1
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Nomura T. Function and application of a non-ester-hydrolyzing carboxylesterase discovered in tulip. Biosci Biotechnol Biochem 2017; 81:81-94. [DOI: 10.1080/09168451.2016.1240608] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Plants have evolved secondary metabolite biosynthetic pathways of immense rich diversity. The genes encoding enzymes for secondary metabolite biosynthesis have evolved through gene duplication followed by neofunctionalization, thereby generating functional diversity. Emerging evidence demonstrates that some of those enzymes catalyze reactions entirely different from those usually catalyzed by other members of the same family; e.g. transacylation catalyzed by an enzyme similar to a hydrolytic enzyme. Tuliposide-converting enzyme (TCE), which we recently discovered from tulip, catalyzes the conversion of major defensive secondary metabolites, tuliposides, to antimicrobial tulipalins. The TCEs belong to the carboxylesterase family in the α/β-hydrolase fold superfamily, and specifically catalyze intramolecular transesterification, but not hydrolysis. This non-ester-hydrolyzing carboxylesterase is an example of an enzyme showing catalytic properties that are unpredictable from its primary structure. This review describes the biochemical and physiological aspects of tulipalin biogenesis, and the diverse functions of plant carboxylesterases in the α/β-hydrolase fold superfamily.
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Affiliation(s)
- Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
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2
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Mindrebo JT, Nartey CM, Seto Y, Burkart MD, Noel JP. Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. Curr Opin Struct Biol 2016; 41:233-246. [PMID: 27662376 PMCID: PMC5687975 DOI: 10.1016/j.sbi.2016.08.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/13/2022]
Abstract
The alpha/beta hydrolase (ABH) superfamily is a widespread and functionally malleable protein fold recognized for its diverse biochemical activities across all three domains of life. ABH enzymes possess unexpected catalytic activity in the green plant lineage through selective alterations in active site architecture and chemistry. Furthermore, the ABH fold serves as the core structure for phytohormone and ligand receptors in the gibberellin, strigolactone, and karrikin signaling pathways in plants. Despite recent discoveries, the ABH family is sparsely characterized in plants, a sessile kingdom known to evolve complex and specialized chemical adaptations as survival responses to widely varying biotic and abiotic ecologies. This review calls attention to the ABH superfamily in the plant kingdom to highlight the functional adaptability of the ABH fold.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, The University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charisse M Nartey
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yoshiya Seto
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, The University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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3
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Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs. J Biotechnol 2016; 235:24-31. [DOI: 10.1016/j.jbiotec.2016.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 11/21/2022]
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4
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Zhao Y, Chen N, Wang C, Cao Z. A Comprehensive Understanding of Enzymatic Catalysis by Hydroxynitrile Lyases with S Stereoselectivity from the α/β-Hydrolase Superfamily: Revised Role of the Active-Site Lysine and Kinetic Behavior of Substrate Delivery and Sequential Product Release. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02855] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuan Zhao
- The Key Laboratory of Natural Medicine
and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine
and Immuno-Engineering, Henan University, Kaifeng 475004, People’s Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and
Fujian Provincial Key Laboratory of Theoretical and Computational
Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People’s Republic of China
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5
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Rauwerdink A, Lunzer M, Devamani T, Jones B, Mooney J, Zhang ZJ, Xu JH, Kazlauskas RJ, Dean AM. Evolution of a Catalytic Mechanism. Mol Biol Evol 2015; 33:971-9. [PMID: 26681154 DOI: 10.1093/molbev/msv338] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The means by which superfamilies of specialized enzymes arise by gene duplication and functional divergence are poorly understood. The escape from adaptive conflict hypothesis, which posits multiple copies of a gene encoding a primitive inefficient and highly promiscuous generalist ancestor, receives support from experiments showing that resurrected ancestral enzymes are indeed more substrate-promiscuous than their modern descendants. Here, we provide evidence in support of an alternative model, the innovation-amplification-divergence hypothesis, which posits a single-copied ancestor as efficient and specific as any modern enzyme. We argue that the catalytic mechanisms of plant esterases and descendent acetone cyanohydrin lyases are incompatible with each other (e.g., the reactive substrate carbonyl must bind in opposite orientations in the active site). We then show that resurrected ancestral plant esterases are as catalytically specific as modern esterases, that the ancestor of modern acetone cyanohydrin lyases was itself only very weakly promiscuous, and that improvements in lyase activity came at the expense of esterase activity. These observations support the innovation-amplification-divergence hypothesis, in which an ancestor gains a weak promiscuous activity that is improved by selection at the expense of the ancestral activity, and not the escape from adaptive conflict in which an inefficient generalist ancestral enzyme steadily loses promiscuity throughout the transition to a highly active specialized modern enzyme.
