutaneous infusion of Simvastatin or Lovastatin in NAR coincides with, and may be related to inflammatory changes caused by administering these compounds into the dermis.
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5

Davidson, Jaysón, Kyndall Nicholas, Jeremy Young, Deborah G. Conrady, Stephen Mayclin, Sandhya Subramanian, Bart L. Staker, Peter J. Myler, and Oluwatoyin A. Asojo. "Crystal structure of a putative short-chain dehydrogenase/reductase from Paraburkholderia xenovorans." Acta Crystallographica Section F Structural Biology Communications 78, no. 1 (January 1, 2022): 25–30. http://dx.doi.org/10.1107/s2053230x21012632.

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Paraburkholderia xenovorans degrades organic wastes, including polychlorinated biphenyls. The atomic structure of a putative dehydrogenase/reductase (SDR) from P. xenovorans (PxSDR) was determined in space group P21 at a resolution of 1.45 Å. PxSDR shares less than 37% sequence identity with any known structure and assembles as a prototypical SDR tetramer. As expected, there is some conformational flexibility and difference in the substrate-binding cavity, which explains the substrate specificity. Uniquely, the cofactor-binding cavity of PxSDR is not well conserved and differs from those of other SDRs. PxSDR has an additional seven amino acids that form an additional unique loop within the cofactor-binding cavity. Further studies are required to determine how these differences affect the enzymatic functions of the SDR.
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6

Nguyen, Giang Thu, Shinae Kim, Hyeonseok Jin, Dong-Hyung Cho, Hang-Suk Chun, Woo-Keun Kim, and Jeong Ho Chang. "Crystal Structure of NADPH-Dependent Methylglyoxal Reductase Gre2 from Candida Albicans." Crystals 9, no. 9 (September 10, 2019): 471. http://dx.doi.org/10.3390/cryst9090471.

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Gre2 is a key enzyme in the methylglyoxal detoxification pathway; it uses NADPH or NADH as an electron donor to reduce the cytotoxic methylglyoxal to lactaldehyde. This enzyme is a member of the short-chain dehydrogenase/reductase (SDR) superfamily whose members catalyze this type of reaction with a broad range of substrates. To elucidate the structural features, we determined the crystal structures of the NADPH-dependent methylglyoxal reductase Gre2 from Candida albicans (CaGre2) for both the apo-form and NADPH-complexed form at resolutions of 2.8 and 3.02 Å, respectively. The CaGre2 structure is composed of two distinct domains: the N-terminal cofactor-binding domain and the C-terminal substrate-binding domain. Extensive comparison of CaGre2 with its homologous structures reveals conformational changes in α12 and β3′ of the NADPH-complex forms. This study may provide insights into the structural and functional variation of SDR family proteins.
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7

Sameeullah, Muhammad, Muhammet Yildirim, Noreen Aslam, Mehmet Cengiz Baloğlu, Buhara Yucesan, Andreas G. Lössl, Kiran Saba, Mohammad Tahir Waheed, and Ekrem Gurel. "Plastidial Expression of 3β-Hydroxysteroid Dehydrogenase and Progesterone 5β-Reductase Genes Confer Enhanced Salt Tolerance in Tobacco." International Journal of Molecular Sciences 22, no. 21 (October 29, 2021): 11736. http://dx.doi.org/10.3390/ijms222111736.

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The short-chain dehydrogenase/reductase (SDR) gene family is widely distributed in all kingdoms of life. The SDR genes, 3β-hydroxysteroid dehydrogenase (3β-HSD) and progesterone 5-β-reductases (P5βR1, P5βR2) play a crucial role in cardenolide biosynthesis pathway in the Digitalis species. However, their role in plant stress, especially in salinity stress management, remains unexplored. In the present study, transplastomic tobacco plants were developed by inserting the 3β-HSD, P5βR1 and P5βR2 genes. The integration of transgenes in plastomes, copy number and transgene expression at transcript and protein level in transplastomic plants were confirmed by PCR, end-to-end PCR, qRT-PCR and Western blot analysis, respectively. Subcellular localization analysis showed that 3β-HSD and P5βR1 are cytoplasmic, and P5βR2 is tonoplast-localized. Transplastomic lines showed enhanced growth in terms of biomass and chlorophyll content compared to wild type (WT) under 300 mM salt stress. Under salt stress, transplastomic lines remained greener without negative impact on shoot or root growth compared to the WT. The salt-tolerant transplastomic lines exhibited enhanced levels of a series of metabolites (sucrose, glutamate, glutamine and proline) under control and NaCl stress. Furthermore, a lower Na+/K+ ratio in transplastomic lines was also observed. The salt tolerance, mediated by plastidial expression of the 3β-HSD, P5βR1 and P5βR2 genes, could be due to the involvement in the upregulation of nitrogen assimilation, osmolytes as well as lower Na+/K+ ratio. Taken together, the plastid-based expression of the SDR genes leading to enhanced salt tolerance, which opens a window for developing saline-tolerant plants via plastid genetic engineering.
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8

Jacob, Asha I., Sirin A. I. Adham, David S. Capstick, Scott R. D. Clark, Tara Spence, and Trevor C. Charles. "Mutational Analysis of the Sinorhizobium meliloti Short-Chain Dehydrogenase/Reductase Family Reveals Substantial Contribution to Symbiosis and Catabolic Diversity." Molecular Plant-Microbe Interactions® 21, no. 7 (July 2008): 979–87. http://dx.doi.org/10.1094/mpmi-21-7-0979.

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The short-chain dehydrogenase/reductase (SDR) family is one of the largest and most ubiquitous protein families in bacterial genomes. Despite there being a few well-characterized examples, the substrate specificities or functions of most members of the family are unknown. In this study, we carried out a large-scale mutagenesis of the SDR gene family in the alfalfa root nodule symbiont Sinorhizobium meliloti. Subsequent phenotypic analysis revealed phenotypes for mutants of 21 of the SDR-encoding genes. This brings the total number of S. meliloti SDR-encoding genes with known function or associated phenotype to 25. Several of the mutants were deficient in the utilization of specific carbon sources, while others exhibited symbiotic deficiencies on alfalfa (Medicago sativa), ranging from partial ineffectiveness to complete inability to form root nodules. Five of the mutants had both symbiotic and carbon utilization phenotypes. These results clearly demonstrate the importance of the SDR family in both symbiosis and saprotrophy, and reinforce the complex nature of the interaction of S. meliloti with its plant hosts. Further analysis of the genes identified in this study will contribute to the overall understanding of the biology and metabolism of S. meliloti in relation to its interaction with alfalfa.
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9

Stambergova, Hana, Lucie Skarydova, James E. Dunford, and Vladimir Wsol. "Biochemical properties of human dehydrogenase/reductase (SDR family) member 7." Chemico-Biological Interactions 207 (January 2014): 52–57. http://dx.doi.org/10.1016/j.cbi.2013.11.003.

