Academic literature on the topic 'Short-chain dehydrogenase/reductase (SDR)'
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Journal articles on the topic "Short-chain dehydrogenase/reductase (SDR)"
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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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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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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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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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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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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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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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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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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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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.
Dissertations / Theses on the topic "Short-chain dehydrogenase/reductase (SDR)"
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Olandersson, Sandra. "Evaluation of Machine Learning Algorithms for Classification of Short-Chain Dehydrogenase/Reductase Protein Sequences." Thesis, Blekinge Tekniska Högskola, Institutionen för programvaruteknik och datavetenskap, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:bth-3828.
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The classification of protein sequences is a subfield in the area of Bioinformatics that attracts a substantial interest today. Machine Learning algorithms are here believed to be able to improve the performance of the classification phase. This thesis considers the application of different Machine Learning algorithms to the classification problem of a data set of short-chain dehydrogenases/reductases (SDR) proteins. The classification concerns both the division of the proteins into the two main families, Classic and Extended, and into their different subfamilies. The results of the different algorithms are compared to select the most appropriate algorithm for this particular classification problem.Klassificeringen av proteinsekvenser är ett område inom Bioinformatik, vilket idag drar till sig ett stort intresse. Maskininlärningsalgoritmer anses här kunna förbättra utförandet av klassificeringsfasen. Denna uppsats rör tillämpandet av olika maskininlärningsalgoritmer för klassificering av ett dataset med short-chain dehydrogenases/reductases (SDR) proteiner. Klassificeringen rör både indelningen av proteinerna i två huvudklasser, Classic och Extended, och deras olika subklasser. Resultaten av de olika algoritmerna jämförs för att välja ut den mest lämpliga algoritmen för detta specifika klassificeringsproblem.
Sandra Olandersson Blåbärsvägen 27 372 38 Ronneby home: 0457-12084
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ROTONDO, ROSSELLA. "New enzymatic pathway(s) in 4-hydroxynonenal metabolism." Doctoral thesis, Università di Siena, 2017. http://hdl.handle.net/11365/1007903.
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The main effect of lipid peroxidation, which often occurs in response to oxidative stress, is the production of different toxic aldehydes. In particular, over the years, the lipid peroxidation-derived aldehyde 4-hydroxy-trans-2-nonenal (HNE) has received much attention for its dual role in the pathogenesis of several diseases and as signaling molecule. HNE metabolism is reported to mainly occur through its conjugation with glutathione (GSH) and the subsequent formation of 3-glutathionyl-4-hydroxynonanal (GSHNE) [1, 2]. This molecule is susceptible to both oxidative and reductive transformations, which occur through the action of either the NADPH-dependent activity of aldose reductase (AKR1B1) [1] or through the NAD(P)+ -dependent activity of aldehyde dehydrogenase, respectively [3, 4]. Recently, we have demonstrated the implication of a new NADP+-dependent enzymatic activity able to oxidize GSHNE to its corresponding acid 3-glutathionyl-nonanoic-γ-lactone (GSHNA-γ-lactone) [5]. The enzyme was purified from a human astrocytoma cells line (ADF) to electrophoretic homogeneity as protein doublet in SDS-PAGE, with an apparent molecular weight of 31-32 kDa. Proteomic analysis identified both proteins as human CBR1, also known as NADP+ 15-hydroxyprostaglandine dehydrogenase with 74% of homology and proved their migration