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Affiliation(s)
- Alissa Rauwerdink
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota
| | - Mark Lunzer
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota
| | - Titu Devamani
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota
| | - Bryan Jones
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota
| | - Joanna Mooney
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota
| | - Zhi-Jun Zhang
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota Department of Biotechnology, East China University of Science and Technology, Shanghai, PR China
| | - Jian-He Xu
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota Department of Biotechnology, East China University of Science and Technology, Shanghai, PR China
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota
| | - Antony M Dean
- Department of Biochemistry, Molecular Biology & Biophysics and the Biotechnology Institute, University of Minnesota Department of Ecology, Evolution and Behavior, University of Minnesota College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, PR China
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6
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Zhao Y, Chen N, Mo Y, Cao Z. A full picture of enzymatic catalysis by hydroxynitrile lyases from Hevea brasiliensis: protonation dependent reaction steps and residue-gated movement of the substrate and the product. Phys Chem Chem Phys 2014; 16:26864-75. [DOI: 10.1039/c4cp04032e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydroxynitrile lyases (HNLs) defend plants from herbivores and microbial attack by releasing cyanide from hydroxynitriles.
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Affiliation(s)
- Yuan Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005, P. R. China
| | - Nanhao Chen
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, P. R. China
| | - Yirong Mo
- Department of Chemistry
- Western Michigan University
- Kalamazoo, USA
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005, P. R. China
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7
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8
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García-Urdiales E, Alfonso I, Gotor V. Update 1 of: Enantioselective Enzymatic Desymmetrizations in Organic Synthesis. Chem Rev 2011; 111:PR110-80. [DOI: 10.1021/cr100330u] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eduardo García-Urdiales
- Departamento de Química
Orgánica e Inorgánica, Facultad de Química, Universidad
de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain,
and
| | - Ignacio Alfonso
- Departamento de Química Biológica
y Modelización Molecular, Instituto de Química Avanzada
de Cataluña (IQAC, CSIC), Jordi Girona, 18-26, 08034, Barcelona,
Spain
| | - Vicente Gotor
- Departamento de Química
Orgánica e Inorgánica, Facultad de Química, Universidad
de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain,
and
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9
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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10
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Kamiya K, Boero M, Shiraishi K, Oshiyama A, Shigeta Y. Energy Compensation Mechanism for Charge-Separated Protonation States in Aspartate−Histidine Amino Acid Residue Pairs. J Phys Chem B 2010; 114:6567-78. [DOI: 10.1021/jp906148m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katsumasa Kamiya
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Mauro Boero
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Kenji Shiraishi
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Atsushi Oshiyama
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
| | - Yasuteru Shigeta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo, 678-1297, Japan, CREST, Japan Science and Technology Agency, Sanban-cho, Tokyo 102-0075, Japan, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23, rue du Loess, F-67034 Strasbourg 2, France, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan, Center for Computational
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11
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Dreveny I, Andryushkova AS, Glieder A, Gruber K, Kratky C. Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity. Biochemistry 2009; 48:3370-7. [PMID: 19256550 PMCID: PMC2669238 DOI: 10.1021/bi802162s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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In a large number of plant species hydroxynitrile lyases catalyze the decomposition of cyanohydrins in order to generate hydrogen cyanide upon tissue damage. Hydrogen cyanide serves as a deterrent against herbivores and fungi. In vitro hydroxynitrile lyases are proficient biocatalysts for the stereospecific synthesis of cyanohydrins. Curiously, hydroxynitrile lyases from different species are completely unrelated in structure and substrate specificity despite catalyzing the same reaction. The hydroxynitrile lyase from almond shows close resemblance to flavoproteins of the glucose−methanol−choline oxidoreductase family. We report here 3D structural data of this lyase with the reaction product benzaldehyde bound within the active site, which allow unambiguous assignment of the location of substrate binding. Based on the binding geometry, a reaction mechanism is proposed that involves one of the two conserved active site histidine residues acting as a general base abstracting the proton from the cyanohydrin hydroxyl group. Site-directed mutagenesis shows that both active site histidines are required for the reaction to occur. There is no evidence that the flavin cofactor directly participates in the reaction. Comparison with other hydroxynitrile lyases reveals a large diversity of active site architectures, which, however, share the common features of a general active site base and a nearby patch with positive electrostatic potential. On the basis of the difference in substrate binding geometry between the FAD-dependent HNL from almond and the related oxidases, we can rationalize why the HNL does not act as an oxidase.
