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de Carvalho CC, Murray IP, Nguyen H, Nguyen T, Cantu DC. Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms. Proteins 2024; 92:157-169. [PMID: 37776148 DOI: 10.1002/prot.26599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023]
Abstract
Acyltransferases (AT) are enzymes that catalyze the transfer of acyl group to a receptor molecule. This review focuses on ATs that act on thioester-containing substrates. Although many ATs can recognize a wide variety of substrates, sequence similarity analysis allowed us to classify the ATs into fifteen distinct families. Each AT family is originated from enzymes experimentally characterized to have AT activity, classified according to sequence similarity, and confirmed with tertiary structure similarity for families that have crystallized structures available. All the sequences and structures of the AT families described here are present in the thioester-active enzyme (ThYme) database. The AT sequences and structures classified into families and available in the ThYme database could contribute to enlightening the understanding acyl transfer to thioester-containing substrates, most commonly coenzyme A, which occur in multiple metabolic pathways, mostly with fatty acids.
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Affiliation(s)
- Caio C de Carvalho
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| | - Ian P Murray
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| | - Hung Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama, USA
| | - Tin Nguyen
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
- Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama, USA
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
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2
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Wozniak JM, Li W, Governa P, Chen LY, Jadhav A, Dongre A, Forli S, Parker CG. Enhanced mapping of small-molecule binding sites in cells. Nat Chem Biol 2024:10.1038/s41589-023-01514-z. [PMID: 38167919 DOI: 10.1038/s41589-023-01514-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Photoaffinity probes are routinely utilized to identify proteins that interact with small molecules. However, despite this common usage, resolving the specific sites of these interactions remains a challenge. Here we developed a chemoproteomic workflow to determine precise protein binding sites of photoaffinity probes in cells. Deconvolution of features unique to probe-modified peptides, such as their tendency to produce chimeric spectra, facilitated the development of predictive models to confidently determine labeled sites. This yielded an expansive map of small-molecule binding sites on endogenous proteins and enabled the integration with multiplexed quantitation, increasing the throughput and dimensionality of experiments. Finally, using structural information, we characterized diverse binding sites across the proteome, providing direct evidence of their tractability to small molecules. Together, our findings reveal new knowledge for the analysis of photoaffinity probes and provide a robust method for high-resolution mapping of reversible small-molecule interactions en masse in native systems.
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Affiliation(s)
- Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Paolo Governa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Li-Yun Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Appaso Jadhav
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashok Dongre
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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3
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Singh R, Kundu P, Mishra VK, Singh BK, Bhattacharyya S, Das AK. Crystal structure of FadA2 thiolase from Mycobacterium tuberculosis and prediction of its substrate specificity and membrane-anchoring properties. FEBS J 2023; 290:3997-4022. [PMID: 37026388 DOI: 10.1111/febs.16792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/17/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023]
Abstract
Tuberculosis (TB) is one of the leading causes of human death caused by Mycobacterium tuberculosis (Mtb). Mtb can enter into a long-lasting persistence where it can utilize fatty acids as the carbon source. Hence, fatty acid metabolism pathway enzymes are considered promising and pertinent mycobacterial drug targets. FadA2 (thiolase) is one of the enzymes involved in Mtb's fatty acid metabolism pathway. FadA2 deletion construct (ΔL136-S150) was designed to produce soluble protein. The crystal structure of FadA2 (ΔL136-S150) at 2.9 Å resolution was solved and analysed for membrane-anchoring region. The four catalytic residues of FadA2 are Cys99, His341, His390 and Cys427, and they belong to four loops with characteristic sequence motifs, i.e., CxT, HEAF, GHP and CxA. FadA2 is the only thiolase of Mtb which belongs to the CHH category containing the HEAF motif. Analysing the substrate-binding channel, it has been suggested that FadA2 is involved in the β-oxidation pathway, i.e., the degradative pathway, as the long-chain fatty acid can be accommodated in the channel. The catalysed reaction is favoured by the presence of two oxyanion holes, i.e., OAH1 and OAH2. OAH1 formation is unique in FadA2, formed by the NE2 of His390 present in the GHP motif and NE2 of His341 present in the HEAF motif, whereas OAH2 formation is similar to CNH category thiolase. Sequence and structural comparison with the human trifunctional enzyme (HsTFE-β) suggests the membrane-anchoring region in FadA2. Molecular dynamics simulations of FadA2 with a membrane containing POPE lipid were conducted to understand the role of a long insertion sequence of FadA2 in membrane anchoring.
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Affiliation(s)
- Rashika Singh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Prasun Kundu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | | | - Bina Kumari Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Sudipta Bhattacharyya
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
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Fedoryshchak RO, Gorelik A, Shen M, Shchepinova MM, Pérez-Dorado I, Tate EW. Discovery of lipid-mediated protein-protein interactions in living cells using metabolic labeling with photoactivatable clickable probes. Chem Sci 2023; 14:2419-2430. [PMID: 36873846 PMCID: PMC9977449 DOI: 10.1039/d2sc06116c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023] Open
Abstract
Protein-protein interactions (PPIs) are essential and pervasive regulatory elements in biology. Despite the development of a range of techniques to probe PPIs in living systems, there is a dearth of approaches to capture interactions driven by specific post-translational modifications (PTMs). Myristoylation is a lipid PTM added to more than 200 human proteins, where it may regulate membrane localization, stability or activity. Here we report the design and synthesis of a panel of novel photocrosslinkable and clickable myristic acid analog probes, and their characterization as efficient substrates for human N-myristoyltransferases NMT1 and NMT2, both biochemically and through X-ray crystallography. We demonstrate metabolic incorporation of probes to label NMT substrates in cell culture and in situ intracellular photoactivation to form a covalent crosslink between modified proteins and their interactors, capturing a snapshot of interactions in the presence of the lipid PTM. Proteomic analyses revealed both known and multiple novel interactors of a series of myristoylated proteins, including ferroptosis suppressor protein 1 (FSP1) and spliceosome-associated RNA helicase DDX46. The concept exemplified by these probes offers an efficient approach for exploring the PTM-specific interactome without the requirement for genetic modification, which may prove broadly applicable to other PTMs.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Andrii Gorelik
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Mengjie Shen
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Maria M Shchepinova
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Inmaculada Pérez-Dorado
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
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Ma Z, Huang Z, Zhang C, Liu X, Zhang J, Shu H, Ma Y, Liu Z, Feng Y, Chen X, Kuang S, Zhang Y, Jia Z. Hepatic Acat2 overexpression promotes systemic cholesterol metabolism and adipose lipid metabolism in mice. Diabetologia 2023; 66:390-405. [PMID: 36378328 PMCID: PMC9665029 DOI: 10.1007/s00125-022-05829-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
AIMS/HYPOTHESIS Acetyl coenzyme A acetyltransferase (ACAT), also known as acetoacetyl-CoA thiolase, catalyses the formation of acetoacetyl-CoA from acetyl-CoA and forms part of the isoprenoid biosynthesis pathway. Thus, ACAT plays a central role in cholesterol metabolism in a variety of cells. Here, we aimed to assess the effect of hepatic Acat2 overexpression on cholesterol metabolism and systemic energy metabolism. METHODS We generated liver-targeted adeno-associated virus 9 (AAV9) to achieve hepatic Acat2 overexpression in mice. Mice were injected with AAV9 through the tail vein and subjected to morphological, physiological (body composition, indirect calorimetry, treadmill, GTT, blood biochemistry, cardiac ultrasonography and ECG), histochemical, gene expression and metabolomic analysis under normal diet or feeding with high-fat diet to investigate the role of ACAT2 in the liver. RESULTS Hepatic Acat2 overexpression reduced body weight and total fat mass, elevated the metabolic rate, improved glucose tolerance and lowered the serum cholesterol level of mice. In addition, the overexpression of Acat2 inhibited fatty acid, glucose and ketone metabolic pathways but promoted cholesterol metabolism and changed the bile acid pool and composition of the liver. Hepatic Acat2 overexpression also decreased the size of white adipocytes and promoted lipid metabolism in white adipose tissue. Furthermore, hepatic Acat2 overexpression protected mice from high-fat-diet-induced weight gain and metabolic defects CONCLUSIONS/INTERPRETATION: Our study identifies an essential role for ACAT2 in cholesterol metabolism and systemic energy expenditure and provides key insights into the metabolic benefits of hepatic Acat2 overexpression. Thus, adenoviral Acat2 overexpression in the liver may be a potential therapeutic tool in the treatment of obesity and hypercholesterolaemia.
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Affiliation(s)
- Zhimin Ma
- Endocrinology Department, Suzhou Science & Technology Town Hospital, Suzhou, China
| | - Zhengyun Huang
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China
| | - Chi Zhang
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China
| | - Xiangpeng Liu
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China
| | - Jie Zhang
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China
| | - Hui Shu
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yue Ma
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yu Feng
- Department of Endocrinology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiyue Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Yong Zhang
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China
| | - Zhihao Jia
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College, Soochow University, Suzhou, China.
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Vrzoňová R, Tóth R, Siváková B, Moťovská A, Gaplovská-Kyselá K, Baráth P, Tomáška Ľ, Gácser A, Gabaldón T, Nosek J, Neboháčová M. OCT1 - a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway. FEMS Yeast Res 2021; 21:6293844. [PMID: 34089318 DOI: 10.1093/femsyr/foab034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In contrast to baker's yeast Saccharomyces cerevisiae, yeast species from the Debaryomycetaceae family also encode a thiolase with predicted mitochondrial localization. These yeasts are able to utilize a range of hydroxyaromatic compounds via the 3-oxoadipate pathway the last step of which is catalyzed by 3-oxoadipyl-CoA thiolase and presumably occurs in mitochondria. In this work, we studied Oct1p, an ortholog of this enzyme from Candida parapsilosis. We found that the cells grown on a 3-oxoadipate pathway substrate exhibit increased levels of the OCT1 mRNA. Deletion of both OCT1 alleles impairs the growth of C. parapsilosis cells on 3-oxoadipate pathway substrates and this defect can be rescued by expression of the OCT1 gene from a plasmid vector. Subcellular localization experiments and LC-MS/MS analysis of enriched organellar fraction-proteins confirmed the presence of Oct1p in mitochondria. Phylogenetic profiling of Oct1p revealed an intricate evolutionary pattern indicating multiple horizontal gene transfers among different fungal groups.