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10

Bryndová, J., P. Klusoňová, M. Kučka, K. Mazancová-Vagnerová, I. Mikšík, and J. Pácha. "Cloning and expression of chicken 20-hydroxysteroid dehydrogenase." Journal of Molecular Endocrinology 37, no. 3 (December 2006): 453–62. http://dx.doi.org/10.1677/jme.1.02025.

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The ligand specificity and activation of steroid receptors depend considerably on the enzymatic activities involved in local pre-receptor synthesis and the metabolism of the steroids. Several enzymes in particular, steroid dehydrogenases have been shown to participate in this process. Here we report the isolation of 20-hydroxysteroid dehydrogenase (ch20HSD) cDNA from chicken intestine and the distribution of ch20HSD mRNA and 20-reductase activity in various avian tissues. Using a reverse transcription PCR and comparison with the known sequences of mammalian 20βHSDs, we have isolated a new ch20HSD cDNA. This cDNA predicted 276 amino acid residues that shared about 75% homology with mammalian 20βHSD. Sequences specific to the short-chain dehydrogenase/reductase superfamily (SDR) were found, the Gly-X-X-X-Gly-X-Gly cofactor-binding motif (residues 11–17) and the catalytic activity motif Tyr-X-X-X-Lys (residues 193–197). The cDNA coding for ch20HSD was expressed in Escherichia coli by placing it under isopropylthiogalactoside (IPTG) inducible control. Both the IPTG cells of E. coli and the isolated recombinant protein reduced progesterone to 20-dihydroprogesterone, corticosterone to 20-dihydrocorticosterone and 5α-dihydrotestosterone to its 3-ol derivative. The 20-reductase and 3-reductase activities of ch20HSD catalyzed both 3α/β- and 20α/20β-epimers. The mRNA transcripts of ch20HSD were found in the kidney, colon, and testes; weaker expression was also found in the heart, ovaries, oviduct, brain, liver, and ileum. 20-Reductase activity has been proven in tissue slices of kidney, colon, ileum, liver, oviduct, testis, and ovary; whereas the activity was nearly absent in the heart and brain. A similar distribution of 20-reductase activity was found in tissue homogenates measured under Vmax conditions. These results suggest that chicken 20HSD is the latest member of the SDR superfamily to be found, is expressed in many avian tissues and whose precise role remains to be determined.
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11

FRANSEN, Marc, Paul P. VAN VELDHOVEN, and Suresh SUBRAMANI. "Identification of peroxisomal proteins by using M13 phage protein VI phage display: molecular evidence that mammalian peroxisomes contain a 2,4-dienoyl-CoA reductase." Biochemical Journal 340, no. 2 (May 25, 1999): 561–68. http://dx.doi.org/10.1042/bj3400561.

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To elucidate unknown mammalian peroxisomal enzymes and functions, we subjected M13 phage expressing fusions between the gene encoding protein VI and a rat liver cDNA library to an immunoaffinity selection process in vitro (biopanning) with the use of antibodies raised against peroxisomal subfractions. In an initial series of biopanning experiments, four different cDNA clones were obtained. These cDNA species encoded two previously identified peroxisomal enzymes, catalase and urate oxidase, and two novel proteins that contained a C-terminal peroxisomal targeting signal (PTS1). A primary structure analysis of these novel proteins revealed that one, ending in the tripeptide AKL, is homologous to the yeast peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34; DCR), an enzyme required for the degradation of unsaturated fatty acids, and that the other, ending in the tripeptide SRL, is a putative member of the short-chain dehydrogenase/reductase (SDR) family, with three isoforms. Green fluorescent protein (GFP) fusions encoding GFP-DCR-AKL, GFP-DCR, GFP-SDR-SRL and GFP-SDR were expressed in mammalian cells. The analysis of the subcellular location of the recombinant fusion proteins confirmed the peroxisomal localization of GFP-DCR-AKL and GFP-SDR-SRL, as well as the functionality of the PTS1. That the AKL protein is indeed an NADPH-dependent DCR was demonstrated by showing DCR activity of the bacterially expressed protein. These results demonstrate at the molecular level that mammalian peroxisomes do indeed contain a DCR. In addition, the results presented here indicate that the protein VI display system is suitable for the isolation of rare cDNA clones from cDNA libraries and that this technology facilitates the identification of novel peroxisomal proteins.
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12

Ferrandi, Erica Elisa, Ivan Bassanini, Susanna Bertuletti, Sergio Riva, Chiara Tognoli, Marta Vanoni, and Daniela Monti. "Functional Characterization and Synthetic Application of Is2-SDR, a Novel Thermostable and Promiscuous Ketoreductase from a Hot Spring Metagenome." International Journal of Molecular Sciences 23, no. 20 (October 12, 2022): 12153. http://dx.doi.org/10.3390/ijms232012153.

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In a metagenome mining-based search of novel thermostable hydroxysteroid dehydrogenases (HSDHs), enzymes that are able to selectively oxidize/reduce steroidal compounds, a novel short-chain dehydrogenase/reductase (SDR), named Is2-SDR, was recently discovered. This enzyme, found in an Icelandic hot spring metagenome, shared a high sequence similarity with HSDHs, but, unexpectedly, showed no activity in the oxidation of the tested steroid substrates, e.g., cholic acid. Despite that, Is2-SDR proved to be a very active and versatile ketoreductase, being able to regio- and stereoselectively reduce a diversified panel of carbonylic substrates, including bulky ketones, α- and β-ketoesters, and α-diketones of pharmaceutical relevance. Further investigations showed that Is2-SDR was indeed active in the regio- and stereoselective reduction of oxidized steroid derivatives, and this outcome was rationalized by docking analysis in the active site model. Moreover, Is2-SDR showed remarkable thermostability, with an apparent melting temperature (TM) around 75 °C, as determined by circular dichroism analysis, and no significant decrease in catalytic activity, even after 5 h at 80 °C. A broad tolerance to both water-miscible and water-immiscible organic solvents was demonstrated as well, thus, confirming the potential of this new biocatalyst for its synthetic application.
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13

Persson, Bengt, Yvonne Kallberg, James E. Bray, Elspeth Bruford, Stephen L. Dellaporta, Angelo D. Favia, Roser Gonzalez Duarte, et al. "The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative." Chemico-Biological Interactions 178, no. 1-3 (March 2009): 94–98. http://dx.doi.org/10.1016/j.cbi.2008.10.040.

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14

Bray, James E., Brian D. Marsden, and Udo Oppermann. "The human short-chain dehydrogenase/reductase (SDR) superfamily: A bioinformatics summary." Chemico-Biological Interactions 178, no. 1-3 (March 2009): 99–109. http://dx.doi.org/10.1016/j.cbi.2008.10.058.

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15

Shah, Bhumika S., Sasha G. Tetu, Stephen J. Harrop, Ian T. Paulsen, and Bridget C. Mabbutt. "Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain ofAcinetobacter baumannii." Acta Crystallographica Section F Structural Biology Communications 70, no. 10 (September 25, 2014): 1318–23. http://dx.doi.org/10.1107/s2053230x14019785.