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Affiliation(s)
- Ingrid Dreveny
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Humboldtstrasse 50/III, A-8010 Graz, Austria.
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12
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Schmidt A, Gruber K, Kratky C, Lamzin VS. Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis. J Biol Chem 2008; 283:21827-36. [PMID: 18524775 DOI: 10.1074/jbc.m801056200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydroxynitrile lyases are versatile enzymes that enantiospecifically cope with cyanohydrins, important intermediates in the production of various agrochemicals or pharmaceuticals. We determined four atomic resolution crystal structures of hydroxynitrile lyase from Hevea brasiliensis: one native and three complexes with acetone, isopropyl alcohol, and thiocyanate. We observed distinct distance changes among the active site residues related to proton shifts upon substrate binding. The combined use of crystallography and ab initio quantum chemical calculations allowed the determination of the protonation states in the enzyme active site. We show that His(235) of the catalytic triad must be protonated in order for catalysis to proceed, and we could reproduce the cyanohydrin synthesis in ab initio calculations. We also found evidence for the considerable pK(a) shifts that had been hypothesized earlier. We envision that this knowledge can be used to enhance the catalytic properties and the stability of the enzyme for industrial production of enantiomerically pure cyanohydrins.
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Affiliation(s)
- Andrea Schmidt
- EMBL Hamburg c/o Deutsches Elektronen Synchrotron, Notkestrasse 85, Hamburg, Germany.
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13
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Stöckigt J, Panjikar S. Structural biology in plant natural product biosynthesis--architecture of enzymes from monoterpenoid indole and tropane alkaloid biosynthesis. Nat Prod Rep 2007; 24:1382-400. [PMID: 18033585 DOI: 10.1039/b711935f] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several cDNAs of enzymes catalyzing biosynthetic pathways of plant-derived alkaloids have recently been heterologously expressed, and the production of appropriate enzymes from ajmaline and tropane alkaloid biosynthesis in bacteria allows their crystallization. This review describes the architecture of these enzymes with and without their ligands.
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Affiliation(s)
- Joachim Stöckigt
- College of Pharmaceutical Sciences, Zijingang Campus, Zhejiang University, 310058, Hangzhou, China
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14
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Purkarthofer T, Gruber K, Gruber-Khadjawi M, Waich K, Skranc W, Mink D, Griengl H. A biocatalytic Henry reaction--the hydroxynitrile lyase from Hevea brasiliensis also catalyzes nitroaldol reactions. Angew Chem Int Ed Engl 2007; 45:3454-6. [PMID: 16634109 DOI: 10.1002/anie.200504230] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Gruber-Khadjawi M, Purkarthofer T, Skranc W, Griengl H. Hydroxynitrile Lyase-Catalyzed Enzymatic Nitroaldol (Henry) Reaction. Adv Synth Catal 2007. [DOI: 10.1002/adsc.200700064] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Fechter MH, Gruber K, Avi M, Skranc W, Schuster C, Pöchlauer P, Klepp KO, Griengl H. Stereoselective Biocatalytic Synthesis of (S)-2-Hydroxy-2-Methylbutyric Acid via Substrate Engineering by Using “Thio-Disguised” Precursors and Oxynitrilase Catalysis. Chemistry 2007; 13:3369-76. [PMID: 17226866 DOI: 10.1002/chem.200601114] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
3-Tetrahydrothiophenone (4) and 4-phenylthiobutan-2-one (7) were used as masked 2-butanone equivalents to give the corresponding cyanohydrins 5 (79 % yield, 91 % ee) and 8 (95 % yield, 96 % ee) in an enzymatic cyanohydrin reaction applying the hydroxynitrile lyase (HNL) from Hevea brasiliensis. After hydrolysis and desulphurisation the desired intermediate (S)-2-hydroxy-2-methylbutyric acid (10) was obtained with 99 % ee. Interestingly, when applying (R)-selective HNL from Prunus amygdalus again the (S)-cyanohydrin 5 was formed (62 % ee). The absolute configuration of 5 was verified by crystal structure determination of the corresponding hydrolysis derived carboxylate. The fact that both enzymes yield the same enantiomer was analysed and interpreted by molecular modelling calculations.