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Affiliation(s)
- Romana Vrzoňová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Renáta Tóth
- Department of Microbiology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.,MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Barbara Siváková
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Anna Moťovská
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Katarína Gaplovská-Kyselá
- Faculty of Natural Sciences, Department of Genetics, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Ľubomír Tomáška
- Faculty of Natural Sciences, Department of Genetics, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Attila Gácser
- Department of Microbiology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.,MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB), Jordi Girona 29, 08034 Barcelona, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jozef Nosek
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Martina Neboháčová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
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7
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Fang SM. Genome-wide identification and analysis of the thiolase family in insects. PeerJ 2020; 8:e10393. [PMID: 33240678 PMCID: PMC7682436 DOI: 10.7717/peerj.10393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2020] [Indexed: 12/30/2022] Open
Abstract
Thiolases are important enzymes involved in lipid metabolism in both prokaryotes and eukaryotes, and are essential for a range of metabolic pathways, while, little is known for this important family in insects. To shed light on the evolutionary models and functional diversities of the thiolase family, 137 thiolase genes were identified in 20 representative insect genomes. They were mainly classified into five classes, namely cytosolic thiolase (CT-thiolase), T1-thiolase, T2-thiolase, trifunctional enzyme thiolase (TFE-thiolase), and sterol carrier protein 2 thiolase (SCP2-thiolase). The intron number and exon/intron structures of the thiolase genes reserve large diversification. Subcellular localization prediction indicated that all the thiolase proteins were mitochondrial, cytosolic, or peroxisomal enzymes. Four highly conserved sequence fingerprints were found in the insect thiolase proteins, including CxS-, NEAF-, GHP-, and CxGGGxG-motifs. Homology modeling indicated that insect thiolases share similar 3D structures with mammals, fishes, and microorganisms. In Bombyx mori, microarray data and reverse transcription-polymerase chain reaction (RT-PCR) analysis suggested that some thiolases might be involved in steroid metabolism, juvenile hormone (JH), and sex pheromone biosynthesis pathways. In general, sequence and structural characteristics were relatively conserved among insects, bacteria and vertebrates, while different classes of thiolases might have differentiation in specific functions and physiological processes. These results will provide an important foundation for future functional validation of insect thiolases.
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Affiliation(s)
- Shou-Min Fang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China.,College of Life Science, China West Normal University, Nanchong, Sichuan, China
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8
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Liu L, Zhou S, Deng Y. The 3-ketoacyl-CoA thiolase: an engineered enzyme for carbon chain elongation of chemical compounds. Appl Microbiol Biotechnol 2020; 104:8117-8129. [PMID: 32830293 DOI: 10.1007/s00253-020-10848-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Because of their function of catalyzing the rearrangement of the carbon chains, thiolases have attracted increasing attentions over the past decades. The 3-ketoacyl-CoA thiolase (KAT) is a member of the thiolase, which is capable of catalyzing the Claisen condensation reaction between the two acyl-CoAs, thereby achieving carbon chain elongation. In this way, diverse value-added compounds might be synthesized starting from simple small CoA thioesters. However, most KATs are hampered by low stability and poor substrate specificity, which has hindered the development of large-scale biosynthesis. In this review, the common characteristics in the three-dimensional structure of KATs from different sources are summarized. Moreover, structure-guided rational engineering is discussed as a strategy for enhancing the performance of KATs. Finally, we reviewed the metabolic engineering applications of KATs for producing various energy-storage molecules, such as n-butanol, fatty acids, dicarboxylic acids, and polyhydroxyalkanoates. KEY POINTS: • Summarize the structural characteristics and catalyzation mechanisms of KATs. • Review on the rational engineering to enhance the performance of KATs. • Discuss the applications of KATs for producing energy-storage molecules.
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Affiliation(s)
- Lixia Liu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.
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Babbi G, Baldazzi D, Savojardo C, Martelli PL, Casadio R. Highlighting Human Enzymes Active in Different Metabolic Pathways and Diseases: The Case Study of EC 1.2.3.1 and EC 2.3.1.9. Biomedicines 2020; 8:biomedicines8080250. [PMID: 32751059 PMCID: PMC7459455 DOI: 10.3390/biomedicines8080250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 11/22/2022] Open
Abstract
Enzymes are key proteins performing the basic functional activities in cells. In humans, enzymes can be also responsible for diseases, and the molecular mechanisms underlying the genotype to phenotype relationship are under investigation for diagnosis and medical care. Here, we focus on highlighting enzymes that are active in different metabolic pathways and become relevant hubs in protein interaction networks. We perform a statistics to derive our present knowledge on human metabolic pathways (the Kyoto Encyclopaedia of Genes and Genomes (KEGG)), and we found that activity aldehyde dehydrogenase (NAD(+)), described by Enzyme Commission number EC 1.2.1.3, and activity acetyl-CoA C-acetyltransferase (EC 2.3.1.9) are the ones most frequently involved. By associating functional activities (EC numbers) to enzyme proteins, we found the proteins most frequently involved in metabolic pathways. With our analysis, we found that these proteins are endowed with the highest numbers of interaction partners when compared to all the enzymes in the pathways and with the highest numbers of predicted interaction sites. As specific enzyme protein test cases, we focus on Alpha-Aminoadipic Semialdehyde Dehydrogenase (ALDH7A1, EC 2.3.1.9) and Acetyl-CoA acetyltransferase, cytosolic and mitochondrial (gene products of ACAT2 and ACAT1, respectively; EC 2.3.1.9). With computational approaches we show that it is possible, by starting from the enzyme structure, to highlight clues of their multiple roles in different pathways and of putative mechanisms promoting the association of genes to disease.
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10
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Aspergillus fumigatus Mitochondrial Acetyl Coenzyme A Acetyltransferase as an Antifungal Target. Appl Environ Microbiol 2020; 86:AEM.02986-19. [PMID: 32005728 PMCID: PMC7082573 DOI: 10.1128/aem.02986-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 01/15/2020] [Indexed: 12/27/2022] Open
Abstract
Ergosterol plays an important role in maintaining cell membrane sterol homeostasis in fungi, and as such, it is considered an effective target in antifungal chemotherapy. In yeast, the enzyme acetyl-coenzyme A (CoA) acetyltransferase (ERG10) catalyzes the Claisen condensation of two acetyl-CoA molecules to acetoacetyl-CoA in the ergosterol biosynthesis pathway and is reported as being critical for cell viability. Using yeast ERG10 for alignment, two orthologues, AfERG10A (AFUB_000550) and AfERG10B (AFUB_083570), were discovered in the opportunistic fungal pathogen Aspergillus fumigatus Despite the essentiality of AfERG10B having been previously validated, the biological function of AfERG10A remains unclear. In this study, we have characterized recombinant AfERG10A as a functional acetyl-CoA acetyltransferase catalyzing both synthetic and degradative reactions. Unexpectedly, AfERG10A localizes to the mitochondria in A. fumigatus, as shown by C-terminal green fluorescent protein (GFP) tag fusion. Both knockout and inducible promoter strategies demonstrate that Aferg10A is essential for the survival of A. fumigatus The reduced expression of Aferg10A leads to severe morphological defects and increased susceptibility to oxidative and cell wall stresses. Although the catalytic mechanism of acetyl-CoA acetyltransferase family is highly conserved, the crystal structure of AfERG10A and its complex with CoA are solved, revealing four substitutions within the CoA binding site that are different from human orthologues. Taken together, our combination of genetic and structural studies demonstrates that mitochondrial AfERG10A is essential for A. fumigatus cell viability and could be a potential drug target to feed the antifungal drug development pipeline.IMPORTANCE A growing number of people worldwide are suffering from invasive aspergillosis caused by the human opportunistic fungal pathogen A. fumigatus Current therapeutic options rely on a limited repertoire of antifungals. Ergosterol is an essential component of the fungal cell membrane as well as a target of current antifungals. Approximately 20 enzymes are involved in ergosterol biosynthesis, of which acetyl-CoA acetyltransferase (ACAT) is the first enzyme. Two ACATs in A. fumigatus are AfErg10A and AfErg10B. However, the biological function of AfErg10A is yet to be investigated. In this study, we showed that AfErg10A is localized in the mitochondria and is essential for A. fumigatus survival and morphological development. In combination with structural studies, we validated AfErg10A as a potential drug target that will facilitate the development of novel antifungals and improve the efficiency of existing drugs.
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11
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Zhang Y, Wang M, Lin H. A Regulatory Cysteine Residue Mediates Reversible Inactivation of NAD +-Dependent Aldehyde Dehydrogenases to Promote Oxidative Stress Response. ACS Chem Biol 2020; 15:28-32. [PMID: 31820916 DOI: 10.1021/acschembio.9b00662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aldehyde dehydrogenases (ALDHs) are a large family of enzymes that oxidize aldehydes into carboxylic acids. All ALDHs have a conserved catalytic cysteine residue but different cofactor preferences for NAD+ or NADP+. We discovered a CC motif composed of the catalytic and an adjacent cysteine, which are prone to disulfide bond formation under oxidative stress. This facilitates rapid detection of and response to oxidants, as well as protects the catalytic cysteine from overoxidation into irreversible products. In ALDHs, the CC motif only exists in NAD+-dependent ones, which leads to selective inhibition of NAD+-dependent ALDHs under oxidative stress, diverting carbon sources to the NADPH producing ALDHs. This alleviates the oxidative stress and promotes cell survival. Our findings revealed a novel regulatory mechanism for ALDHs that functions in the oxidative stress response. Many enzymes with catalytic cysteine residues have proximal cysteine, suggesting that such a regulatory mechanism may be general.