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Over 15% of the genome of an Australian clinical isolate ofAcinetobacter baumanniioccurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access.
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16

Contreras, Ángela, Irene Merino, Enrique Álvarez, David Bolonio, José-Eugenio Ortiz, Luis Oñate-Sánchez, and Luis Gómez. "A poplar short-chain dehydrogenase reductase plays a potential key role in biphenyl detoxification." Proceedings of the National Academy of Sciences 118, no. 35 (August 26, 2021): e2103378118. http://dx.doi.org/10.1073/pnas.2103378118.

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Polychlorinated biphenyls (PCBs) are persistent organic pollutants with severe effects on human health and the biosphere. Plant-based remediation offers many benefits over conventional PCB remediation, but its development has been hampered by our poor understanding of biphenyl metabolism in eukaryotes, among other factors. We report here a major PCB-responsive protein in poplar, a plant model system capable of PCB uptake and translocation. We provide structural and functional evidence that this uncharacterized protein, termed SDR57C, belongs to the heterogeneous short-chain dehydrogenase reductase (SDR) superfamily. Despite sequence divergence, structural modeling hinted at structural and functional similarities between SDR57C and BphB, a central component of the Bph pathway for biphenyl/PCB degradation in aerobic bacteria. By combining gas chromatography/mass spectrometry (GC/MS) profiling with a functional complementation scheme, we found that poplar SDR57C can replace BphB activity in the upper Bph pathway of Pseudomonas furukawaii KF707 and therefore catalyze the oxidation of 2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DHDB) to 2,3-dihydroxybiphenyl (2,3-DHB). Consistent with this biochemical activity, we propose a mechanism of action based on prior quantum studies, general properties of SDR enzymes, and the modeled docking of 2,3-DHDB to the SDR57C-NAD+ complex. The putative detoxifying capacity of SDR57C was substantiated through reverse genetics in Arabidopsis thaliana. Phenotypic characterization of the SDR lines underscored an inducible plant pathway with the potential to catabolize toxic biphenyl derivatives. Partial similarities with aerobic bacterial degradation notwithstanding, real-time messenger RNA quantification indicates the occurrence of plant-specific enzymes and features. Our results may help explain differences in degradative abilities among plant genotypes and also provide elements to improve them.
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17

Bhinija, Kisana, Pattana Srifah Huehne, Skorn Mongkolsuk, Somkid Sitthimonchai, and Jutamaad Satayavivad. "A short-chain dehydrogenase/reductase (SDR) detection for the isoflavone reductase gene in Bulbophyllum and other orchids." South African Journal of Botany 144 (January 2022): 295–304. http://dx.doi.org/10.1016/j.sajb.2021.08.034.

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18

Pang, Yu, Wen-Qiang Song, Fang-Yuan Chen, and Yong-Mei Qin. "A new cotton SDR family gene encodes a polypeptide possessing aldehyde reductase and 3-ketoacyl-CoA reductase activities." Biochemistry (Moscow) 75, no. 3 (March 2010): 320–26. http://dx.doi.org/10.1134/s0006297910030089.

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19

Rodarte, Justas V., Jan Abendroth, Thomas E. Edwards, Donald D. Lorimer, Bart L. Staker, Sunny Zhang, Peter J. Myler, and Krystle J. McLaughlin. "Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis." Acta Crystallographica Section F Structural Biology Communications 77, no. 2 (February 1, 2021): 54–60. http://dx.doi.org/10.1107/s2053230x21001497.

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Rickettsia felis, a Gram-negative bacterium that causes spotted fever, is of increasing interest as an emerging human pathogen. R. felis and several other Rickettsia strains are classed as National Institute of Allergy and Infectious Diseases priority pathogens. In recent years, R. felis has been shown to be adaptable to a wide range of hosts, and many fevers of unknown origin are now being attributed to this infectious agent. Here, the structure of acetoacetyl-CoA reductase from R. felis is reported at a resolution of 2.0 Å. While R. felis acetoacetyl-CoA reductase shares less than 50% sequence identity with its closest homologs, it adopts a fold common to other short-chain dehydrogenase/reductase (SDR) family members, such as the fatty-acid synthesis II enzyme FabG from the prominent pathogens Staphylococcus aureus and Bacillus anthracis. Continued characterization of the Rickettsia proteome may prove to be an effective means of finding new avenues of treatment through comparative structural studies.
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20

Yu, Shuhan, Qiguo Sun, Jiaxuan Wu, Pengcheng Zhao, Yanmei Sun, and Zhenfei Guo. "Genome-Wide Identification and Characterization of Short-Chain Dehydrogenase/Reductase (SDR) Gene Family in Medicago truncatula." International Journal of Molecular Sciences 22, no. 17 (August 31, 2021): 9498. http://dx.doi.org/10.3390/ijms22179498.

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Short-chain dehydrogenase/reductase (SDR) belongs to the NAD(P)(H)-dependent oxidoreductase superfamily. Limited investigations reveal that SDRs participate in diverse metabolisms. A genome-wide identification of the SDR gene family in M. truncatula was conducted. A total of 213 MtSDR genes were identified, and they were distributed on all chromosomes unevenly. MtSDR proteins were categorized into seven subgroups based on phylogenetic analysis and three types including ‘classic’, ‘extended’, and ‘atypical’, depending on the cofactor-binding site and active site. Analysis of the data from M. truncatula Gene Expression Atlas (MtGEA) showed that above half of MtSDRs were expressed in at least one organ, and lots of MtSDRs had a preference in a tissue-specific expression. The cis-acting element responsive to plant hormones (salicylic acid, ABA, auxin, MeJA, and gibberellin) and stresses were found in the promoter of some MtSDRs. Many genes of MtSDR7C,MtSDR65C, MtSDR110C, MtSDR114C, and MtSDR108E families were responsive to drought, salt, and cold. The study provides useful information for further investigation on biological functions of MtSDRs, especially in abiotic stress adaptation, in the future.
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Heibel, Sandra, Celine Chen, Joseph Urban, and Harry Dawson. "Effect of 1,25-dihydroxyvitamin D on all-trans retinoic acid metabolism and interleukin-4 signaling in porcine alternatively activated lung macrophages. (IRM7P.493)." Journal of Immunology 192, no. 1_Supplement (May 1, 2014): 126.18. http://dx.doi.org/10.4049/jimmunol.192.supp.126.18.