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Affiliation(s)
- Martin H Fechter
- Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
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17
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Gartler G, Kratky C, Gruber K. Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis. J Biotechnol 2007; 129:87-97. [PMID: 17250917 DOI: 10.1016/j.jbiotec.2006.12.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Revised: 07/28/2006] [Accepted: 08/15/2006] [Indexed: 10/23/2022]
Abstract
The hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis (HbHNL) is utilized as a biocatalyst in stereospecific syntheses of alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed reaction represents one of the few industrially relevant examples of enzyme mediated C-C coupling reactions. In this work, we determined the X-ray crystal structures (at 1.54 and 1.76 Angstroms resolution) of HbHNL complexes with two chiral substrates -- mandelonitrile and 2,3-dimethyl-2-hydroxy-butyronitrile -- by soaking and rapid freeze quenching techniques. This is the first structural observation of the complex between a HNL and chiral substrates. Consistent with the known selectivity of the enzyme, only the S-enantiomers of the two substrates were observed in the active site. The binding modes of the chiral substrates were identical to that observed for the biological substrate acetone cyanohydrin. This indicates that the transformation of these non-natural substrates follows the same mechanism. A large hydrophobic pocket was identified in the active site of HbHNL which accommodates the more voluminous substituents of the two substrates. A three-point binding mode of the substrates -- hydrophobic pocket, hydrogen bonds between the hydroxyl group and Ser80 and Thr11, electrostatic interaction of the cyano group with Lys236 -- offers a likely structural explanation for the enantioselectivity of the enzyme. The structural data rationalize the observed (S)-enantioselectivity and form the basis for modifying the stereospecificity through rational design. The structures also revealed the necessity of considerable flexibility of the sidechain of Trp128 in order to bind and transform larger substrates.
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Affiliation(s)
- Günter Gartler
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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18
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Purkarthofer T, Gruber K, Gruber-Khadjawi M, Waich K, Skranc W, Mink D, Griengl H. Eine biokatalytische Henry-Reaktion – die Hydroxynitrillyase ausHevea brasiliensis katalysiert auch Nitroaldolreaktionen. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504230] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Bugg TDH. Diverse catalytic activities in the alphabeta-hydrolase family of enzymes: activation of H2O, HCN, H2O2, and O2. Bioorg Chem 2005; 32:367-75. [PMID: 15381402 DOI: 10.1016/j.bioorg.2004.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Indexed: 11/17/2022]
Abstract
The article describes the observation of novel catalytic activities in the alphabeta-hydrolase superfamily apparently unrelated to ester hydrolysis and unexpected biochemical observations relating to the structure and function of the serine catalytic triad in these enzymes. One common feature of these novel activities is the activation of a small diatomic molecule, but via diverse chemistry. Possible mechanisms of catalysis are discussed.