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Affiliation(s)
- Yugang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Miao Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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12
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Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100018. [PMID: 32647822 PMCID: PMC7337054 DOI: 10.1016/j.yjsbx.2019.100018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/17/2019] [Accepted: 12/27/2019] [Indexed: 11/23/2022]
Abstract
Thiolases are a well characterized family of enzymes with two distinct categories: degradative, β-ketoadipyl-CoA thiolases and biosynthetic, acetoacetyl-CoA thiolases. Both classes share an identical catalytic triad but catalyze reactions in opposite directions. Moreover, it is established that in contrast to the biosynthetic thiolases the degradative thiolases can accept substrates with broad chain lengths. Hitherto, no residue or structural pattern has been recognized that might help to discern the two thiolases, here we exploit, a tetrameric degradative thiolase from Pseudomonas putida KT2440 annotated as PcaF, as a model system to understand features which distinguishes the two classes using structural studies and bioinformatics analyses. Degradative thiolases have different active site architecture when compared to biosynthetic thiolases, demonstrating the dissimilar chemical nature of the active site architecture. Both thiolases deploy different "anchoring residues" to tether the large Coenzyme A (CoA) or CoA derivatives. Interestingly, the H356 of the catalytic triad in PcaF is directly involved in tethering the CoA/CoA derivatives into the active site and we were able to trap a gridlocked thiolase structure of the H356A mutant, where the CoA was found to be covalently linked to the catalytic cysteine residue, inhibiting the overall reaction. Further, X-ray structures with two long chain CoA derivatives, hexanal-CoA and octanal-CoA helped in delineating the long tunnel of 235 Å2 surface area in PcaF and led to identification of a unique covering loop exclusive to degradative thiolases that plays an active role in determining the tunnel length and the nature of the binding substrate.
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Key Words
- A-mutant-HAL-CoA, A-mutant-hexanal CoA complex
- A-mutant-Hex-CoA, A-mutant-Hexanoyl CoA complex
- A-mutants, H356A Mutant
- AA-mutants, H356A-C386A Mutant
- AS-mutant-OAL-CoA, AS-mutant-octanal CoA complex
- AS-mutant-Oct-CoA, AS-mutant-Octanoyl CoA complex
- AS-mutants, H356A-C90S Mutant
- Covalent locking
- Covering loop
- HAL, hexanal
- Hex-CoA, Hexanoyl CoA
- Hexanoyl CoA
- Mtb-thiolase, Mycobacterium tuberculosis thiolase
- OAL, octanal
- Oct-CoA, Octanoyl CoA
- Octanoyl CoA
- PcaF, β-ketoadipyl-CoA thiolase
- Tunnel
- Zr-thiolase, Zoogleria ramigera thiolase
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13
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The peroxisomal zebrafish SCP2-thiolase (type-1) is a weak transient dimer as revealed by crystal structures and native mass spectrometry. Biochem J 2019; 476:307-332. [PMID: 30573650 DOI: 10.1042/bcj20180788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/12/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022]
Abstract
The SCP2 (sterol carrier protein 2)-thiolase (type-1) functions in the vertebrate peroxisomal, bile acid synthesis pathway, converting 24-keto-THC-CoA and CoA into choloyl-CoA and propionyl-CoA. This conversion concerns the β-oxidation chain shortening of the steroid fatty acyl-moiety of 24-keto-THC-CoA. This class of dimeric thiolases has previously been poorly characterized. High-resolution crystal structures of the zebrafish SCP2-thiolase (type-1) now reveal an open catalytic site, shaped by residues of both subunits. The structure of its non-dimerized monomeric form has also been captured in the obtained crystals. Four loops at the dimer interface adopt very different conformations in the monomeric form. These loops also shape the active site and their structural changes explain why a competent active site is not present in the monomeric form. Native mass spectrometry studies confirm that the zebrafish SCP2-thiolase (type-1) as well as its human homolog are weak transient dimers in solution. The crystallographic binding studies reveal the mode of binding of CoA and octanoyl-CoA in the active site, highlighting the conserved geometry of the nucleophilic cysteine, the catalytic acid/base cysteine and the two oxyanion holes. The dimer interface of SCP2-thiolase (type-1) is equally extensive as in other thiolase dimers; however, it is more polar than any of the corresponding interfaces, which correlates with the notion that the enzyme forms a weak transient dimer. The structure comparison of the monomeric and dimeric forms suggests functional relevance of this property. These comparisons provide also insights into the structural rearrangements that occur when the folded inactive monomers assemble into the mature dimer.
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14
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Galpaz N, Gonda I, Shem-Tov D, Barad O, Tzuri G, Lev S, Fei Z, Xu Y, Mao L, Jiao C, Harel-Beja R, Doron-Faigenboim A, Tzfadia O, Bar E, Meir A, Sa'ar U, Fait A, Halperin E, Kenigswald M, Fallik E, Lombardi N, Kol G, Ronen G, Burger Y, Gur A, Tadmor Y, Portnoy V, Schaffer AA, Lewinsohn E, Giovannoni JJ, Katzir N. Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:169-191. [PMID: 29385635 DOI: 10.1111/tpj.13838] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/19/2017] [Accepted: 01/08/2018] [Indexed: 05/18/2023]
Abstract
Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic and transcriptomic data from a melon recombinant inbred line (RIL) population. RNA sequencing (RNA-Seq) of fruit from 96 RILs yielded a highly saturated collection of > 58 000 single-nucleotide polymorphisms, identifying 6636 recombination events that separated the genome into 3663 genomic bins. Bin-based QTL analysis of 79 RILs and 129 fruit-quality traits affecting taste, aroma and color resulted in the mapping of 241 QTL. Thiol acyltransferase (CmThAT1) gene was identified within the QTL interval of its product, S-methyl-thioacetate, a key component of melon fruit aroma. Metabolic activity of CmThAT1-encoded protein was validated in bacteria and in vitro. QTL analysis of flesh color intensity identified a candidate white-flesh gene (CmPPR1), one of two major loci determining fruit flesh color in melon. CmPPR1 encodes a member of the pentatricopeptide protein family, involved in processing of RNA in plastids, where carotenoid and chlorophyll pigments accumulate. Network analysis of > 12 000 eQTL mapped for > 8000 differentially expressed fruit genes supported the role of CmPPR1 in determining the expression level of plastid targeted genes. We highlight the potential of RNA-Seq-based QTL analysis of small to moderate size, advanced RIL populations for precise marker-assisted breeding and gene discovery. We provide the following resources: a RIL population genotyped with a unique set of SNP markers, confined genomic segments that harbor QTL governing 129 traits and a saturated set of melon eQTLs.
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Affiliation(s)
- Navot Galpaz
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Itay Gonda
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Doron Shem-Tov
- NRGENE, Park HaMada Ness Ziona, Israel
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Galil Tzuri
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Shery Lev
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
- Institute of Life Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - Yimin Xu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Linyong Mao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Chen Jiao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Rotem Harel-Beja
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Adi Doron-Faigenboim
- Department of Vegetable and Field Crops, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Oren Tzfadia
- VIB Department of Plant Systems Biology, Ghent University, Gent, Belgium
| | - Einat Bar
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Ayala Meir
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Uzi Sa'ar
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Aaron Fait
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eran Halperin
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Merav Kenigswald
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
- Institute of Life Science, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Postharvest Science of Fresh Produce, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Elazar Fallik
- Department of Postharvest Science of Fresh Produce, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Nadia Lombardi
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
- Department of Agricultural Sciences, University of Naples, Portici, Italy
| | - Guy Kol
- NRGENE, Park HaMada Ness Ziona, Israel
| | - Gil Ronen
- NRGENE, Park HaMada Ness Ziona, Israel
| | - Yosef Burger
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Amit Gur
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Ya'akov Tadmor
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Vitaly Portnoy
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Arthur A Schaffer
- Department of Vegetable and Field Crops, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Efraim Lewinsohn
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - Nurit Katzir
- Department of Vegetable and Field Crops, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
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15
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Marshall AC, Bond CS, Bruning JB. Structure of Aspergillus fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation by Monovalent Cations. ACS Catal 2018. [DOI: 10.1021/acscatal.7b02873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrew C. Marshall
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Charles S. Bond
- School
of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - John B. Bruning
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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16
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Blaisse MR, Fu B, Chang MCY. Structural and Biochemical Studies of Substrate Selectivity in Ascaris suum Thiolases. Biochemistry 2018; 57:3155-3166. [PMID: 29381332 DOI: 10.1021/acs.biochem.7b01123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thiolases are a class of carbon-carbon bond forming enzymes with important applications in biotechnology and metabolic engineering as they provide a general method for the condensation of two acyl coenzyme A (CoA) substrates. As such, developing a greater understanding of their substrate selectivity would expand our ability to engineer the enzymatic or microbial production of a broad range of small-molecule targets. Here, we report the crystal structures and biochemical characterization of Acat2 and Acat5, two biosynthetic thiolases from Ascaris suum with varying selectivity toward branched compared to linear compounds. The structure of the Acat2-C91S mutant bound to propionyl-CoA shows that the terminal methyl group of the substrate, representing the α-branch point, is directed toward the conserved Phe 288 and Met 158 residues. In Acat5, the Phe ring is rotated to accommodate a hydroxyl-π interaction with an adjacent Thr side chain, decreasing space in the binding pocket and possibly accounting for its strong preference for linear substrates compared to Acat2. Comparison of the different Acat thiolase structures shows that Met 158 is flexible, adopting alternate conformations with the side chain rotated toward or away from a covering loop at the back of the active site. Mutagenesis of residues in the covering loop in Acat5 with the corresponding residues from Acat2 allows for highly increased accommodation of branched substrates, whereas the converse mutations do not significantly affect Acat2 substrate selectivity. Our results suggest an important contribution of second-shell residues to thiolase substrate selectivity and offer insights into engineering this enzyme class.
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17
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Zhou P, Zhu Z, Hidayatullah Khan M, Zheng P, Teng M, Niu L. Crystal structure of cytoplasmic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2018; 74:6-13. [PMID: 29372902 PMCID: PMC5947687 DOI: 10.1107/s2053230x17016971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/25/2017] [Indexed: 11/10/2022] Open
Abstract
Thiolases are vital enzymes which participate in both degradative and biosynthetic pathways. Biosynthetic thiolases catalyze carbon-carbon bond formation by a Claisen condensation reaction. The cytoplasmic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae, ERG10, catalyses carbon-carbon bond formation in the mevalonate pathway. The structure of a S. cerevisiae biosynthetic thiolase has not previously been reported. Here, crystal structures of apo ERG10 and its Cys91Ala variant were solved at resolutions of 2.2 and 1.95 Å, respectively. The structure determined shows that ERG10 shares the characteristic thiolase superfamily fold, with a similar active-site architecture to those of type II thiolases and a similar binding pocket, apart from Ala159 at the entrance to the pantetheine-binding cavity, which appears to be a determinant of the poor binding ability of the substrate. Moreover, comparative binding-pocket analysis of molecule B in the asymmetric unit of the apo structure with that of the CoA-bound complex of human mitochondrial acetoacetyl-CoA thiolase indicates the canonical binding mode of CoA. Furthermore, the steric hindrance revealed in a structural comparison of molecule A with the CoA-bound form raise the possibility of conformational changes that are associated with substrate binding.