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Abstract All-trans retinoic acid (ATRA), the most active vitamin A (VA) metabolite, and 1,25-dihydroxyvitamin D (VD3), the most active form of vitamin D (VD), and interleukin-4 (IL-4) each positively regulate the development of alternatively activated macrophages (AAM) however, their interactions are unknown. We have previously shown that VA, ATRA, and IL-4 have differing mechanisms for sustaining a Th2-type AAM response. Herein, we demonstrate that VD3 regulates the contribution of ATRA and IL-4 inducible signals to this system. While ATRA (10-7 M) increases mRNA expression of retinol producing dehydrogenase/reductase (SDR family) member, 4 fold, VD3 (10-7 M) decreases its expression 3-fold and additively increases expression of retinal producing, Aldehyde dehydrogenase 1 family, member A2, and dehydrogenase/reductase (SDR family) member 9 by 5 fold when present along with ATRA. Conversely, VD3 decreases IL-4 (10 ng/ml) -induced chemokine (C-C motif) ligand 17 by 4 fold, and C-type lectin CD209 antigen by 60 fold. These results suggest that VD3 increases expression of genes involved in ATRA anabolism while decreasing expression of IL-4 responsive genes. In conclusion, VD3 may regulate the development of AAM by increasing levels of ATRA and decreasing the effect of IL-4, thereby supporting an alternate signal for AAM development.
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22

Sałuda-Gorgul, Anna, Karolina Seta, Magdalena Nowakowska, and Andrzej K. Bednarek. "WWOX Oxidoreductase – Substrate and Enzymatic Characterization." Zeitschrift für Naturforschung C 66, no. 1-2 (February 1, 2011): 73–82. http://dx.doi.org/10.1515/znc-2011-1-210.

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WWOX is a tumour suppressor gene that spans the common fragile site FRA16D. Analysis of the WWOX expression pattern in normal human tissues showed the highest expression in testis, prostate, and ovary. Its altered expression has been demonstrated in different tissues and tumour types. The WWOX gene encodes a 414-amino acids protein, which is the first discovered protein with a short-chain dehydrogenase/reductase (SDR) central domain and two WW domains at the NH2 terminus. Due to its potential role in sex-steroid metabolism, using two bacterial expression systems, we have cloned WWOX fusion proteins showing oxidoreductase activity in a crude extract, defined a course of enzymatic reactions for selected steroid substrates, and determined related Km values. Our results show that the SDR domain of the WWOX protein has dehydrogenase activity and is reactive both in the presence of NAD+ and NADP+ for all examined steroid substrates. On the other hand, with the same substrates and reduced cofactors (NADH and NADPH) reduction activity was not observed.
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Büsing, Imke, H. Wolfgang Höffken, Michael Breuer, Lars Wöhlbrand, Bernhard Hauer, and Ralf Rabus. "Molecular Genetic and Crystal Structural Analysis of 1-(4-Hydroxyphenyl)-Ethanol Dehydrogenase from ‘Aromatoleum aromaticum' EbN1." Journal of Molecular Microbiology and Biotechnology 25, no. 5 (2015): 327–39. http://dx.doi.org/10.1159/000439113.

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The dehydrogenation of 1-(4-hydroxyphenyl)-ethanol to 4-hydroxyacetophenone represents the second reaction step during anaerobic degradation of <i>p</i>-ethylphenol in the denitrifying bacterium ‘<i>Aromatoleum aromaticum</i>' EbN1. Previous proteogenomic studies identified two different proteins (ChnA and EbA309) as possible candidates for catalyzing this reaction [Wöhlbrand et al: J Bacteriol 2008;190:5699-5709]. Physiological-molecular characterization of newly generated unmarked <i>in-frame</i> deletion and complementation mutants allowed defining ChnA (renamed here as Hped) as the enzyme responsible for 1-(4-hydroxyphenyl)-ethanol oxidation. Hped [1-(4-hydroxyphenyl)-ethanol dehydrogenase] belongs to the ‘classical' family within the short-chain alcohol dehydrogenase/reductase (SDR) superfamily. Hped was overproduced in <i>Escherichia coli</i>, purified and crystallized. The X-ray structures of the apo- and NAD<sup>+</sup>-soaked form were resolved at 1.5 and 1.1 Å, respectively, and revealed Hped as a typical homotetrameric SDR. Modeling of the substrate 4-hydroxyacetophenone (reductive direction of Hped) into the active site revealed the structural determinants of the strict <i>(R)</i>-specificity of Hped (Phe<sup>187</sup>), contrasting the <i>(S)</i>-specificity of previously reported 1-phenylethanol dehydrogenase (Ped; Tyr<sup>93</sup>) from strain EbN1 [Höffken et al: Biochemistry 2006;45:82-93].
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Szeliga, Magdalena, Joanna Ciura, and Mirosław Tyrka. "Representational Difference Analysis of Transcripts Involved in Jervine Biosynthesis." Life 10, no. 6 (June 19, 2020): 88. http://dx.doi.org/10.3390/life10060088.

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Veratrum-type steroidal alkaloids (VSA) are the major bioactive ingredients that strongly determine the pharmacological activities of Veratrum nigrum. Biosynthesis of VSA at the molecular and genetic levels is not well understood. Next-generation sequencing of representational difference analysis (RDA) products after elicitation and precursor feeding was applied to identify candidate genes involved in VSA biosynthesis. A total of 12,048 contigs with a median length of 280 bases were received in three RDA libraries obtained after application of methyl jasmonate, squalene and cholesterol. The comparative analysis of annotated sequences was effective in identifying candidate genes. GABAT2 transaminase and hydroxylases active at C-22, C-26, C-11, and C-16 positions in late stages of jervine biosynthesis were selected. Moreover, genes coding pyrroline-5-carboxylate reductase and enzymes from the short-chain dehydrogenases/reductases family (SDR) associated with the reduction reactions of the VSA biosynthesis process were proposed. The data collected contribute to better understanding of jervine biosynthesis and may accelerate implementation of biotechnological methods of VSA biosynthesis.
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25

Kowalik, Dorota, Ferdinand Haller, Jerzy Adamski, and Gabriele Moeller. "In search for function of two human orphan SDR enzymes: Hydroxysteroid dehydrogenase like 2 (HSDL2) and short-chain dehydrogenase/reductase-orphan (SDR-O)." Journal of Steroid Biochemistry and Molecular Biology 117, no. 4-5 (November 2009): 117–24. http://dx.doi.org/10.1016/j.jsbmb.2009.08.001.

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26

Shafqat, Naeem, Joao R. C. Muniz, Ewa S. Pilka, Evangelos Papagrigoriou, Frank von Delft, Udo Oppermann, and Wyatt W. Yue. "Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits." Biochemical Journal 452, no. 1 (April 25, 2013): 27–36. http://dx.doi.org/10.1042/bj20121580.

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MAT (methionine adenosyltransferase) utilizes L-methionine and ATP to form SAM (S-adenosylmethionine), the principal methyl donor in biological methylation. Mammals encode a liver-specific isoenzyme, MAT1A, that is genetically linked with an inborn metabolic disorder of hypermethioninaemia, as well as a ubiquitously expressed isoenzyme, MAT2A, whose enzymatic activity is regulated by an associated subunit MAT2B. To understand the molecular mechanism of MAT functions and interactions, we have crystallized the ligand-bound complexes of human MAT1A, MAT2A and MAT2B. The structures of MAT1A and MAT2A in binary complexes with their product SAM allow for a comparison with the Escherichia coli and rat structures. This facilitates the understanding of the different substrate or product conformations, mediated by the neighbouring gating loop, which can be accommodated by the compact active site during catalysis. The structure of MAT2B reveals an SDR (short-chain dehydrogenase/reductase) core with specificity for the NADP/H cofactor, and harbours the SDR catalytic triad (YxxxKS). Extended from the MAT2B core is a second domain with homology with an SDR sub-family that binds nucleotide-sugar substrates, although the equivalent region in MAT2B presents a more open and extended surface which may endow a different ligand/protein-binding capability. Together, the results of the present study provide a framework to assign structural features to the functional and catalytic properties of the human MAT proteins, and facilitate future studies to probe new catalytic and binding functions.
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27

TANAKA, Nobutada. "Structure and Function of the enzymes belonging to the SDR(Short-chain Dehydrogenase/Reductase) Family." Nihon Kessho Gakkaishi 38, no. 3 (1996): 235–43. http://dx.doi.org/10.5940/jcrsj.38.235.