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Affiliation(s)
- Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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García-Urdiales E, Alfonso I, Gotor V. Enantioselective enzymatic desymmetrizations in organic synthesis. Chem Rev 2005; 105:313-54. [PMID: 15720156 DOI: 10.1021/cr040640a] [Citation(s) in RCA: 393] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eduardo García-Urdiales
- Departamento de Química Orgánica e Inorgánica, Facultad de Química, Universidad de Oviedo, Julián Clavería, 8, 33071 Oviedo, Spain
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Avi M, Fechter MH, Gruber K, Belaj F, Pöchlauer P, Griengl H. Hydroxynitrile lyase catalysed synthesis of heterocyclic (R)- and (S)-cyanohydrins. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.07.099] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Gruber K, Gartler G, Krammer B, Schwab H, Kratky C. Reaction mechanism of hydroxynitrile lyases of the alpha/beta-hydrolase superfamily: the three-dimensional structure of the transient enzyme-substrate complex certifies the crucial role of LYS236. J Biol Chem 2004; 279:20501-10. [PMID: 14998991 DOI: 10.1074/jbc.m401575200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hydroxynitrile lyases (HNLs) from Hevea brasiliensis (HbHNL) and from Manihot esculenta (MeHNL) are both members of the alpha/beta-hydrolase superfamily. Mechanistic proposals have been put forward in the past for both enzymes; they differed with respect to the role of the active-site lysine residue for which a catalytic function was claimed for the Hevea enzyme but denied for the Manihot enzyme. We applied a freeze-quench method to prepare crystals of the complex of HbHNL with the biological substrate acetone cyanohydrin and determined its three-dimensional structure. Site-directed mutagenesis was used to prepare the mutant K236L, which is inactive although its three-dimensional structure is similar to the wild-type enzyme. However, the structure of the K236L-acetone cyanohydrin complex shows the substrate in a different orientation from the wild-type complex. Finite difference Poisson-Boltzmann calculations show that in the absence of Lys(236) the catalytic base His(235) would be protonated at neutral pH. All of this suggests that Lys(236) is instrumental for catalysis in several ways, i.e. by correctly positioning the substrate, by stabilizing the negatively charged reaction product CN(-), and by modulating the basicity of the catalytic base. These data complete the elucidation of the reaction mechanism of alpha/beta-hydrolase HNLs, in which the catalytic triad acts as a general base rather than as a nucleophile; proton abstraction from the substrate is performed by the serine, and reprotonation of the product cyanide is performed by the histidine residues. Together with a threonine side chain, the active-site serine and lysine are also involved in substrate binding.
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Affiliation(s)
- Karl Gruber
- Institut für Chemie, Physikalische Chemie, Karl-Franzens Universitaät Heinrichstrasse 28, A-8010 Graz, Austria
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Baxter SM, Rosenblum JS, Knutson S, Nelson MR, Montimurro JS, Di Gennaro JA, Speir JA, Burbaum JJ, Fetrow JS. Synergistic Computational and Experimental Proteomics Approaches for More Accurate Detection of Active Serine Hydrolases in Yeast. Mol Cell Proteomics 2004; 3:209-25. [PMID: 14645503 DOI: 10.1074/mcp.m300082-mcp200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An analysis of the structurally and catalytically diverse serine hydrolase protein family in the Saccharomyces cerevisiae proteome was undertaken using two independent but complementary, large-scale approaches. The first approach is based on computational analysis of serine hydrolase active site structures; the second utilizes the chemical reactivity of the serine hydrolase active site in complex mixtures. These proteomics approaches share the ability to fractionate the complex proteome into functional subsets. Each method identified a significant number of sequences, but 15 proteins were identified by both methods. Eight of these were unannotated in the Saccharomyces Genome Database at the time of this study and are thus novel serine hydrolase identifications. Three of the previously uncharacterized proteins are members of a eukaryotic serine hydrolase family, designated as Fsh (family of serine hydrolase), identified here for the first time. OVCA2, a potential human tumor suppressor, and DYR-SCHPO, a dihydrofolate reductase from Schizosaccharomyces pombe, are members of this family. Comparing the combined results to results of other proteomic methods showed that only four of the 15 proteins were identified in a recent large-scale, "shotgun" proteomic analysis and eight were identified using a related, but similar, approach (neither identifies function). Only 10 of the 15 were annotated using alternate motif-based computational tools. The results demonstrate the precision derived from combining complementary, function-based approaches to extract biological information from complex proteomes. The chemical proteomics technology indicates that a functional protein is being expressed in the cell, while the computational proteomics technology adds details about the specific type of function and residue that is likely being labeled. The combination of synergistic methods facilitates analysis, enriches true positive results, and increases confidence in novel identifications. This work also highlights the risks inherent in annotation transfer and the use of scoring functions for determination of correct annotations.
