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Coenzyme Activity of NAD Analogs for 3-Isopropylmalate Dehydrogenase fromThermus thermophilusHB8. Biosci Biotechnol Biochem 2014; 63:1647-9. [DOI: 10.1271/bbb.63.1647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Yin BL, Zhang ZR, Xu LW, Jiang H. Highly Facialselective Synthesis of Pyranose 1,3-Oxazines and Their Ring Opening with Nucleophiles: A Novel Entry to 2-C-Branched Glycosides. Org Lett 2011; 13:5088-91. [DOI: 10.1021/ol2019604] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Biao-Lin Yin
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, 510640, China, and Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, P. R. China
| | - Ze-Ren Zhang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, 510640, China, and Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, P. R. China
| | - Li-Wen Xu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, 510640, China, and Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, P. R. China
| | - Huanfeng Jiang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, 510640, China, and Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, P. R. China
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Nango E, Yamamoto T, Kumasaka T, Eguchi T. Crystal structure of 3-isopropylmalate dehydrogenase in complex with NAD(+) and a designed inhibitor. Bioorg Med Chem 2009; 17:7789-94. [PMID: 19833522 DOI: 10.1016/j.bmc.2009.09.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 09/12/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
Abstract
Isopropylmalate dehydrogenase (IPMDH) is the third enzyme specific to leucine biosynthesis in microorganisms and plants, and catalyzes the oxidative decarboxylation of (2R,3S)-3-isopropylmalate to alpha-ketoisocaproate using NAD(+) as an oxidizing agent. In this study, a thia-analogue of the substrate was designed and synthesized as an inhibitor for IPMDH. The analogue showed strong competitive inhibitory activity with K(i)=62nM toward IPMDH derived from Thermus thermophilus. Moreover, the crystal structure of T. thermophilus IPMDH in a ternary complex with NAD(+) and the inhibitor has been determined at 2.8A resolution. The inhibitor exists as a decarboxylated product with an enol/enolate form in the active site. The product interacts with Arg 94, Asn 102, Ser 259, Glu 270, and a water molecule hydrogen-bonding with Arg 132. All interactions between the product and the enzyme were observed in the position associated with keto-enol tautomerization. This result implies that the tautomerization step of the thia-analogue during the IPMDH reaction is involved in the inhibition.
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Affiliation(s)
- Eriko Nango
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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Fujita M, Tamegai H, Eguchi T, Kakinuma K. Novel substrate specificity of designer 3-isopropylmalate dehydrogenase derived from Thermus thermophilus HB8. Biosci Biotechnol Biochem 2001; 65:2695-700. [PMID: 11826966 DOI: 10.1271/bbb.65.2695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Redesigning of an enzyme for a new catalytic reaction and modified substrate specificity was exploited with 3-isopropylmalate dehydrogenase (IPMDH). Point-mutation on Gly-89, which is not in the catalytic site but near it, was done by changing it to Ala, Ser, Val, and Pro, and all the mutations changed the substrate specificity. The mutant enzymes showed higher catalytic efficiency (kcat/Km) than the native IPMDH when malate was used as a substrate instead of 3-isopropylmalate. More interestingly, an additional insertion of Gly between Gly-89 and Leu-90 significantly altered the substrate-specificity, although the overall catalytic activity was decreased. Particularly, this mutant turned out to efficiently accept D-lactic acid, which was not accepted as a substrate by wild-type IPMDH at all. These results demonstrate the opportunity for creating nove,enzymes by modification of amino acid residues that do not directly participate in catalysis, or by insertion of additional residues.
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Affiliation(s)
- M Fujita
- Department of Chemistry, Tokyo Institute of Technology, Japan
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Fujita M, Toyooka Y, Tamegai H, Eguchi T, Kakinuma K. Arg-94 is crucial to the catalysis of 3-isopropylmalate dehydrogenase from Thermus thermophilus HB8. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(99)00091-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Chiba A, Arai N, Eguchi T, Kakinuma K. 3-Isopropylidenemalic Acid: A Mechanism-based Inhibitor of 3-Isopropylmalate Dehydrogenase. CHEM LETT 1999. [DOI: 10.1246/cl.1999.1313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Chiba A, Aoyama T, Suzuki R, Eguchi T, Oshima T, Kakinuma K. Synthetic and Mechanistic Studies of (2R,3S)-3-Vinylmalic Acid as a Mechanism-Based Inhibitor of 3-Isopropylmalate Dehydrogenase. J Org Chem 1999. [DOI: 10.1021/jo982206c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akira Chiba
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Tetsuya Aoyama
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Rieko Suzuki
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Tairo Oshima
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
| | - Katsumi Kakinuma
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan, and Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji-shi, Tokyo 192-0392, Japan
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Chiba A, Eguchi T, Oshima T, Kakinuma K. Synthesis of cyclopropane substrate analog for 3-isopropylmalate dehydrogenase and its mechanism-based inhibition. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00074-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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