differences due to the occurrence of a carboxyethyl moiety at Lys239 [5]. This modification has been already described for the human enzyme and has been demonstrated to have no effect on the protein activity and specificity [6, 7]. The enzyme efficiently catalyzes the oxidation of GSHNE, while it is practically inactive towards 4-hydroxy trans-2-nonenal and other HNE-S-thiolated adducts containing an incomplete glutathionyl moiety [5]. Nucleotide sequence analysis of hCBR1 cDNA from ADF cells completely matched with the human wild type counterpart [5], excluding any gain-of-function mutations in the cDNA-derived protein sequence of hCBR1 [8, 9]. Highly purified human recombinant carbonyl reductase 1 (E.C. 1.1.1.184, hCBR1), which preserves its ability to oxidize specifically GSHNE, is also shown to efficiently act as aldehyde reductase on glutathionylated alkanals, namely 3-glutathionyl-4-hydroxynonanal (GSHNE), 3-glutathionyl-nonanal, 3-glutathionyl-hexanal and 3-glutathionyl-propanal [10]. The presence of the glutathionyl moiety appears as a necessary requirement for the susceptibility of these compounds to the NADPH-dependent reduction by hCBR1. In fact the corresponding alkanals and alkenals, and the cysteinyl and γ-glutamyl-cysteinyl alkanals adducts were either ineffective or very poorly active as CBR1 substrates [10]. Mass spectrometry analysis reveals the ability of hCBR1 to reduce GSHNE to the corresponding 3-glutathionyl-1,4-dihydroxynonane (GSDHN) and at the same time to catalyze the oxidation of the hemiacetal form of GSHNE, generating the 3-glutathionylnonanoic-γ-lactone. These data are indicative of the ability of the enzyme to catalyze a disproportion reaction of the substrate through the redox recycle of the pyridine cofactor [10]. A rationale for the observed preferential activity of hCBR1 on different GSHNE diastereoisomers is given by molecular modelling. These results evidence the potential of hCBR1 acting on GSHNE to accomplish a dual role, both in terms of HNE detoxification and, through the production of GSDHN, in terms of involvement into the signalling cascade of the cellular inflammatory response.
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Gong, Wenjie [Verfasser]. "Characterization of the LysR-type Transcriptional Regulator HsdR Gene and Its Adjacent Short-chain Dehydrogenase, Reductase SDRx Gene in Comamonas testosteroni ATCC 11996 / Wenjie Gong." Kiel : Universitätsbibliothek Kiel, 2011. http://d-nb.info/1020244666/34.
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Scherbak, Nikolai, Anneli Ala-Häiväla, Mikael Brosché, Nathalie Böwer, Hilja Strid, John R. Gittins, Elin M. Grahn, Leif A. Eriksson, and Åke Strid. "The pea SAD short-chain dehydrogenase/reductase : quinone reduction, tissue distribution, and heterologous expression." Örebro universitet, Akademin för naturvetenskap och teknik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-15765.
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The pea (Pisum sativum) tetrameric short-chain alcohol dehydrogenase-like protein (SAD) family consists of at least three highly similar members (SAD-A, -B, and -C). According to mRNA data, environmental stimuli induce SAD expression. The aim of this study was to characterize the SAD proteins by examining their catalytic function, distribution in pea, and induction in different tissues. In enzyme activity assays using a range of potential substrates, the SAD-C enzyme was shown to reduce one- or two-ring-membered quinones lacking long hydrophobic hydrocarbon tails. Immunological assays using a specific antiserum against the protein demonstrated that different tissues and cell types contain small amounts of SAD protein that was predominantly located within epidermal or subepidermal cells and around vascular tissue. Particularly high local concentrations were observed in the protoderm of the seed cotyledonary axis. Two bow-shaped rows of cells in the ovary and the placental surface facing the ovule also exhibited considerable SAD staining. Ultraviolet-B irradiation led to increased staining in epidermal and subepidermal cells of leaves and stems. The different localization patterns of SAD suggest functions both in development and in responses to environmental stimuli. Finally, the pea SAD-C promoter was shown to confer heterologous wound-induced expression in Arabidopsis (Arabidopsis thaliana), which confirmed that the inducibility of its expression is regulated at the transcriptional level.
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Luba, James. "Studies of Leishmania major Pteridine Reductase 1, a Novel Short Chain Dehydrogenase." eScholarship@UMMS, 1997. https://escholarship.umassmed.edu/gsbs_diss/45.