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Affiliation(s)
- Pengfei Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Muhammad Hidayatullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Peiyi Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
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18
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Ithayaraja M, Janardan N, Wierenga RK, Savithri HS, Murthy MRN. Crystal structure of a thiolase from Escherichia coli at 1.8 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:534-44. [PMID: 27380370 PMCID: PMC4933003 DOI: 10.1107/s2053230x16008451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/25/2016] [Indexed: 11/10/2022] Open
Abstract
Thiolases catalyze the Claisen condensation of two acetyl-CoA molecules to give acetoacetyl-CoA, as well as the reverse degradative reaction. Four genes coding for thiolases or thiolase-like proteins are found in the Escherichia coli genome. In this communication, the successful cloning, purification, crystallization and structure determination at 1.8 Å resolution of a homotetrameric E. coli thiolase are reported. The structure of E. coli thiolase co-crystallized with acetyl-CoA at 1.9 Å resolution is also reported. As observed in other tetrameric thiolases, the present E. coli thiolase is a dimer of two tight dimers and probably functions as a biodegradative enzyme. Comparison of the structure and biochemical properties of the E. coli enzyme with those of other well studied thiolases reveals certain novel features of this enzyme, such as the modification of a lysine in the dimeric interface, the possible oxidation of the catalytic Cys88 in the structure of the enzyme obtained in the presence of CoA and active-site hydration. The tetrameric enzyme also displays an interesting departure from exact 222 symmetry, which is probably related to the deformation of the tetramerization domain that stabilizes the oligomeric structure of the protein. The current study allows the identification of substrate-binding amino-acid residues and water networks at the active site and provides the structural framework required for understanding the biochemical properties as well as the physiological function of this E. coli thiolase.
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Affiliation(s)
- M. Ithayaraja
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - N. Janardan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Rik K. Wierenga
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90014 Oulu, Finland
| | - H. S. Savithri
- Biochemistry Department, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - M. R. N. Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
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19
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Nakao N, Kaneda H, Tsushima N, Tanaka M. Characterization of primary structure and post-hatching increase in chicken cytosolic acetoacetyl-coA thiolase in the liver. Poult Sci 2016; 95:1406-10. [PMID: 26944984 DOI: 10.3382/ps/pew045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 12/03/2015] [Indexed: 11/20/2022] Open
Abstract
Acetoacetyl-CoA thiolase (EC 2.3.1.9) catalyzes the cleavage of acetoacetyl-CoA into acetyl-CoA and its reverse reaction, the synthesis of acetoacetyl-CoA. Cytosolic acetoacetyl-CoA thiolase ( CT: ) is a key enzyme in the initial step of the cholesterol synthesis pathway. In the present study, we characterized the amino acid sequence of chicken CT and the tissue distribution of its mRNA and protein, together with their developmental changes in the liver. The amino acid sequence encoded by the nucleotide sequence of chicken CT cDNA showed a higher overall identity with those of human (74.3%) and rat (74.6%) CTs. Amino acid residues known to participate in enzymatic activity in human CT are conserved in chicken CT. Real-time PCR analysis revealed the expression of CT mRNA in the liver, kidney, adrenal gland, jejunum and ovary of adult hens, with higher levels in the liver, kidney, adrenal gland and ovary. Western blot analysis detected an immunoreactive protein of 41 kDa from cytoplasmic fraction but not particulate fractions of adult chicken liver. The immunoreactive protein was detected in all the tissues. The mRNA levels in the liver rapidly increased after hatching, with a maximum on d 5 post-hatching, after which they gradually decreased to adult levels. A similar change was observed in the protein levels. The increase in transcription and protein synthesis of CT suggests that the synthetic pathway of cholesterol from acetyl-CoA produced by CT replaces the hydrolysis of accumulated cholesteryl ester in the liver, in response to a change in the nutrient source from the lipid-rich yolk to a lower-lipid diet during the early post-hatching period.
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Affiliation(s)
- N Nakao
- Laboratory of Animal Physiology, Department of Animal Science, Faculty of Applied Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonancho, Musashino, Tokyo, 180-8602, Japan
| | - H Kaneda
- Laboratory of Animal Physiology, Department of Animal Science, Faculty of Applied Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonancho, Musashino, Tokyo, 180-8602, Japan
| | - N Tsushima
- Laboratory of Animal Physiology, Department of Animal Science, Faculty of Applied Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonancho, Musashino, Tokyo, 180-8602, Japan
| | - M Tanaka
- Laboratory of Animal Physiology, Department of Animal Science, Faculty of Applied Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonancho, Musashino, Tokyo, 180-8602, Japan
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20
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Harijan RK, Mazet M, Kiema TR, Bouyssou G, Alexson SEH, Bergmann U, Moreau P, Michels PAM, Bringaud F, Wierenga RK. The SCP2-thiolase-like protein (SLP) of Trypanosoma brucei is an enzyme involved in lipid metabolism. Proteins 2016; 84:1075-96. [PMID: 27093562 DOI: 10.1002/prot.25054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 04/03/2016] [Accepted: 04/08/2016] [Indexed: 11/06/2022]
Abstract
Bioinformatics studies have shown that the genomes of trypanosomatid species each encode one SCP2-thiolase-like protein (SLP), which is characterized by having the YDCF thiolase sequence fingerprint of the Cβ2-Cα2 loop. SLPs are only encoded by the genomes of these parasitic protists and not by those of mammals, including human. Deletion of the Trypanosoma brucei SLP gene (TbSLP) increases the doubling time of procyclic T. brucei and causes a 5-fold reduction of de novo sterol biosynthesis from glucose- and acetate-derived acetyl-CoA. Fluorescence analyses of EGFP-tagged TbSLP expressed in the parasite located the TbSLP in the mitochondrion. The crystal structure of TbSLP (refined at 1.75 Å resolution) confirms that TbSLP has the canonical dimeric thiolase fold. In addition, the structures of the TbSLP-acetoacetyl-CoA (1.90 Å) and TbSLP-malonyl-CoA (2.30 Å) complexes reveal that the two oxyanion holes of the thiolase active site are preserved. TbSLP binds malonyl-CoA tightly (Kd 90 µM), acetoacetyl-CoA moderately (Kd 0.9 mM) and acetyl-CoA and CoA very weakly. TbSLP possesses low malonyl-CoA decarboxylase activity. Altogether, the data show that TbSLP is a mitochondrial enzyme involved in lipid metabolism. Proteins 2016; 84:1075-1096. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rajesh K Harijan
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland.,Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461, USA
| | - Muriel Mazet
- Centre De Résonance Magnétique Des Systèmes Biologiques (RMSB), UMR5536, Université De Bordeaux, CNRS, 146 Rue Léo Saignat, Bordeaux, 33076, France.,Laboratoire De Microbiologie Fondamentale Et Pathogénicité (MFP), UMR5234, Université De Bordeaux, CNRS, 146 Rue Léo Saignat, Bordeaux, 33076, France
| | - Tiila R Kiema
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland
| | - Guillaume Bouyssou
- Laboratoire De Biogenèse Membranaire, UMR-5200, Université De Bordeaux, CNRS, Bâtiment A3 - 1er Étage, INRA Bordeaux Aquitaine BP81, 71 Avenue Edouard Bourlaux, Villenave D'Ornon Cedex, 33883, France
| | - Stefan E H Alexson
- Karolinska Institutet, Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska University Hospital, Stockholm, SE 141 86, Sweden
| | - Ulrich Bergmann
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland
| | - Patrick Moreau
- Laboratoire De Biogenèse Membranaire, UMR-5200, Université De Bordeaux, CNRS, Bâtiment A3 - 1er Étage, INRA Bordeaux Aquitaine BP81, 71 Avenue Edouard Bourlaux, Villenave D'Ornon Cedex, 33883, France
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, the King's Buildings, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| | - Frédéric Bringaud
- Centre De Résonance Magnétique Des Systèmes Biologiques (RMSB), UMR5536, Université De Bordeaux, CNRS, 146 Rue Léo Saignat, Bordeaux, 33076, France.,Laboratoire De Microbiologie Fondamentale Et Pathogénicité (MFP), UMR5234, Université De Bordeaux, CNRS, 146 Rue Léo Saignat, Bordeaux, 33076, France
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland
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21
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Wu DM, He Z, Chen T, Liu Y, Ma LP, Ping J. DNA hypermethylation of acetoacetyl-CoA synthetase contributes to inhibited cholesterol supply and steroidogenesis in fetal rat adrenals under prenatal nicotine exposure. Toxicology 2016; 340:43-52. [PMID: 26776438 DOI: 10.1016/j.tox.2016.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 12/28/2015] [Accepted: 01/10/2016] [Indexed: 11/16/2022]
Abstract
Prenatal nicotine exposure is a risk factor for intrauterine growth retardation (IUGR). Steroid hormones synthesized from cholesterol in the fetal adrenal play an important role in the fetal development. The aim of this study is to investigate the effects of prenatal nicotine exposure on steroidogenesis in fetal rat adrenals from the perspective of cholesterol supply and explore the underlying epigenetic mechanisms. Pregnant Wistar rats were administered 1.0mg/kg nicotine subcutaneously twice a day from gestational day (GD) 7 to GD17. The results showed that prenatal nicotine exposure increased IUGR rates. Histological changes, decreased steroid hormone concentrations and decreased cholesterol supply were observed in nicotine-treated fetal adrenals. In the gene expression array, the expression of genes regulating ketone metabolic process decreased in nicotine-treated fetal adrenals. The following conjoint analysis of DNA methylation array with these differentially expressed genes suggested that acetoacetyl-CoA synthetase (AACS), the enzyme utilizing ketones for cholesterol supply, may play an important role in nicotine-induced cholesterol supply deficiency. Moreover, the decreased expression of AACS and increased DNA methylation in the proximal promoter of AACS in the fetal adrenal was verified by real-time reverse-transcription PCR (RT-PCR) and bisulfite sequencing PCR (BSP), respectively. In conclusion, prenatal nicotine exposure can cause DNA hypermethylation of the AACS promoter in the rat fetal adrenal. These changes may result in decreased AACS expression and cholesterol supply, which inhibits steroidogenesis in the fetal adrenal.