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Affiliation(s)
- Susan M Baxter
- GeneFormatics, Inc., 5830 Oberlin Drive, Suite 200, San Diego, CA 92121, USA
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25
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Brookhaven National Laboratory, Building 725 A X9, Upton, New York 11973, USA
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Stranzl GR, Gruber K, Steinkellner G, Zangger K, Schwab H, Kratky C. Observation of a Short, Strong Hydrogen Bond in the Active Site of Hydroxynitrile Lyase from Hevea brasiliensis Explains a Large pK Shift of the Catalytic Base Induced by the Reaction Intermediate. J Biol Chem 2004; 279:3699-707. [PMID: 14597632 DOI: 10.1074/jbc.m306814200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The hydroxynitrile lyase from Hevea brasiliensis (HbHNL) uses a catalytic triad consisting of Ser(80)-His(235)-Asp(207) to enhance the basicity of Ser(80)-O gamma for abstracting a proton from the OH group of the substrate cyanohydrin. Following the observation of a relatively short distance between a carboxyl oxygen of Asp(207) and the N delta(1)(His(235)) in a 1.1 A crystal structure of HbHNL, we here show by (1)H and (15)N-NMR spectroscopy that a short, strong hydrogen bond (SSHB) is formed between the two residues upon binding of the competitive inhibitor thiocyanate to HbHNL: the proton resonance of H-N delta 1(His(235)) moves from 15.41 ppm in the free enzyme to 19.35 ppm in the complex, the largest downfield shift observed so far upon inhibitor binding. Simultaneously, the D/H fractionation factor decreases from 0.98 to 0.35. In the observable pH range, i.e. between pH 4 and 10, no significant changes in chemical shifts (and therefore hydrogen bond strength) were observed for free HbHNL. For the complex with thiocyanate, the 19.35 ppm signal returned to 15.41 ppm at approximately pH 8, which indicates a pK(a) near this value for the H-N epsilon(2)(His(235)). These NMR results were analyzed on the basis of finite difference Poisson-Boltzmann calculations, which yielded the relative free energies of four protonation states of the His(235)-Asp(207) pair in solution as well as in the protein environment with and without bound inhibitor. The calculations explain all the NMR features, i.e. they suggest why a short, strong hydrogen bond is formed upon inhibitor binding and why this short, strong hydrogen bond reverts back to a normal one at approximately pH 8. Importantly, the computations also yield a shift of the free energy of the anionic state relative to the zwitterionic reference state by about 10.6 kcal/mol, equivalent to a shift in the apparent pK(a) of His(235) from 2.5 to 10. This huge inhibitor-induced increase in basicity is a prerequisite for His(235) to act as general base in the HbHNL-catalyzed cyanohydrin reaction.
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Affiliation(s)
- Gudrun R Stranzl
- Institut für Chemie, Physikalische Chemie, Karl-Franzens Universität Heinrichstrasse 28, A-8010 Graz, Austria
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27
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Novel access to chiral 1,1′-disubstituted ferrocene derivatives via double stereoselective cyanohydrin synthesis exploiting the hydroxynitrile lyase from Hevea brasiliensis. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0957-4166(02)00826-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Gruber K, Kratky C. Biopolymers for biocatalysis: Structure and catalytic mechanism of hydroxynitrile lyases. ACTA ACUST UNITED AC 2003. [DOI: 10.1002/pola.10845] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Mattern-Dogru E, Ma X, Hartmann J, Decker H, Stöckigt J. Potential active-site residues in polyneuridine aldehyde esterase, a central enzyme of indole alkaloid biosynthesis, by modelling and site-directed mutagenesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:2889-96. [PMID: 12071952 DOI: 10.1046/j.1432-1033.2002.02956.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the biosynthesis of the antiarrhythmic alkaloid ajmaline, polyneuridine aldehyde esterase (PNAE) catalyses a central reaction by transforming polyneuridine aldehyde into epi-vellosimine, which is the immediate precursor for the synthesis of the ajmalane skeleton. The PNAE cDNA was previously heterologously expressed in E. coli. Sequence alignments indicated that PNAE has a 43% identity to a hydroxynitrile lyase from Hevea brasiliensis, which is a member of the alpha/beta hydrolase superfamily. The catalytic triad, which is typical for this family, is conserved. By site-directed mutagenesis, the members of the catalytic triad were identified. For further detection of the active residues, a model of PNAE was constructed based on the X-ray crystallographic structure of hydroxynitrile lyase. The potential active site residues were selected on this model, and were mutated in order to better understand the relationship of PNAE with the alpha/beta hydrolases, and as well its mechanism of action. The results showed that PNAE is a novel member of the alpha/beta hydrolase enzyme superfamily.