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28

Fujimoto, Kengo, Masayuki Hara, Hirotaka Yamada, Masato Sakurai, Akemi Inaba, Akito Tomomura, and Setsuko Katoh. "Role of the conserved Ser–Tyr–Lys triad of the SDR family in sepiapterin reductase." Chemico-Biological Interactions 130-132 (January 2001): 825–32. http://dx.doi.org/10.1016/s0009-2797(00)00238-6.

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29

Endo, Satoshi, Namiki Miyagi, Toshiyuki Matsunaga, Akira Hara, and Akira Ikari. "Human dehydrogenase/reductase (SDR family) member 11 is a novel type of 17β-hydroxysteroid dehydrogenase." Biochemical and Biophysical Research Communications 472, no. 1 (March 2016): 231–36. http://dx.doi.org/10.1016/j.bbrc.2016.01.190.

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30

Alenazi, Jawaher, Stephen Mayclin, Sandhya Subramanian, Peter J. Myler, and Oluwatoyin A. Asojo. "Crystal structure of a short-chain dehydrogenase/reductase from Burkholderia phymatum in complex with NAD." Acta Crystallographica Section F Structural Biology Communications 78, no. 2 (January 27, 2022): 52–58. http://dx.doi.org/10.1107/s2053230x22000218.

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Burkholderia phymatum is an important symbiotic nitrogen-fixing betaproteobacterium. B. phymatum is beneficial, unlike other Burkholderia species, which cause disease or are potential bioagents. Structural genomics studies at the SSGCID include characterization of the structures of short-chain dehydrogenases/reductases (SDRs) from multiple Burkholderia species. The crystal structure of a short-chain dehydrogenase from B. phymatum (BpSDR) was determined in space group C2221 at a resolution of 1.80 Å. BpSDR shares less than 38% sequence identity with any known structure. The monomer is a prototypical SDR with a well conserved cofactor-binding domain despite its low sequence identity. The substrate-binding cavity is unique and offers insights into possible functions and likely inhibitors of the enzymatic functions of BpSDR.
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31

Chen, Weiguo, Min-Sun Song, and Joseph L. Napoli. "SDR-O : an orphan short-chain dehydrogenase/reductase localized at mouse chromosome 10/human chromosome 12." Gene 294, no. 1-2 (July 2002): 141–46. http://dx.doi.org/10.1016/s0378-1119(02)00757-6.

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Lundová, Tereza, Hana Štambergová, Lucie Zemanová, Markéta Svobodová, Jana Havránková, Miroslav Šafr, and Vladimír Wsól. "Human dehydrogenase/reductase (SDR family) member 8 (DHRS8): a description and evaluation of its biochemical properties." Molecular and Cellular Biochemistry 411, no. 1-2 (October 16, 2015): 35–42. http://dx.doi.org/10.1007/s11010-015-2566-0.

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33

Cheng, Zhong, Yao Li, Chun Sui, Xiaobo Sun, and Yong Xie. "Synthesis, purification and crystallographic studies of the C-terminal sterol carrier protein type 2 (SCP-2) domain of human hydroxysteroid dehydrogenase-like protein 2." Acta Crystallographica Section F Structural Biology Communications 71, no. 7 (June 27, 2015): 901–5. http://dx.doi.org/10.1107/s2053230x15008559.

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Human hydroxysteroid dehydrogenase-like protein 2 (HSDL2) is a member of the short-chain dehydrogenase/reductase (SDR) subfamily of oxidoreductases and contains an N-terminal catalytic domain and a C-termianl sterol carrier protein type 2 (SCP-2) domain. In this study, the C-terminal SCP-2 domain of human HSDL2, including residues Lys318–Arg416, was produced inEscherichia coli, purified and crystallized. X-ray diffraction data were collected to 2.10 Å resolution. The crystal belonged to the trigonal space groupP3121 (orP3221), with unit-cell parametersa=b= 70.4,c= 60.6 Å, α = β = 90, γ = 120°. Two protein molecules are present in the asymmetric unit, resulting in a Matthews coefficient of 2.16 Å3 Da−1and an approximate solvent content of 43%.
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34

Zhou, Yan, Yifeng Wei, Lianyun Lin, Tong Xu, Ee Lui Ang, Huimin Zhao, Zhiguang Yuchi, and Yan Zhang. "Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca." Biochemical Journal 476, no. 4 (February 28, 2019): 733–46. http://dx.doi.org/10.1042/bcj20190005.

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Abstract Sulfoacetaldehyde reductase (IsfD) is a member of the short-chain dehydrogenase/reductase (SDR) family, involved in nitrogen assimilation from aminoethylsulfonate (taurine) in certain environmental and human commensal bacteria. IsfD catalyzes the reversible NADPH-dependent reduction of sulfoacetaldehyde, which is generated by transamination of taurine, forming hydroxyethylsulfonate (isethionate) as a waste product. In the present study, the crystal structure of Klebsiella oxytoca IsfD in a ternary complex with NADPH and isethionate was solved at 2.8 Å, revealing residues important for substrate binding. IsfD forms a homotetramer in both crystal and solution states, with the C-terminal tail of each subunit interacting with the C-terminal tail of the diagonally opposite subunit, forming an antiparallel β sheet that constitutes part of the substrate-binding site. The sulfonate group of isethionate is stabilized by a hydrogen bond network formed by the residues Y148, R195, Q244 and a water molecule. In addition, F249 from the diagonal subunit restrains the conformation of Y148 to further stabilize the orientation of the sulfonate group. Mutation of any of these four residues into alanine resulted in a complete loss of catalytic activity for isethionate oxidation. Biochemical investigations of the substrate scope of IsfD, and bioinformatics analysis of IsfD homologs, suggest that IsfD is related to the promiscuous 3-hydroxyacid dehydrogenases with diverse metabolic functions.
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Endo, Satoshi, Namiki Miyagi, Toshiyuki Matsunaga, and Akira Ikari. "Rabbit dehydrogenase/reductase SDR family member 11 (DHRS11): Its identity with acetohexamide reductase with broad substrate specificity and inhibitor sensitivity, different from human DHRS11." Chemico-Biological Interactions 305 (May 2019): 12–20. http://dx.doi.org/10.1016/j.cbi.2019.03.026.