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Affiliation(s)
- Dong-Mei Wu
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Zheng He
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Ting Chen
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Yang Liu
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Liang-Peng Ma
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, China
| | - Jie Ping
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Diseases, Wuhan 430071, China.
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Liu W, Xu X, Zhang R, Cheng T, Cao Y, Li X, Guo J, Liu H, Xian M. Engineering Escherichia coli for high-yield geraniol production with biotransformation of geranyl acetate to geraniol under fed-batch culture. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:58. [PMID: 26973712 PMCID: PMC4787002 DOI: 10.1186/s13068-016-0466-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/19/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Geraniol is an acyclic monoterpene alcohol, which exhibits good prospect as a gasoline alternative. Geraniol is naturally encountered in plants at low concentrations and an attractive target for microbial engineering. Geraniol has been heterologously produced in Escherichia coli, but the low titer hinders its industrial applications. Moreover, bioconversion of geraniol by E. coli remains largely unknown. RESULTS Recombinant overexpression of Ocimum basilicum geraniol synthase, Abies grandis geranyl diphosphate synthase, and a heterotic mevalonate pathway in E. coli BL21 (DE3) enabled the production of up to 68.6 ± 3 mg/L geraniol in shake flasks. Initial fed-batch fermentation only increased geraniol production to 78.8 mg/L. To further improve the production yield, the fermentation conditions were optimized. Firstly, 81.4 % of volatile geraniol was lost during the first 5 h of fermentation in a solvent-free system. Hence, isopropyl myristate was added to the culture medium to form an aqueous-organic two-phase culture system, which effectively prevented volatilization of geraniol. Secondly, most of geraniol was eventually biotransformed into geranyl acetate by E. coli, thus decreasing geraniol production. For the first time, we revealed the role of acetylesterase (Aes, EC 3.1.1.6) from E. coli in hydrolyzing geranyl acetate to geraniol, and production of geraniol was successfully increased to 2.0 g/L under controlled fermentation conditions. CONCLUSIONS An efficient geraniol production platform was established by overexpressing several key pathway proteins in engineered E. coli strain combined with a controlled fermentation system. About 2.0 g/L geraniol was obtained using our controllable aqueous-organic two-phase fermentation system, which is the highest yield to date. In addition, the interconversion between geraniol and geranyl acetate by E. coli was first elucidated. This study provided a new and promising strategy for geraniol biosynthesis, which laid a basis for large-scale industrial application.
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Affiliation(s)
- Wei Liu
- />CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 10090 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xin Xu
- />CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Rubing Zhang
- />CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tao Cheng
- />CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Yujin Cao
- />CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Xiaoxiao Li
- />CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Jiantao Guo
- />Department of Chemistry, University of Nebraska–Lincoln, Lincoln, NE 68588 USA
| | - Huizhou Liu
- />CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Mo Xian
- />CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
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Janardan N, Harijan RK, Kiema TR, Wierenga RK, Murthy MRN. Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase fromMycobacterium smegmatis. ACTA ACUST UNITED AC 2015; 71:2479-93. [DOI: 10.1107/s1399004715019331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/12/2015] [Indexed: 11/10/2022]
Abstract
Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) fromMycobacterium smegmatisin apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domainviaflexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The Lα1–covering loop–Lα2 region, together with the Nβ2–Nα2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.
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Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum. Nat Commun 2015; 6:8410. [PMID: 26391388 PMCID: PMC4595758 DOI: 10.1038/ncomms9410] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/19/2015] [Indexed: 01/02/2023] Open
Abstract
Thiolase is the first enzyme catalysing the condensation of two acetyl-coenzyme A (CoA) molecules to form acetoacetyl-CoA in a dedicated pathway towards the biosynthesis of n-butanol, an important solvent and biofuel. Here we elucidate the crystal structure of Clostridium acetobutylicum thiolase (CaTHL) in its reduced/oxidized states. CaTHL, unlike those from other aerobic bacteria such as Escherichia coli and Zoogloea ramegera, is regulated by the redox-switch modulation through reversible disulfide bond formation between two catalytic cysteine residues, Cys88 and Cys378. When CaTHL is overexpressed in wild-type C. acetobutylicum, butanol production is reduced due to the disturbance of acidogenic to solventogenic shift. The CaTHL(V77Q/N153Y/A286K) mutant, which is not able to form disulfide bonds, exhibits higher activity than wild-type CaTHL, and enhances butanol production upon overexpression. On the basis of these results, we suggest that CaTHL functions as a key enzyme in the regulation of the main metabolism of C. acetobutylicum through a redox-switch regulatory mechanism.
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25
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Schaefer CM, Lu R, Nesbitt NM, Schiebel J, Sampson NS, Kisker C. FadA5 a thiolase from Mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. Structure 2014; 23:21-33. [PMID: 25482540 DOI: 10.1016/j.str.2014.10.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/18/2014] [Accepted: 10/06/2014] [Indexed: 11/29/2022]
Abstract
With the exception of HIV, tuberculosis (TB) is the leading cause of mortality among infectious diseases. The urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant Mycobacterium tuberculosis (Mtb) strains. Proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against TB. FadA5, a thiolase from Mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation under release of critical metabolites and was shown to be of importance during the chronic stage of TB infections. To gain structural and mechanistic insight on FadA5, we characterized the enzyme in different stages of the cleavage reaction and with a steroid bound to the binding pocket. Structural comparisons to human thiolases revealed that it should be possible to target FadA5 specifically, and the steroid-bound structure provides a solid basis for the development of inhibitors against FadA5.
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Affiliation(s)
- Christin M Schaefer
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Rui Lu
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Natasha M Nesbitt
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
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26
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Kiema TR, Harijan RK, Strozyk M, Fukao T, Alexson SEH, Wierenga RK. The crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase (T1): insight into the reaction mechanism of its thiolase and thioesterase activities. ACTA ACUST UNITED AC 2014; 70:3212-25. [PMID: 25478839 DOI: 10.1107/s1399004714023827] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/28/2014] [Indexed: 11/10/2022]
Abstract
Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The active site is surprisingly similar to the active site of the Zoogloea ramigera biosynthetic tetrameric thiolase (PDB entries 1dm3 and 1m1o) and different from the active site of the peroxisomal dimeric degradative thiolase (PDB entries 1afw and 2iik). A cavity analysis suggests a mode of binding for the fatty-acyl tail in a tunnel lined by the Nβ2-Nα2 loop of the adjacent subunit and the Lα1 helix of the loop domain. Soaking of the apo hT1 crystals with octanoyl-CoA resulted in a crystal structure in complex with CoA owing to the intrinsic acyl-CoA thioesterase activity of hT1. Solution studies confirm that hT1 has low acyl-CoA thioesterase activity for fatty acyl-CoA substrates. The fastest rate is observed for the hydrolysis of butyryl-CoA. It is also shown that T1 has significant biosynthetic thiolase activity, which is predicted to be of physiological importance.
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Affiliation(s)
- Tiila Riikka Kiema
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Rajesh K Harijan
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Malgorzata Strozyk
- Karolinska Institutet, Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Toshiyuki Fukao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Stefan E H Alexson
- Karolinska Institutet, Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
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Anbazhagan P, Harijan RK, Kiema TR, Janardan N, Murthy M, Michels PA, Juffer AH, Wierenga RK. Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis. Tuberculosis (Edinb) 2014; 94:405-12. [DOI: 10.1016/j.tube.2014.03.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
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28
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Genetic profiling of the isoprenoid and sterol biosynthesis pathway genes of Trypanosoma cruzi. PLoS One 2014; 9:e96762. [PMID: 24828104 PMCID: PMC4020770 DOI: 10.1371/journal.pone.0096762] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/04/2014] [Indexed: 12/02/2022] Open
Abstract
In Trypanosoma cruzi the isoprenoid and sterol biosynthesis pathways are validated targets for chemotherapeutic intervention. In this work we present a study of the genetic diversity observed in genes from these pathways. Using a number of bioinformatic strategies, we first identified genes that were missing and/or were truncated in the T. cruzi genome. Based on this analysis we obtained the complete sequence of the ortholog of the yeast ERG26 gene and identified a non-orthologous homolog of the yeast ERG25 gene (sterol methyl oxidase, SMO), and we propose that the orthologs of ERG25 have been lost in trypanosomes (but not in Leishmanias). Next, starting from a set of 16 T. cruzi strains representative of all extant evolutionary lineages, we amplified and sequenced ∼24 Kbp from 22 genes, identifying a total of 975 SNPs or fixed differences, of which 28% represent non-synonymous changes. We observed genes with a density of substitutions ranging from those close to the average (∼2.5/100 bp) to some showing a high number of changes (11.4/100 bp, for the putative lathosterol oxidase gene). All the genes of the pathway are under apparent purifying selection, but genes coding for the sterol C14-demethylase, the HMG-CoA synthase, and the HMG-CoA reductase have the lowest density of missense SNPs in the panel. Other genes (TcPMK, TcSMO-like) have a relatively high density of non-synonymous SNPs (2.5 and 1.9 every 100 bp, respectively). However, none of the non-synonymous changes identified affect a catalytic or ligand binding site residue. A comparative analysis of the corresponding genes from African trypanosomes and Leishmania shows similar levels of apparent selection for each gene. This information will be essential for future drug development studies focused on this pathway.
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Crystal structures of SCP2-thiolases of Trypanosomatidae, human pathogens causing widespread tropical diseases: the importance for catalysis of the cysteine of the unique HDCF loop. Biochem J 2013; 455:119-30. [PMID: 23909465 DOI: 10.1042/bj20130669] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Thiolases are essential CoA-dependent enzymes in lipid metabolism. In the present study we report the crystal structures of trypanosomal and leishmanial SCP2 (sterol carrier protein, type-2)-thiolases. Trypanosomatidae cause various widespread devastating (sub)-tropical diseases, for which adequate treatment is lacking. The structures reveal the unique geometry of the active site of this poorly characterized subfamily of thiolases. The key catalytic residues of the classical thiolases are two cysteine residues, functioning as a nucleophile and an acid/base respectively. The latter cysteine residue is part of a CxG motif. Interestingly, this cysteine residue is not conserved in SCP2-thiolases. The structural comparisons now show that in SCP2-thiolases the catalytic acid/base is provided by the cysteine residue of the HDCF motif, which is unique for this thiolase subfamily. This HDCF cysteine residue is spatially equivalent to the CxG cysteine residue of classical thiolases. The HDCF cysteine residue is activated for acid/base catalysis by two main chain NH-atoms, instead of two water molecules, as present in the CxG active site. The structural results have been complemented with enzyme activity data, confirming the importance of the HDCF cysteine residue for catalysis. The data obtained suggest that these trypanosomatid SCP2-thiolases are biosynthetic thiolases. These findings provide promise for drug discovery as biosynthetic thiolases catalyse the first step of the sterol biosynthesis pathway that is essential in several of these parasites.