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Pteridine reductase 1 (PTR1) is an NADPH dependent reductase that catalyzes the reduction of several pterins and folates. The gene encoding this enzyme was originally identified in Leishmania based on its ability to provide resistance to the drug methotrexate (MTX). The DNA and amino acid sequences are known, and overproducing strains of Escherichia coli are available. PTR1 has been previously shown to be required for the salvage of oxidized pteridines (folate, biopterin, and others). Since Leishmaniaare folate and pterin auxotrophes, PTR1 is a possible target for novel anti-folate drugs for the treatment of leishmaniasis.
PTR1 catalyzes the transfer of hydride from NADPH to the 2-amino-4-oxo-pteridine ring system yielding 7, 8-dihydropteridines, and to the pteridine ring system of 7, 8-dihydropteridines yielding 5,6, 7, 8-tetrahydropteridines. PTR1 shows a pH dependent substrate specificity. At pH 4.6 the specific activity of PTR1 is highest with pterins, while at pH 6.0 the specific activity of PTR1 was highest with folates.
The sequence of PTR1 is only 20-30% homologous to the sequences of members of the short chain dehydrogenase/reductase enzyme family. Although this is typical for members of this enzyme family, it does not allow for unambiguous classification in this family. In fact, when the DNA sequence of PTR1was first determined, PTR1 was classified as an aldoketo reductase. To classify PTR1 definitively, further biochemical characterization was required. To provide this information, the work described here was undertaken: (i) the stereochemical and kinetic course of PTR1 was determined; (ii) residues important in catalysis and ligand binding were identified; and (iii) conditions for the crystallization of PTR1 were developed.
The stereochemistry of hydride transfer
The use of [3H]-folate, showed that the ultimate product of PTR1 was 5, 6, 7, 8-tetrahydrofolate. 4R-[3H]-NADPH and 4S-[3H]-NADPH were synthesized enzymatically and used as the cofactor for the reduction of folate. PTR1 was coupled to thymidylate synthase (TS), and tritium from 4S-[3H]-NADPH was transferred to thymidylate. Therefore, the pro-S hydride of NADPH was transferred to the si face of dihydrofolate (DHF; see figure I-1). The transfer of the pro-Shydride indicates that PTR1 is a B-side dehydrogenase which is consistent with its membership in the short chain dehydrogenase (SDR) family.
The kinetic mechanism of PTR1
When NADPH was varied at several fixed concentrations of folate (and vice-versa) V/K (Vmax/KM) showed a dependence upon concentration of the fixed substrate. This is consistent with a ternary complex mechanism, in contrast to a substituted enzyme mechanism that exhibits no dependence of V/K on fixed substrate. Product inhibition patterns using NADP+ and 5-deazatetrahydrofolate (5dTHF, a stable product analog) were consistent with an ordered ternary complex mechanism in which NADPH binds first and NADP+ dissociates last. However, an enzyme-DHF binary complex was detected by fluorescence. Isotope partitioning experiments showed that the enzyme-DHF binary complex was not catalytically competent whereas the enzyme-NADPH complex was. Measurement of the tritium isotope effect on V/K (T(V/K)) at high and low dihydrofolate confirmed that PTR1 proceeds via a steady state ordered mechanism. Rapid quench analysis showed that dihydrofolate was a transient intermediate during the reduction of folate to tetrahydrofolate and that folate reduction is biphasic.