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36

Cassetta, Alberto, Ivet Krastanova, Katja Kristan, Mojca Brunskole Švegelj, Doriano Lamba, Tea Lanišnik Rižner, and Jure Stojan. "Insights into subtle conformational differences in the substrate-binding loop of fungal 17β-hydroxysteroid dehydrogenase: a combined structural and kinetic approach." Biochemical Journal 441, no. 1 (December 14, 2011): 151–60. http://dx.doi.org/10.1042/bj20110567.

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The 17β-HSD (17β-hydroxysteroid dehydrogenase) from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) is a NADP(H)-dependent enzyme that preferentially catalyses the interconversion of inactive 17-oxo-steroids and their active 17β-hydroxy counterparts. 17β-HSDcl belongs to the SDR (short-chain dehydrogenase/reductase) superfamily. It is currently the only fungal 17β-HSD member that has been described and represents one of the model enzymes of the cP1 classical subfamily of NADPH-dependent SDR enzymes. A thorough crystallographic analysis has been performed to better understand the structural aspects of this subfamily and provide insights into the evolution of the HSD enzymes. The crystal structures of the 17β-HSDcl apo, holo and coumestrol-inhibited ternary complex, and the active-site Y167F mutant reveal subtle conformational differences in the substrate-binding loop that probably modulate the catalytic activity of 17β-HSDcl. Coumestrol, a plant-derived non-steroidal compound with oestrogenic activity, inhibits 17β-HSDcl [IC50 2.8 μM; at 100 μM substrate (4-oestrene-3,17-dione)] by occupying the putative steroid-binding site. In addition to an extensive hydrogen-bonding network, coumestrol binding is stabilized further by π–π stacking interactions with Tyr212. A stopped-flow kinetic experiment clearly showed the coenzyme dissociation as the slowest step of the reaction and, in addition to the low steroid solubility, it prevents the accumulation of enzyme–coenzyme–steroid ternary complexes.
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37

Janssen, D. B., M. Majerić-Elenkov, G. Hasnaoui, B. Hauer, and J. H. Lutje Spelberg. "Enantioselective formation and ring-opening of epoxides catalysed by halohydrin dehalogenases." Biochemical Society Transactions 34, no. 2 (March 20, 2006): 291–95. http://dx.doi.org/10.1042/bst0340291.

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Halohydrin dehalogenases catalyse the conversion of vicinal halohydrins into their corresponding epoxides, while releasing halide ions. They can be found in several bacteria that use halogenated alcohols or compounds that are degraded via halohydrins as a carbon source for growth. Biochemical and structural studies have shown that halohydrin dehalogenases are evolutionarily and mechanistically related to enzymes of the SDR (short-chain dehydrogenase/reductase) superfamily. In the reverse reaction, which is epoxide-ring opening, different nucleophiles can be accepted, including azide, nitrite and cyanide. This remarkable catalytic promiscuity allows the enzymatic production of a broad range of β-substituted alcohols from epoxides. In these oxirane-ring-opening reactions, the halohydrin dehalogenase from Agrobacterium radiobacter displays high enantioselectivity, making it possible to use the enzyme for the preparation of enantiopure building blocks for fine chemicals.
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38

Sirko, A., A. Wegleńska, M. Hryniewicz, and D. M. Hulanicka. "Characterization of the Escherichia coli gene encoding a new member of the short-chain dehydrogenase/reductase (SDR) family." Acta Biochimica Polonica 44, no. 1 (March 31, 1997): 153–57. http://dx.doi.org/10.18388/abp.1997_4453.

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The nucleotide sequence of a chromosomal DNA fragment located upstream from the cysPTWAM operon of Escherichia coli was established. Sequence analysis indicates the presence of an open reading frame which has been designated ucpA (upstream cys P). The potential protein products exhibits strong sequence homology to the members of a large protein family, short-chain dehydrogenases/reductases. Involvement of Crp, FruR and IHF in the regulation of ucpA transcription in vivo was demonstrated.
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39

Pennacchio, Angela, Biagio Pucci, Francesco Secundo, Francesco La Cara, Mosè Rossi, and Carlo A. Raia. "Purification and Characterization of a Novel Recombinant Highly Enantioselective Short-Chain NAD(H)-Dependent Alcohol Dehydrogenase from Thermus thermophilus." Applied and Environmental Microbiology 74, no. 13 (May 2, 2008): 3949–58. http://dx.doi.org/10.1128/aem.00217-08.

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ABSTRACT The gene encoding a novel alcohol dehydrogenase (ADH) that belongs to the short-chain dehydrogenase/reductase (SDR) superfamily was identified in the extremely thermophilic, halotolerant gram-negative eubacterium Thermus thermophilus HB27. The T. thermophilus ADH gene (adh Tt) was heterologously overexpressed in Escherichia coli, and the protein (ADHTt) was purified to homogeneity and characterized. ADHTt is a tetrameric enzyme consisting of identical 26,961-Da subunits composed of 256 amino acids. The enzyme has remarkable thermophilicity and thermal stability, displaying activity at temperatures up to ∼73°C and a 30-min half-inactivation temperature of ∼90°C, as well as good tolerance to common organic solvents. ADHTt has a strict requirement for NAD(H) as the coenzyme, a preference for reduction of aromatic ketones and α-keto esters, and poor activity on aromatic alcohols and aldehydes. This thermophilic enzyme catalyzes the following reactions with Prelog specificity: the reduction of acetophenone, 2,2,2-trifluoroacetophenone, α-tetralone, and α-methyl and α-ethyl benzoylformates to (S)-(−)-1-phenylethanol (>99% enantiomeric excess [ee]), (R)-α-(trifluoromethyl)benzyl alcohol (93% ee), (S)-α-tetralol (>99% ee), methyl (R)-(−)-mandelate (92% ee), and ethyl (R)-(−)-mandelate (95% ee), respectively, by way of an efficient in situ NADH-recycling system involving 2-propanol and a second thermophilic ADH. This study further supports the critical role of the D37 residue in discriminating NAD(H) from NADP(H) in members of the SDR superfamily.
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Kisiela, Michael, Annette Faust, Bettina Ebert, Edmund Maser, and Axel J. Scheidig. "Crystal structure and catalytic characterization of the dehydrogenase/reductase SDR family member 4 ( DHRS 4) from Caenorhabditis elegans." FEBS Journal 285, no. 2 (November 28, 2017): 275–93. http://dx.doi.org/10.1111/febs.14337.

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41

Isotani, Kentaro, Junji Kurokawa, Fumiko Suzuki, Syunsuke Nomoto, Takashi Negishi, Michiko Matsuda, and Nobuya Itoh. "Gene Cloning and Characterization of Two NADH-Dependent 3-Quinuclidinone Reductases from Microbacterium luteolum JCM 9174." Applied and Environmental Microbiology 79, no. 4 (December 21, 2012): 1378–84. http://dx.doi.org/10.1128/aem.03099-12.