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30
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A comprehensive machine-readable view of the mammalian cholesterol biosynthesis pathway. Biochem Pharmacol 2013; 86:56-66. [PMID: 23583456 PMCID: PMC3912678 DOI: 10.1016/j.bcp.2013.03.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/22/2013] [Accepted: 03/26/2013] [Indexed: 01/17/2023]
Abstract
Cholesterol biosynthesis serves as a central metabolic hub for numerous biological processes in health and disease. A detailed, integrative single-view description of how the cholesterol pathway is structured and how it interacts with other pathway systems is lacking in the existing literature. Here we provide a systematic review of the existing literature and present a detailed pathway diagram that describes the cholesterol biosynthesis pathway (the mevalonate, the Kandutch-Russell and the Bloch pathway) and shunt pathway that leads to 24(S),25-epoxycholesterol synthesis. The diagram has been produced using the Systems Biology Graphical Notation (SBGN) and is available in the SBGN-ML format, a human readable and machine semantically parsable open community file format.
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31
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Akri KE, Mouhibi R, Zahouily M, Hanafi N, Bahlaoui MA. Physicochemical 2D-Qsar and 3D Molecular Docking Studies on N-Chlorosulfonyl Isocyanate Analogs as Sterol O-Acyl-Transferase-1 “Soat-1” Inhibitors. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojmc.2013.34013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Sun S, Kang XP, Tian YS, Zheng SW, Hao RJ, Liu QL, Zhang JC, Xing GM. Cloning and Bioinformatic Analysis of a Novel Thiolase II Gene (BPLTHI2)from Betula Platyphylla. BIOTECHNOL BIOTEC EQ 2013. [DOI: 10.5504/bbeq.2013.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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33
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Janardan N, Harijan RK, Wierenga RK, Murthy MRN. Crystal structure of a monomeric thiolase-like protein type 1 (TLP1) from Mycobacterium smegmatis. PLoS One 2012; 7:e41894. [PMID: 22844533 PMCID: PMC3406046 DOI: 10.1371/journal.pone.0041894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 06/29/2012] [Indexed: 11/29/2022] Open
Abstract
An analysis of the Mycobacterium smegmatis genome suggests that it codes for several thiolases and thiolase-like proteins. Thiolases are an important family of enzymes that are involved in fatty acid metabolism. They occur as either dimers or tetramers. Thiolases catalyze the Claisen condensation of two acetyl-Coenzyme A molecules in the synthetic direction and the thiolytic cleavage of 3-ketoacyl-Coenzyme A molecules in the degradative direction. Some of the M. smegmatis genes have been annotated as thiolases of the poorly characterized SCP2-thiolase subfamily. The mammalian SCP2-thiolase consists of an N-terminal thiolase domain followed by an additional C-terminal domain called sterol carrier protein-2 or SCP2. The M. smegmatis protein selected in the present study, referred to here as the thiolase-like protein type 1 (MsTLP1), has been biochemically and structurally characterized. Unlike classical thiolases, MsTLP1 is a monomer in solution. Its structure has been determined at 2.7 Å resolution by the single wavelength anomalous dispersion method. The structure of the protomer confirms that the N-terminal domain has the thiolase fold. An extra C-terminal domain is indeed observed. Interestingly, it consists of six β-strands forming an anti-parallel β-barrel which is completely different from the expected SCP2-fold. Detailed sequence and structural comparisons with thiolases show that the residues known to be essential for catalysis are not conserved in MsTLP1. Consistent with this observation, activity measurements show that MsTLP1 does not catalyze the thiolase reaction. This is the first structural report of a monomeric thiolase-like protein from any organism. These studies show that MsTLP1 belongs to a new group of thiolase related proteins of unknown function.
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Affiliation(s)
- Neelanjana Janardan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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34
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The characterization and evolutionary relationships of a trypanosomal thiolase. Int J Parasitol 2011; 41:1273-83. [DOI: 10.1016/j.ijpara.2011.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/22/2011] [Accepted: 07/19/2011] [Indexed: 11/23/2022]
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35
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Fischer JJ, Michaelis S, Schrey AK, Diehl A, Graebner OY, Ungewiss J, Horzowski S, Glinski M, Kroll F, Dreger M, Koester H. SAHA Capture Compound--a novel tool for the profiling of histone deacetylases and the identification of additional vorinostat binders. Proteomics 2011; 11:4096-104. [PMID: 21898820 DOI: 10.1002/pmic.201000717] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 06/10/2011] [Accepted: 07/29/2011] [Indexed: 11/10/2022]
Abstract
Suberoylanilide hydroxamic acid (SAHA) is a potent histone deacetylase (HDAC) inhibitor. Inhibitors of HDACs are used in cancer therapy based on the role HDACs play in transcription by regulating chromatin compaction and non-histone proteins such as transcription factors. Profiling of HDAC expression is of interest in the functional proteomics analysis of cancer. Also, non-HDAC proteins may interact with HDAC inhibitor drugs and contribute to the drug mode of action. We here present a tool for the unbiased chemical proteomic profiling of proteins that specifically interact with SAHA. We designed and synthesized a trifunctional Capture Compound containing SAHA as selectivity and identified HDACs1, 2, 3 and 6, known and predicted HDAC interactors from human-derived HepG2 cell lysate, as well as a set of new potential non-HDAC targets of SAHA. One of these non-HDAC targets, isochorismatase domain-containing protein 2 (ISOC2) is putative hydrolase associated with the negative regulation of the tumor-suppressor p16(INK4a). We demonstrated the direct and dose-dependent interaction of SAHA to the purified recombinant ISOC2 protein. Using SAHA Capture Compound mass spectrometry, we thus identified potential new SAHA target proteins in an entirely unbiased chemical proteomics approach.
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36
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Janardan N, Paul A, Harijan RK, Wierenga RK, Murthy MRN. Cloning, expression, purification and preliminary X-ray diffraction studies of a putative Mycobacterium smegmatis thiolase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:817-20. [PMID: 21795802 PMCID: PMC3144804 DOI: 10.1107/s1744309111019324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 05/21/2011] [Indexed: 11/10/2022]
Abstract
Thiolases are important in fatty-acid degradation and biosynthetic pathways. Analysis of the genomic sequence of Mycobacterium smegmatis suggests the presence of several putative thiolase genes. One of these genes appears to code for an SCP-x protein. Human SCP-x consists of an N-terminal domain (referred to as SCP2 thiolase) and a C-terminal domain (referred as sterol carrier protein 2). Here, the cloning, expression, purification and crystallization of this putative SCP-x protein from M. smegmatis are reported. The crystals diffracted X-rays to 2.5 Å resolution and belonged to the triclinic space group P1. Calculation of rotation functions using X-ray diffraction data suggests that the protein is likely to possess a hexameric oligomerization with 32 symmetry which has not been observed in the other six known classes of this enzyme.