Catalytic Residues of PTR1
The amino acid sequences of dihydropteridine reductase and 3-α, 20-β, hydroxy steroid dehydrogenase were aligned to that of PTR1. Based on the results of the alignment, site directed mutagenesis was used to investigate the role of specific residues in the catalytic cycle of PTR1. Variant enzymes were screened based on their ability to rescue a dihydrofolate reductase (DHFR) deficient strain of E. coli. Selected PTR1 variants (some complementing and some non-complementing) were purified and further characterized. Tyrosine 193 of the wild type enzyme was found to be involved in the reduction of pteridines, but not in the reduction of 7, 8-dihydropteridines, and eliminated the substrate inhibition of 7, 8-dihydropteridines observed with the wild type enzyme. Both PTR1(K197Q) and PTR1(Y193F/K197Q) had decreased activity for all substrates and low affinity for NADPH. In contrast to the wild type enzyme, NADPH displayed substrate inhibition towards PTR1(K197Q). All PTR1(D180) variants that were purified were inactive except for PTR1(D180C), which showed 2.5% of wild type activity with DHF. The binary complexes of PTR1(D180A) and PTR1(D180S) with NADPH showed a decrease in affinity for folate. Based on the kinetic properties of the PTR1 variants, roles for Y193, K197, and D180 are proposed. In conjunction with D180, Y193 acts as a proton donor to N8 of folate. K197 forms hydrogen bonds with NADPH in the active site and lowers the pKaof Y193. D180 participates in the protonation of N8 of folate and N5 of DHF.
Crystallization of PTR1 and PTR1-ligand complexes
The crystallization of PTR1 from L. major and L. tarentolea as unliganded and as binary and ternary complexes was attempted. Several crystal forms were obtained including L. major PTR1-NADPH-MTX crystals that diffracted to ~ 3.2 Å resolution. It was not possible to collect a full data set of any of the crystals. At their current stage, none of the crystal forms is suitable for structural work.
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Keller, Brigitte D. "Search for new steroid hormone metabolizing enzymes functional genomics of the short chain dehydrogenase, reductase superfamily /." [S.l.] : [s.n.], 2006. http://mediatum2.ub.tum.de/doc/603773/document.pdf.
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Hoffmann, Frank [Verfasser]. "Carbonyl Reductases and Pluripotent Hydroxysteroid Dehydrogenases of the Short-Chain Dehydrogenase/Reductase Superfamily : Structural Aspects of Oligomerization in 3-Hydroxysteroid Dehydrogenase/Carbonyl Reductase from Comamonas testosteroni / Frank Hoffmann." Hamburg : Diplom.de, 2009. http://d-nb.info/1117660591/34.
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Takase, Ryuichi. "Studies on Structure-Function Relationship and Conversion of Coenzyme Requirement in Bacterial α-Keto Acid Reductases Responsible for Metabolism of Acidic Polysaccharides." Kyoto University, 2015. http://hdl.handle.net/2433/200458.
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Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第19195号
農博第2134号
新制||農||1034(附属図書館)
学位論文||H27||N4941(農学部図書室)
32187
京都大学大学院農学研究科食品生物科学専攻
(主査)教授 谷 史人, 教授 保川 清, 准教授 橋本 渉
学位規則第4条第1項該当
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Jacob, Asha Ivy. "STUDY OF SHORT CHAIN DEHYDROGENASE / REDUCTASES (SDRs) IN SINORHIZOBIUM MELILOTI." Thesis, 2007. http://hdl.handle.net/10012/3346.
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Sinorhizobium meliloti maintains a complex lifestyle, including saprotrophy, rhizophere colonization and root hair infection leading to the formation of root nodules in which the plant provides sustenance in return for nitrogen fixation. S. meliloti cells use a variety of carbon substrates for growth; this omnivory probably contributes to competitive ability in the soil. Several candidates for contribution to the catabolic capacity are found within the family of short chain dehydrogenases /reductases (SDR), which catalyze NAD(P)(H) dependent oxidation / reduction reactions.