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ABSTRACTWe used the resting-cell reaction to screen approximately 200 microorganisms for biocatalysts which reduce 3-quinuclidinone to optically pure (R)-(−)-3-quinuclidinol.Microbacterium luteolumJCM 9174 was selected as the most suitable organism. The genes encoding the protein products that reduced 3-quinuclidinone were isolated fromM. luteolumJCM 9174. ThebacCgene, which consists of 768 nucleotides corresponding to 255 amino acid residues and is a constituent of the bacilysin synthetic gene cluster, was amplified by PCR based on homology to known genes. Theqnrgene consisted of 759 nucleotides corresponding to 252 amino acid residues. Both enzymes belong to the short-chain alcohol dehydrogenase/reductase (SDR) family. The genes were expressed inEscherichia colias proteins which were His tagged at the N terminus, and the recombinant enzymes were purified and characterized. Both enzymes showed narrow substrate specificity and high stereoselectivity for the reduction of 3-quinuclidinone to (R)-(−)-3-quinuclidinol.
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42

Gao, Miaomiao, Kaili Nie, Meng Qin, Haijun Xu, Fang Wang, and Luo Liu. "Molecular Mechanism Study on Stereo-Selectivity of α or β Hydroxysteroid Dehydrogenases." Crystals 11, no. 3 (February 25, 2021): 224. http://dx.doi.org/10.3390/cryst11030224.

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Hydroxysteroid dehydrogenases (HSDHs) are from two superfamilies of short-chain dehydrogenase (SDR) and aldo–keto reductase (AKR). The HSDHs were summarized and classified according to their structural and functional differences. A typical pair of enzymes, 7α–hydroxysteroid dehydrogenase (7α–HSDH) and 7β–hydroxysteroid dehydrogenase (7β–HSDH), have been reported before. Molecular docking of 7-keto–lithocholic acid(7–KLA) to the binary of 7β–HSDH and nicotinamide adenine dinucleotide phosphate (NADP+) was realized via YASARA, and a possible binding model of 7β–HSDH and 7–KLA was obtained. The α side of 7–KLA towards NADP+ in 7β–HSDH, while the β side of 7–KLA towards nicotinamide adenine dinucleotide (NAD+) in 7α–HSDH, made the orientations of C7–OH different in products. The interaction between Ser193 and pyrophosphate of NAD(P)+ [Ser193–OG⋯3.11Å⋯O1N–PN] caused the upturning of PN–phosphate group, which formed a barrier with the side chain of His95 to make 7–KLA only able to bind to 7β–HSDH with α side towards nicotinamide of NADP+. A possible interaction of Tyr253 and C24 of 7–KLA may contribute to the formation of substrate binding orientation in 7β–HSDH. The results of sequence alignment showed the conservation of His95, Ser193, and Tyr253 in 7β–HSDHs, exhibiting a significant difference to 7α–HSDHs. The molecular docking of other two enzymes, 17β–HSDH from the SDR superfamily and 3(17)α–HSDH from the AKR superfamily, has furtherly verified that the stereospecificity of HSDHs was related to the substrate binding orientation.
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43

Pampa, Kudigana J., Neratur K. Lokanath, Naoki Kunishima, and Ravishankar Vittal Rai. "The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase fromThermus thermophilusHB8." Acta Crystallographica Section D Biological Crystallography 70, no. 4 (March 19, 2014): 994–1004. http://dx.doi.org/10.1107/s1399004713034925.

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2-Keto-3-deoxygluconate (KDG) is one of the important intermediates in pectin metabolism. An enzyme involved in this pathway, 3-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (DDGDH), has been identified which converts 2,5-diketo-3-deoxygluconate to KDG. The enzyme is a member of the short-chain dehydrogenase (SDR) family. To gain insight into the function of this enzyme at the molecular level, the first crystal structure of DDGDH fromThermus thermophilusHB8 has been determined in the apo form, as well as in complexes with the cofactor and with citrate, by X-ray diffraction methods. The crystal structures reveal a tight tetrameric oligomerization. The secondary-structural elements and catalytically important residues of the enzyme were highly conserved amongst the proteins of the NAD(P)-dependent SDR family. The DDGDH protomer contains a dinucleotide-binding fold which binds the coenzyme NAD+in an intersubunit cleft; hence, the observed oligomeric state might be important for the catalytic function. This enzyme prefers NAD(H) rather than NADP(H) as the physiological cofactor. A structural comparison of DDGDH with mouse lung carbonyl reductase suggests that a significant difference in the α–loop–α region of this enzyme is associated with the coenzyme specificity. The structural data allow a detailed understanding of the functional role of the conserved catalytic triad (Ser129–Tyr144–Lys148) in cofactor and substrate recognition, thus providing substantial insights into DDGDH catalysis. From analysis of the three-dimensional structure, intersubunit hydrophobic interactions were found to be important for enzyme oligomerization and thermostability.
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44

Vögeli, Bastian, Raoul G. Rosenthal, Gabriele M. M. Stoffel, Tristan Wagner, Patrick Kiefer, Niña Socorro Cortina, Seigo Shima, and Tobias J. Erb. "InhA, the enoyl-thioester reductase from Mycobacterium tuberculosis forms a covalent adduct during catalysis." Journal of Biological Chemistry 293, no. 44 (September 14, 2018): 17200–17207. http://dx.doi.org/10.1074/jbc.ra118.005405.

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The enoyl-thioester reductase InhA catalyzes an essential step in fatty acid biosynthesis of Mycobacterium tuberculosis and is a key target of antituberculosis drugs to combat multidrug-resistant M. tuberculosis strains. This has prompted intense interest in the mechanism and intermediates of the InhA reaction. Here, using enzyme mutagenesis, NMR, stopped-flow spectroscopy, and LC–MS, we found that the NADH cofactor and the CoA thioester substrate form a covalent adduct during the InhA catalytic cycle. We used the isolated adduct as a molecular probe to directly access the second half-reaction of the catalytic cycle of InhA (i.e. the proton transfer), independently of the first half-reaction (i.e. the initial hydride transfer) and to assign functions to two conserved active-site residues, Tyr-158 and Thr-196. We found that Tyr-158 is required for the stereospecificity of protonation and that Thr-196 is partially involved in hydride transfer and protonation. The natural tendency of InhA to form a covalent C2-ene adduct calls for a careful reconsideration of the enzyme's reaction mechanism. It also provides the basis for the development of effective tools to study, manipulate, and inhibit the catalytic cycle of InhA and related enzymes of the short-chain dehydrogenase/reductase (SDR) superfamily. In summary, our work has uncovered the formation of a covalent adduct during the InhA catalytic cycle and identified critical residues required for catalysis, providing further insights into the InhA reaction mechanism important for the development of antituberculosis drugs.
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45

Kallberg, Yvonne, Udo Oppermann, Hans Jörnvall, and Bengt Persson. "Short-chain dehydrogenase/reductase (SDR) relationships: A large family with eight clusters common to human, animal, and plant genomes." Protein Science 11, no. 3 (April 13, 2009): 636–41. http://dx.doi.org/10.1110/ps.26902.

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46

Endo, Satoshi, Yoshifumi Morikawa, Yudai Kudo, Koichi Suenami, Toshiyuki Matsunaga, Akira Ikari, and Akira Hara. "Human dehydrogenase/reductase SDR family member 11 (DHRS11) and aldo-keto reductase 1C isoforms in comparison: Substrate and reaction specificity in the reduction of 11-keto-C19-steroids." Journal of Steroid Biochemistry and Molecular Biology 199 (May 2020): 105586. http://dx.doi.org/10.1016/j.jsbmb.2020.105586.