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Affiliation(s)
- Neelanjana Janardan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Anju Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Rajesh K. Harijan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Rikkert K. Wierenga
- Department of Biochemistry, Biocenter Oulu, University of Oulu, FIN-90220 Oulu, Finland
| | - M. R. N. Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
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37
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Lasserre JP, Sylvius L, Joubert-Caron R, Caron M, Hardouin J. Organellar Protein Complexes of Caco-2 Human Cells Analyzed by Two-Dimensional Blue Native/SDS-PAGE and Mass Spectrometry. J Proteome Res 2010; 9:5093-107. [DOI: 10.1021/pr100381m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jean-Paul Lasserre
- Laboratoire de Biochimie des Protéines et Protéomique, Université Paris 13, UMR CNRS 7033, 74 rue Marcel Cachin F-93017 Bobigny cedex, France, Institut de Biochimie et Génétique Cellulaires, Université Bordeaux 2, UMR CNRS 5095, 1 rue Camille Saint-Saëns F-33077 Bordeaux Cedex, France, and Laboratoire Polymères, Biopolymères, Surfaces, Equipe BRICS, Université de Rouen, UMR CNRS 6270, Boulevard Maurice de Broglie F-76821 Mont-Saint-Aignan cedex, France
| | - Loïk Sylvius
- Laboratoire de Biochimie des Protéines et Protéomique, Université Paris 13, UMR CNRS 7033, 74 rue Marcel Cachin F-93017 Bobigny cedex, France, Institut de Biochimie et Génétique Cellulaires, Université Bordeaux 2, UMR CNRS 5095, 1 rue Camille Saint-Saëns F-33077 Bordeaux Cedex, France, and Laboratoire Polymères, Biopolymères, Surfaces, Equipe BRICS, Université de Rouen, UMR CNRS 6270, Boulevard Maurice de Broglie F-76821 Mont-Saint-Aignan cedex, France
| | - Raymonde Joubert-Caron
- Laboratoire de Biochimie des Protéines et Protéomique, Université Paris 13, UMR CNRS 7033, 74 rue Marcel Cachin F-93017 Bobigny cedex, France, Institut de Biochimie et Génétique Cellulaires, Université Bordeaux 2, UMR CNRS 5095, 1 rue Camille Saint-Saëns F-33077 Bordeaux Cedex, France, and Laboratoire Polymères, Biopolymères, Surfaces, Equipe BRICS, Université de Rouen, UMR CNRS 6270, Boulevard Maurice de Broglie F-76821 Mont-Saint-Aignan cedex, France
| | - Michel Caron
- Laboratoire de Biochimie des Protéines et Protéomique, Université Paris 13, UMR CNRS 7033, 74 rue Marcel Cachin F-93017 Bobigny cedex, France, Institut de Biochimie et Génétique Cellulaires, Université Bordeaux 2, UMR CNRS 5095, 1 rue Camille Saint-Saëns F-33077 Bordeaux Cedex, France, and Laboratoire Polymères, Biopolymères, Surfaces, Equipe BRICS, Université de Rouen, UMR CNRS 6270, Boulevard Maurice de Broglie F-76821 Mont-Saint-Aignan cedex, France
| | - Julie Hardouin
- Laboratoire de Biochimie des Protéines et Protéomique, Université Paris 13, UMR CNRS 7033, 74 rue Marcel Cachin F-93017 Bobigny cedex, France, Institut de Biochimie et Génétique Cellulaires, Université Bordeaux 2, UMR CNRS 5095, 1 rue Camille Saint-Saëns F-33077 Bordeaux Cedex, France, and Laboratoire Polymères, Biopolymères, Surfaces, Equipe BRICS, Université de Rouen, UMR CNRS 6270, Boulevard Maurice de Broglie F-76821 Mont-Saint-Aignan cedex, France
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First identification of xanthone sulfonamides as potent acyl-CoA:cholesterol acyltransferase (ACAT) inhibitors. Bioorg Med Chem Lett 2010; 20:3094-7. [DOI: 10.1016/j.bmcl.2010.03.101] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/02/2010] [Accepted: 03/27/2010] [Indexed: 11/20/2022]
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39
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Meriläinen G, Poikela V, Kursula P, Wierenga RK. The thiolase reaction mechanism: the importance of Asn316 and His348 for stabilizing the enolate intermediate of the Claisen condensation. Biochemistry 2009; 48:11011-25. [PMID: 19842716 DOI: 10.1021/bi901069h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthetic thiolase catalyzes a Claisen condensation reaction between acetyl-CoA and the enzyme acetylated at Cys89. Two oxyanion holes facilitate this catalysis: oxyanion hole I stabilizes the enolate intermediate generated from acetyl-CoA, whereas oxyanion hole II stabilizes the tetrahedral intermediate of the acetylated enzyme. The latter intermediate is formed when the alpha-carbanion of acetyl-CoA enolate reacts with the carbonyl carbon of acetyl-Cys89, after which C-C bond formation is completed. Oxyanion hole II is made of two main chain peptide NH groups, whereas oxyanion hole I is formed by a water molecule (Wat82) and NE2(His348). Wat82 is anchored in the active site by an optimal set of hydrogen bonding interactions, including a hydrogen bond to ND2(Asn316). Here, the importance of Asn316 and His348 for catalysis has been studied; in particular, the properties of the N316D, N316A, N316H, H348A, and H348N variants have been determined. For the N316D variant, no activity could be detected. For each of the remaining variants, the k(cat)/K(m) value for the Claisen condensation catalysis is reduced by a factor of several hundred, whereas the thiolytic degradation catalysis is much less affected. The crystal structures of the variants show that the structural changes in the active site are minimal. Our studies confirm that oxyanion hole I is critically important for the condensation catalysis. Removing either one of the hydrogen bond donors causes the loss of at least 3.4 kcal/mol of transition state stabilization. It appears that in the thiolytic degradation direction, oxyanion hole I is not involved in stabilizing the transition state of its rate limiting step. However, His348 has a dual role in the catalytic cycle, contributing to oxyanion hole I and activating Cys89. The analysis of the hydrogen bonding interactions in the very polar catalytic cavity shows the importance of two conserved water molecules, Wat82 and Wat49, for the formation of oxyanion hole I and for influencing the reactivity of the catalytic base, Cys378, respectively. Cys89, Asn316, and His348 form the CNH-catalytic triad of the thiolase superfamily. Our findings are also discussed in the context of the importance of this triad for the catalytic mechanism of other enzymes of the thiolase superfamily.
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Affiliation(s)
- Gitte Meriläinen
- Department of Biochemistry, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
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40
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Dyer JH, Maina A, Gomez ID, Cadet M, Oeljeklaus S, Schiedel AC. Cloning, expression and purification of an acetoacetyl CoA thiolase from sunflower cotyledon. Int J Biol Sci 2009; 5:736-44. [PMID: 20011134 PMCID: PMC2793306 DOI: 10.7150/ijbs.5.736] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 11/24/2009] [Indexed: 12/14/2022] Open
Abstract
Thiolase I and II coexist as part of the glyoxysomal beta-oxidation system in sunflower (Helianthus annuus L.) cotyledons, the only system shown to have both forms. The importance of thiolases can be underscored not only by their ubiquity, but also by their involvement in a wide variety of processes in plants, animals and bacteria. Here we describe the cloning, expression and purification of acetoacetyl CoA thiolase (AACT) in enzymatically active form. Use of the extensive amount of sequence information from the databases facilitated the efficient generation of the gene-specific primers used in the RACE protocols. The recombinant AACT (1233 bp) shares 75% similarity with other plant AACTs. Comparison of specific activity of this recombinant AACT to a previously reported enzyme purified from primary sunflower cotyledon tissue was very similar (263 nkat/mg protein vs 220 nkat/mg protein, respectively). Combining the most pure fractions from the affinity column, the enzyme was purified 88-fold with a 55% yield of the enzymatically active, 47 kDa AACT.
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Affiliation(s)
- James H Dyer
- Department of Chemistry and Biochemistry, Montclair State University, NJ 07043, USA.
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41
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Meriläinen G, Schmitz W, Wierenga RK, Kursula P. The sulfur atoms of the substrate CoA and the catalytic cysteine are required for a productive mode of substrate binding in bacterial biosynthetic thiolase, a thioester-dependent enzyme. FEBS J 2008; 275:6136-48. [PMID: 19016856 DOI: 10.1111/j.1742-4658.2008.06737.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thioesters are more reactive than oxoesters, and thioester chemistry is important for the reaction mechanisms of many enzymes, including the members of the thiolase superfamily, which play roles in both degradative and biosynthetic pathways. In the reaction mechanism of the biosynthetic thiolase, the thioester moieties of acetyl-CoA and the acetylated catalytic cysteine react with each other, forming the product acetoacetyl-CoA. Although a number of studies have been carried out to elucidate the thiolase reaction mechanism at the atomic level, relatively little is known about the factors determining the affinity of thiolases towards their substrates. We have carried out crystallographic studies on the biosynthetic thiolase from Zoogloea ramigera complexed with CoA and three of its synthetic analogues to compare the binding modes of these related compounds. The results show that both the CoA terminal SH group and the side chain SH group of the catalytic Cys89 are crucial for the correct positioning of substrate in the thiolase catalytic pocket. Furthermore, calorimetric assays indicate that the mutation of Cys89 into an alanine significantly decreases the affinity of thiolase towards CoA. Thus, although the sulfur atom of the thioester moiety is important for the reaction mechanism of thioester-dependent enzymes, its specific properties can also affect the affinity and competent mode of binding of the thioester substrates to these enzymes.
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42
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Fukao T, Boneh A, Aoki Y, Kondo N. A novel single-base substitution (c.1124A>G) that activates a 5-base upstream cryptic splice donor site within exon 11 in the human mitochondrial acetoacetyl-CoA thiolase gene. Mol Genet Metab 2008; 94:417-421. [PMID: 18511318 DOI: 10.1016/j.ymgme.2008.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 04/17/2008] [Accepted: 04/17/2008] [Indexed: 10/22/2022]
Abstract
Most mutations related to aberrant splicing occur in conserved splice acceptor and donor sites. Some exonic mutations also affect splicing. We identified and characterized a point mutation (c.1124A>G) in an Australian patient (GK43) with mitochondrial acetoacetyl-CoA thiolase (T2) deficiency. GK43 is a homozygote of c.1124A>G, which activates a cryptic splice donor site 5 bases upstream from c.1124A>G within exon 11, causing aberrant splicing in most transcripts. The aberrant splicing results in c.1120-1163 (44-base) deletion, causing a frameshift in T2 mRNA. A mini-gene splicing experiment confirmed that the c.1124A>G substitution was responsible for this aberrant splicing. This cryptic splice site has a Shapiro and Senapathy score (70.0) in a normal sequence but if mutated, the score (84.3) becomes higher than the one in the authentic splice donor site of intron 11 (81.4). This is an example in which a point mutation activates a cryptic splice donor site motif that is used preferentially over a downstream authentic splice site.
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Affiliation(s)
- Toshiyuki Fukao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan; Division of Medical Information Sciences, United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1194, Japan
| | - Avihu Boneh
- Metabolic Service, Murdoch Childrens Research Institute, Royal Children's Hospital, Department of Paediatrics, University of Melbourne, Australia
| | - Yusuke Aoki
- Department of Pediatrics, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Naomi Kondo
- Department of Pediatrics, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
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43
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Wu L, Zeng J, Deng G, Guo F, Li N, Liu X, Chu X, Li D. Inactivation of thiolase by 2-alkynoyl-CoA via its intrinsic isomerase activity. Org Lett 2007; 9:3877-80. [PMID: 17764185 DOI: 10.1021/ol0712677] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective inactivation of cytosolic thiolase by 2-alkynoyl-CoA via its intrinsic isomerase activity was studied, which provides an example for rationally developing mechanism-based inhibitors based on a side activity of the enzyme, and may become a supplemental method for better treatment of cardiovascular disease and cancer.
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Affiliation(s)
- Long Wu
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, PRC
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44
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Sakurai S, Fukao T, Haapalainen AM, Zhang G, Yamada K, Lilliu F, Yano S, Robinson P, Gibson MK, Wanders RJA, Mitchell GA, Wierenga RK, Kondo N. Kinetic and expression analyses of seven novel mutations in mitochondrial acetoacetyl-CoA thiolase (T2): identification of a Km mutant and an analysis of the mutational sites in the structure. Mol Genet Metab 2007; 90:370-8. [PMID: 17236799 DOI: 10.1016/j.ymgme.2006.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 12/03/2006] [Accepted: 12/03/2006] [Indexed: 11/19/2022]
Abstract
Mitochondrial acetoacetyl-CoA thiolase (T2) deficiency is an inborn error of metabolism that affects isoleucine catabolism and ketone body metabolism. We identified 7 novel and 2 previously reported mutations in six T2-deficient patients. Transient expression analysis of wild-type and eight mutant cDNAs was performed at 40, 37 and 30 degrees C. Although no significant residual activity was detected, mutant proteins were detected in the N158D, N158S, R208Q, Y219H and N282H mutants. Accumulation of these mutant proteins was temperature-sensitive with the highest expression levels at lower temperatures. Expression of Q73P and N353K cDNAs yielded neither residual T2 protein nor enzyme activity. An E252del mutant T2 was detected with a relative protein amount and enzyme activity of 30% and 25%, respectively, in comparison to the wild-type at 37 degrees C. The E252del mutant protein was more stable at 30 degrees C expression than 37 degrees C, but was essentially undetectable at 40 degrees C, indicating its temperature-sensitive instability. Kinetic studies revealed a twofold K(m) elevation for substrates coenzyme A and acetoacetyl-CoA in the E252del mutant, while V(max) was comparable to the wild-type. We conclude that the E252del is a temperature-sensitive K(m) mutant. This correlates well with the effect predicted from the T2 tertiary structure analysis, using the crystal structure of the human T2 homotetramer. The probable effect of the other mutations on the T2 tertiary structure was also evaluated.