The 6.7 Mb genome of S. meliloti contains 78 SDR-encoding genes distributed on all three replicons. In this work each of these genes were disrupted by single crossover mutagenesis. These mutants were screened for growth on 93 different compounds as carbon source, and phenotypes were found for 17 of the mutants, providing suggestions for potential substrates of the corresponding enzymes. Carbon sources for which phenotype was observed include sugar alcohols, leucine, lysine, ornithine, galactitol, rhamnose, arabinose, mono-methyl succinate and ribono-γ-lactone. In addition, one of the mutants was found to be a proline auxotroph. In several cases, the phenotypes were consistent with the phenotypes of deletion mutants in which large sections of pSymB were absent. Eight of the mutants exhibited symbiotic deficiency after inoculation of alfalfa, while viable cells of three of the mutants could not be isolated from the nodules even though nitrogen fixation occurred. The results suggest that the corresponding SDR enzymes are involved in a pathway that is required for maintenance of viability by cells throughout infection and nodule development.
This work demonstrates that members of the SDR family contribute to both the catabolic capacity and the symbiotic interactions of S. meliloti. Further experiments will address the details of the biochemical pathways involved. Knowledge of the substrate specificities of these enzymes should also prove informative in the description and annotation of orthologs that are identified in other genome sequences.
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Cho, Yen-Ching, and 卓燕菁. "Stereoselective production of phenylephrine by short-chain dehydrogenase/reductase from Serratia quinivorans BCRC 14811." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/70482776642221323026.
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碩士國立中興大學
生命科學院碩士在職專班
98
In order to avoid involved in the chemical synthesis method, the present study was designed to use a biotransformation approach to produce L-PE from 1-(3-hydroxyphenyl)-2-(methylamino) ethanone (HPMAE). We found that S. quinivorans BCRC 14811 could convert HPMAE to L-PE with 15% of yield. Addition of 2-phenylethanol and acetophenone in the culture medium could increase conversion yield from 15% to 88% and 83%, respectively. A genomic library of S. quinivorans BCRC 14811 was constructed for the screening of clones capable of converting HPMAE to PE using pQE30 as cloning vector and HPMAE-sensitive Escherichia coli NovaBlue as host cell. Luria-Bertani plate containing 1 to 10 mM HPMAE were used as the selection medium. However no positive clone was obtained. Short-chain dehydrogenase / reductase (SDR) was cloned from S. quinivorans BCRC 14811 by PCR. When the sdr gene was expressed in E. coli BL21(DE3), the recombinant E. coli cell can convert 10 mM HPMAE to 8.9 mM D-PE with a yield of about 89% and 60 mM HPMAE to 56.2 mM D-PE with a conversion yield of 94%. The SDR was purified by immobilized metal affinity chromatography. Enzyme activity assay demonstrated that the SDR protein could uses NADPH and NADH as cofactors, which exhibit a specific activities of 257 U/mg and 285 U/mg, respectively.
Book chapters on the topic "Short-chain dehydrogenase/reductase (SDR)"
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Furnham, Nicholas, Gemma L. Holliday, and Janet M. Thornton. "The NAD Binding Domain and the Short-Chain Dehydrogenase/Reductase (SDR) Superfamily." In Protein Families, 191–206. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118743089.ch8.
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Whiteley, John M., Nguyen H. Xuong, and Kottayil I. Varughese. "Is Dihydropteridine Reductase an Anomalous Dihydrofolate Reductase, a Flavin-Like Enzyme, or a Short-Chain Dehydrogenase?" In Advances in Experimental Medicine and Biology, 115–21. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2960-6_23.
Full textReports on the topic "Short-chain dehydrogenase/reductase (SDR)"
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Or, Etti, David Galbraith, and Anne Fennell. Exploring mechanisms involved in grape bud dormancy: Large-scale analysis of expression reprogramming following controlled dormancy induction and dormancy release. United States Department of Agriculture, December 2002. http://dx.doi.org/10.32747/2002.7587232.bard.