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47

Peng, Junbo, Janith V. S. Aluthmuhandiram, K. W. Thilini Chethana, Qi Zhang, Qikai Xing, Hui Wang, Mei Liu, Wei Zhang, Xinghong Li, and Jiye Yan. "An NmrA-Like Protein, Lws1, Is Important for Pathogenesis in the Woody Plant Pathogen Lasiodiplodia theobromae." Plants 11, no. 17 (August 24, 2022): 2197. http://dx.doi.org/10.3390/plants11172197.

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The NmrA-like proteins have been reported to be important nitrogen metabolism regulators and virulence factors in herbaceous plant pathogens. However, their role in the woody plant pathogen Lasiodiplodia theobromae is less clear. In the current study, we identified a putative NmrA-like protein, Lws1, in L. theobromae and investigated its pathogenic role via gene silencing and overexpression experiments. We also evaluated the effects of external carbon and nitrogen sources on Lws1 gene expression via qRT-PCR assays. Moreover, we analyzed the molecular interaction between Lws1 and its target protein via the yeast two-hybrid system. The results show that Lws1 contained a canonical glycine-rich motif shared by the short-chain dehydrogenase/reductase (SDR) superfamily proteins and functioned as a negative regulator during disease development. Transcription profiling revealed that the transcription of Lws1 was affected by external nitrogen and carbon sources. Interaction analyses demonstrated that Lws1 interacted with a putative GATA family transcription factor, LtAreA. In conclusion, these results suggest that Lws1 serves as a critical regulator in nutrition metabolism and disease development during infection.
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48

Orduña, Patricia, Antonia I. Castillo-Rodal, Martha E. Mercado, Samuel Ponce de León, and Yolanda López-Vidal. "Specific Proteins in Nontuberculous Mycobacteria: New Potential Tools." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/964178.

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Nontuberculous mycobacteria (NTM) have been isolated from water, soil, air, food, protozoa, plants, animals, and humans. Although most NTM are saprophytes, approximately one-third of NTM have been associated with human diseases. In this study, we did a comparative proteomic analysis among five NTM strains isolated from several sources. There were different numbers of protein spots fromM. gordonae(1,264),M. nonchromogenicumtype I (894),M. nonchromogenicumtype II (935),M. peregrinum(806), andM. scrofulaceum/Mycobacterium mantenii(1,486) strains, respectively. We identified 141 proteins common to all strains and specific proteins to each NTM strain. A total of 23 proteins were selected for its identification. Two of the common proteins identified (short-chain dehydrogenase/reductase SDR and diguanylate cyclase) did not align withM. tuberculosiscomplex protein sequences, which suggest that these proteins are found only in the NTM strains. Some of the proteins identified as common to all strains can be used as markers of NTM exposure and for the development of new diagnostic tools. Additionally, the specific proteins to NTM strains identified may represent potential candidates for the diagnosis of diseases caused by these mycobacteria.
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49

Lee, Jung-Kul, Bong-Seong Koo, Sang-Yong Kim, and Hyung-Hwan Hyun. "Purification and Characterization of a Novel Mannitol Dehydrogenase from a Newly Isolated Strain of Candida magnoliae." Applied and Environmental Microbiology 69, no. 8 (August 2003): 4438–47. http://dx.doi.org/10.1128/aem.69.8.4438-4447.2003.

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ABSTRACT Mannitol biosynthesis in Candida magnoliae HH-01 (KCCM-10252), a yeast strain that is currently used for the industrial production of mannitol, is catalyzed by mannitol dehydrogenase (MDH) (EC 1.1.1.138). In this study, NAD(P)H-dependent MDH was purified to homogeneity from C. magnoliae HH-01 by ion-exchange chromatography, hydrophobic interaction chromatography, and affinity chromatography. The relative molecular masses of C. magnoliae MDH, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and size-exclusion chromatography, were 35 and 142 kDa, respectively, indicating that the enzyme is a tetramer. This enzyme catalyzed both fructose reduction and mannitol oxidation. The pH and temperature optima for fructose reduction and mannitol oxidation were 7.5 and 37°C and 10.0 and 40°C, respectively. C. magnoliae MDH showed high substrate specificity and high catalytic efficiency (k cat = 823 s−1, K m = 28.0 mM, and k cat /K m = 29.4 mM−1 s−1) for fructose, which may explain the high mannitol production observed in this strain. Initial velocity and product inhibition studies suggest that the reaction proceeds via a sequential ordered Bi Bi mechanism, and C. magnoliae MDH is specific for transferring the 4-pro-S hydrogen of NADPH, which is typical of a short-chain dehydrogenase reductase (SDR). The internal amino acid sequences of C. magnoliae MDH showed a significant homology with SDRs from various sources, indicating that the C. magnoliae MDH is an NAD(P)H-dependent tetrameric SDR. Although MDHs have been purified and characterized from several other sources, C. magnoliae MDH is distinguished from other MDHs by its high substrate specificity and catalytic efficiency for fructose only, which makes C. magnoliae MDH the ideal choice for industrial applications, including enzymatic synthesis of mannitol and salt-tolerant plants.
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50

Zhang, Hui, Bei Wang, Shengli Yang, Hongwei Yu, and Lidan Ye. "Enhancing Acetophenone Tolerance of Anti-Prelog Short-Chain Dehydrogenase/Reductase EbSDR8 Using a Whole-Cell Catalyst by Directed Evolution." Catalysts 12, no. 9 (September 19, 2022): 1071. http://dx.doi.org/10.3390/catal12091071.

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The short-chain dehydrogenase/reductase (SDR) from Empedobacter brevis ZJUY-1401 (EbSDR8, GenBank: ALZ42979.1) is a promising biocatalyst for the reduction of acetophenone to (R)-1-phenylethanol, but its industrial application is restricted by its insufficient tolerance to acetophenone. In this paper, we developed a chromogenic reaction-based high-throughput screening method and employed directed evolution to enhance the acetophenone tolerance of EbSDR8. The resulting variant, M190V, showed 74.8% improvement over the wild-type in specific activity when catalyzing the reduction of 200 mM acetophenone. Kinetic analysis revealed a 70% enhancement in its catalytic efficiency (kcat/Km). Molecular docking was conducted to reveal the possible mechanism behind the improved acetophenone tolerance, and the result implied that the M190V mutation is conducive to the binding and release of coenzyme. Aside from the improved catalytic performance when dealing with a high concentration of acetophenone, other features of M190V, such as a broad pH range (6.0 to 10.5), low optimal cosubstrate concentration (1% isopropanol), and a temperature optimum close to that of E. coli cells (35 °C), also contribute to its practical application as a whole-cell catalyst. In this study, we first designed a directed evolution means to engineer the enzyme and obtained the positive variant which has a high activity under high concentrations of acetophenone. After that, we optimized the catalytic performance of the variant to adapt to industrial applications.
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