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Affiliation(s)
- Satomi Sakurai
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Gifu, Japan
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45
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Haapalainen AM, Meriläinen G, Pirilä PL, Kondo N, Fukao T, Wierenga RK. Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function. Biochemistry 2007; 46:4305-21. [PMID: 17371050 DOI: 10.1021/bi6026192] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiolases are CoA-dependent enzymes which catalyze the formation of a carbon-carbon bond in a Claisen condensation step and its reverse reaction via a thiolytic degradation mechanism. Mitochondrial acetoacetyl-coenzyme A (CoA) thiolase (T2) is important in the pathways for the synthesis and degradation of ketone bodies as well as for the degradation of 2-methylacetoacetyl-CoA. Human T2 deficiency has been identified in more than 60 patients. A unique property of T2 is its activation by potassium ions. High-resolution human T2 crystal structures are reported for the apo form and the CoA complex, with and without a bound potassium ion. The potassium ion is bound near the CoA binding site and the catalytic site. Binding of the potassium ion at this low-affinity binding site causes the rigidification of a CoA binding loop and an active site loop. Unexpectedly, a high-affinity binding site for a chloride ion has also been identified. The chloride ion is copurified, and its binding site is at the dimer interface, near two catalytic loops. A unique property of T2 is its ability to use 2-methyl-branched acetoacetyl-CoA as a substrate, whereas the other structurally characterized thiolases cannot utilize the 2-methylated compounds. The kinetic measurements show that T2 can degrade acetoacetyl-CoA and 2-methylacetoacetyl-CoA with similar catalytic efficiencies. For both substrates, the turnover numbers increase approximately 3-fold when the potassium ion concentration is increased from 0 to 40 mM KCl. The structural analysis of the active site of T2 indicates that the Phe325-Pro326 dipeptide near the catalytic cavity is responsible for the exclusive 2-methyl-branched substrate specificity.
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Affiliation(s)
- Antti M Haapalainen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland
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46
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Steussy CN, Robison AD, Tetrick AM, Knight JT, Rodwell VW, Stauffacher CV, Sutherlin AL. A structural limitation on enzyme activity: the case of HMG-CoA synthase. Biochemistry 2007; 45:14407-14. [PMID: 17128980 DOI: 10.1021/bi061505q] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent structural studies of the HMG-CoA synthase members of the thiolase superfamily have shown that the catalytic loop containing the nucleophilic cysteine follows the phi and psi angle pattern of a II' beta turn. However, the i + 1 residue is conserved as an alanine, which is quite unusual in this position as it must adopt a strained positive phi angle to accommodate the geometry of the turn. To assess the effect of the conserved strain in the catalytic loop, alanine 110 of Enterococcus faecalis 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase was mutated to a glycine. Subsequent enzymatic studies showed that the overall reaction rate of the enzyme was increased 140-fold. An X-ray crystallographic study of the Ala110Gly mutant enzyme demonstrated unanticipated adjustments in the active site that resulted in additional stabilization of all three steps of the reaction pathway. The rates of acetylation and hydrolysis of the mutant enzyme increased because the amide nitrogen of Ser308 shifts 0.4 A toward the catalytic cysteine residue. This motion positions the nitrogen to better stabilize the intermediate negative charge that develops on the carbonyl oxygen of the acetyl group during both the formation of the acyl-enzyme intermediate and its hydrolysis. In addition, the hydroxyl of Ser308 rotates 120 degrees to a position where it is able to stabilize the carbanion intermediate formed by the methyl group of the acetyl-S-enzyme during its condensation with acetoacetyl-CoA.
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Affiliation(s)
- Calvin N Steussy
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
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47
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Sundaramoorthy R, Micossi E, Alphey MS, Germain V, Bryce JH, Smith SM, Leonard GA, Hunter WN. The Crystal Structure of a Plant 3-Ketoacyl-CoA Thiolase Reveals the Potential for Redox Control of Peroxisomal Fatty Acid β-Oxidation. J Mol Biol 2006; 359:347-57. [PMID: 16630629 DOI: 10.1016/j.jmb.2006.03.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/07/2006] [Accepted: 03/15/2006] [Indexed: 11/30/2022]
Abstract
Crystal structures of peroxisomal Arabidopsis thaliana 3-ketoacyl-CoA thiolase (AtKAT), an enzyme of fatty acid beta-oxidation, are reported. The subunit, a typical thiolase, is a combination of two similar alpha/beta domains capped with a loop domain. The comparison of AtKAT with the Saccharomyces cerevisiae homologue (ScKAT) structure reveals a different placement of subunits within the functional dimers and that a polypeptide segment forming an extended loop around the open catalytic pocket of ScKAT converts to alpha-helix in AtKAT, and occludes the active site. A disulfide is formed between Cys192, on this helix, and Cys138, a catalytic residue. Access to Cys138 is determined by the structure of this polypeptide segment. AtKAT represents an oxidized, previously unknown inactive form, whilst ScKAT is the reduced and active enzyme. A high level of sequence conservation is observed, including Cys192, in eukaryotic peroxisomal, but not mitochondrial or prokaryotic KAT sequences, for this labile loop/helix segment. This indicates that KAT activity in peroxisomes is influenced by a disulfide/dithiol change linking fatty acid beta-oxidation with redox regulation.
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Affiliation(s)
- Ramasubramanian Sundaramoorthy
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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48
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Zhang YM, Hurlbert J, White SW, Rock CO. Roles of the Active Site Water, Histidine 303, and Phenylalanine 396 in the Catalytic Mechanism of the Elongation Condensing Enzyme of Streptococcus pneumoniae. J Biol Chem 2006; 281:17390-17399. [PMID: 16618705 DOI: 10.1074/jbc.m513199200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
beta-Ketoacyl-ACP synthases catalyze the condensation steps in fatty acid and polyketide synthesis and are targets for the development of novel antibiotics and anti-obesity and anti-cancer agents. The roles of the active site residues in Streptococcus pneumoniae FabF (beta-ketoacyl-ACP synthase II; SpFabF) were investigated to clarify the mechanism for this enzyme superfamily. The nucleophilic cysteine of the active site triad was required for acyl-enzyme formation and the overall condensation activity. The two active site histidines in the elongation condensing enzyme have different electronic states and functions. His337 is essential for condensation activity, and its protonated Nepsilon stabilizes the negative charge developed on the malonyl thioester carbonyl in the transition state. The Nepsilon of His303 accelerated catalysis by deprotonating a structured active site water for nucleophilic attack on the C3 of malonate, releasing bicarbonate. Lys332 controls the electronic state of His303 and also plays a critical role in the positioning of His337. Phe396 functions as a gatekeeper that controls the order of substrate addition. These data assign specific roles for each active site residue and lead to a revised general mechanism for this important class of enzymes.
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Affiliation(s)
- Yong-Mei Zhang
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Jason Hurlbert
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Stephen W White
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Charles O Rock
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.
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49
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Tsuchiya D, Shimizu N, Ishikawa M, Suzuki Y, Morikawa K. Ligand-induced domain rearrangement of fatty acid beta-oxidation multienzyme complex. Structure 2006; 14:237-46. [PMID: 16472743 DOI: 10.1016/j.str.2005.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Revised: 10/05/2005] [Accepted: 10/12/2005] [Indexed: 11/17/2022]
Abstract
The quaternary structure of a fatty acid beta-oxidation multienzyme complex, catalyzing three sequential reactions, was investigated by X-ray crystallographic and small-angle X-ray solution scattering analyses. X-ray crystallography revealed an intermediate structure of the complex among the previously reported structures. However, the theoretical scattering curves calculated from the crystal structures remarkably disagree with the experimental profiles. Instead, an ensemble of the atomic models, which were all calculated by rigid-body optimization, reasonably explained the experimental data. These structures significantly differ from those in the crystals, but they maintain the substrate binding pocket at the domain boundary. Comparisons among these structures indicated that binding of 3-hydroxyhexadecanoyl-CoA or nicotinamide adenine dinucleotide induces domain rearrangements in the complex. The conformational changes suggest the structural events occurring during the chain reaction catalyzed by the multienzyme complex.
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Affiliation(s)
- Daisuke Tsuchiya
- Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
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50
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Haapalainen AM, Meriläinen G, Wierenga RK. The thiolase superfamily: condensing enzymes with diverse reaction specificities. Trends Biochem Sci 2006; 31:64-71. [PMID: 16356722 DOI: 10.1016/j.tibs.2005.11.011] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 10/25/2005] [Accepted: 11/25/2005] [Indexed: 11/22/2022]
Abstract
The formation of a carbon-carbon bond is an essential step in the biosynthetic pathways by which fatty acids and polyketides are made. The thiolase superfamily enzymes catalyse this carbon-carbon-bond formation via a thioester-dependent Claisen-condensation-reaction mechanism. In this way, fatty-acid chains and polyketides are made by sequentially adding simple building blocks, such as acetate units, to the growing molecule. A common feature of these enzymes is a reactive cysteine residue that is transiently acylated in the catalytic cycle. The wide catalytic diversity of the thiolase superfamily enzymes is of great interest. In particular, the type-III polyketide synthases make complicated compounds of great biological importance using multiple, subsequent condensation reactions, which are all catalysed in the same active-site cavity. The crucial metabolic importance of the bacterial fatty-acid-synthesizing enzymes stimulates in-depth studies that aim to develop efficient anti-bacterial drugs.
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Affiliation(s)
- Antti M Haapalainen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, PO Box 3000, FIN-90014, Finland
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