Full textAbstract:
The timing of dormancy induction and release is very important to the economic production of table grape. Advances in manipulation of dormancy induction and dormancy release are dependent on the establishment of a comprehensive understanding of biological mechanisms involved in bud dormancy. To gain insight into these mechanisms we initiated the research that had two main objectives: A. Analyzing the expression profiles of large subsets of genes, following controlled dormancy induction and dormancy release, and assessing the role of known metabolic pathways, known regulatory genes and novel sequences involved in these processes B. Comparing expression profiles following the perception of various artificial as well as natural signals known to induce dormancy release, and searching for gene showing similar expression patterns, as candidates for further study of pathways having potential to play a central role in dormancy release. We first created targeted EST collections from V. vinifera and V. riparia mature buds. Clones were randomly selected from cDNA libraries prepared following controlled dormancy release and controlled dormancy induction and from respective controls. The entire collection (7920 vinifera and 1194 riparia clones) was sequenced and subjected to bioinformatics analysis, including clustering, annotations and GO classifications. PCR products from the entire collection were used for printing of cDNA microarrays. Bud tissue in general, and the dormant bud in particular, are under-represented within the grape EST database. Accordingly, 59% of the our vinifera EST collection, composed of 5516 unigenes, are not included within the current Vitis TIGR collection and about 22% of these transcripts bear no resemblance to any known plant transcript, corroborating the current need for our targeted EST collection and the bud specific cDNA array. Analysis of the V. riparia sequences yielded 814 unigenes, of which 140 are unique (keilin et al., manuscript, Appendix B). Results from computational expression profiling of the vinifera collection suggest that oxidative stress, calcium signaling, intracellular vesicle trafficking and anaerobic mode of carbohydrate metabolism play a role in the regulation and execution of grape-bud dormancy release. A comprehensive analysis confirmed the induction of transcription from several calcium–signaling related genes following HC treatment, and detected an inhibiting effect of calcium channel blocker and calcium chelator on HC-induced and chilling-induced bud break. It also detected the existence of HC-induced and calcium dependent protein phosphorylation activity. These data suggest, for the first time, that calcium signaling is involved in the mechanism of dormancy release (Pang et al., in preparation). We compared the effects of heat shock (HS) to those detected in buds following HC application and found that HS lead to earlier and higher bud break. We also demonstrated similar temporary reduction in catalase expression and temporary induction of ascorbate peroxidase, glutathione reductase, thioredoxin and glutathione S transferase expression following both treatments. These findings further support the assumption that temporary oxidative stress is part of the mechanism leading to bud break. The temporary induction of sucrose syntase, pyruvate decarboxylase and alcohol dehydrogenase indicate that temporary respiratory stress is developed and suggest that mitochondrial function may be of central importance for that mechanism. These finding, suggesting triggering of identical mechanisms by HS and HC, justified the comparison of expression profiles of HC and HS treated buds, as a tool for the identification of pathways with a central role in dormancy release (Halaly et al., in preparation). RNA samples from buds treated with HS, HC and water were hybridized with the cDNA arrays in an interconnected loop design. Differentially expressed genes from the were selected using R-language package from Bioconductor project called LIMMA and clones showing a significant change following both HS and HC treatments, compared to control, were selected for further analysis. A total of 1541 clones show significant induction, of which 37% have no hit or unknown function and the rest represent 661 genes with identified function. Similarly, out of 1452 clones showing significant reduction, only 53% of the clones have identified function and they represent 573 genes. The 661 induced genes are involved in 445 different molecular functions. About 90% of those functions were classified to 20 categories based on careful survey of the literature. Among other things, it appears that carbohydrate metabolism and mitochondrial function may be of central importance in the mechanism of dormancy release and studies in this direction are ongoing. Analysis of the reduced function is ongoing (Appendix A). A second set of hybridizations was carried out with RNA samples from buds exposed to short photoperiod, leading to induction of bud dormancy, and long photoperiod treatment, as control. Analysis indicated that 42 genes were significant difference between LD and SD and 11 of these were unique.