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Affiliation(s)
- Emine Mattern-Dogru
- Lehrstuhl für Pharmazeutische Biologie, Institut für Pharmazie, Johannes Gutenberg-Universität Mainz, Germany
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30
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Steiner T. Hydrogen bonds from water molecules to aromatic acceptors in very high-resolution protein crystal structures. Biophys Chem 2002; 95:195-201. [PMID: 12062379 DOI: 10.1016/s0301-4622(01)00256-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Short contacts of water molecules with the pi-faces of aromatic residues were studied in a set of 75 very high resolution (<1.1 A) protein X-ray crystal structures. For 18 water molecules found at distances to aromatic midpoints <3.5 A, it was attempted to assign the hydrogen bond configuration (without experimental knowledge of the H-atom positions) by inspection of the surrounding. For approximately one-quarter of the cases, evidence for an O-H...pi hydrogen bond was found, another one-quarter does not form such a hydrogen bond, and for the remaining half, no conclusive assignment could be made. The results confirm the relatively frequent occurrence of aromatic hydrogen bonding in biomolecular hydration, but also underline difficulties in hydrogen bond assignment without reliable knowledge of the H-atom positions.
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Affiliation(s)
- Thomas Steiner
- Institut für Chemie-Kristallographie, Freie Universität Berlin, Takustr. 6, D-14195, Berlin, Germany.
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31
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Dreveny I, Kratky C, Gruber K. The active site of hydroxynitrile lyase from Prunus amygdalus: modeling studies provide new insights into the mechanism of cyanogenesis. Protein Sci 2002; 11:292-300. [PMID: 11790839 PMCID: PMC2373431 DOI: 10.1110/ps.38102] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The FAD-dependent hydroxynitrile lyase from almond (Prunus amygdalus, PaHNL) catalyzes the cleavage of R-mandelonitrile into benzaldehyde and hydrocyanic acid. Catalysis of the reverse reaction-the enantiospecific formation of alpha-hydroxynitriles--is now widely utilized in organic syntheses as one of the few industrially relevant examples of enzyme-mediated C-C bond formation. Starting from the recently determined X-ray crystal structure, systematic docking calculations with the natural substrate were used to locate the active site of the enzyme and to identify amino acid residues involved in substrate binding and catalysis. Analysis of the modeled substrate complexes supports an enzymatic mechanism that includes the flavin cofactor as a mere "spectator" of the reaction and relies on general acid/base catalysis by the conserved His-497. Stabilization of the negative charge of the cyanide ion is accomplished by a pronounced positive electrostatic potential at the binding site. PaHNL activity requires the FAD cofactor to be bound in its oxidized form, and calculations of the pKa of enzyme-bound HCN showed that the observed inactivation upon cofactor reduction is largely caused by the reversal of the electrostatic potential within the active site. The suggested mechanism closely resembles the one proposed for the FAD-independent, and structurally unrelated HNL from Hevea brasiliensis. Although the actual amino acid residues involved in the catalytic cycle are completely different in the two enzymes, a common motif for the mechanism of cyanogenesis (general acid/base catalysis plus electrostatic stabilization of the cyanide ion) becomes evident.
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Affiliation(s)
- Ingrid Dreveny
- Institut für Chemie, Karl-Franzens Universität Graz, A-8010 Graz, Austria
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32
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Dreveny I, Gruber K, Glieder A, Thompson A, Kratky C. The hydroxynitrile lyase from almond: a lyase that looks like an oxidoreductase. Structure 2001; 9:803-15. [PMID: 11566130 DOI: 10.1016/s0969-2126(01)00639-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Cyanogenesis is a defense process of several thousand plant species. Hydroxynitrile lyase, a key enzyme of this process, cleaves a cyanohydrin into hydrocyanic acid and the corresponding aldehyde or ketone. The reverse reaction constitutes an important tool in biocatalysis. Different classes of hydroxynitrile lyases have convergently evolved from FAD-dependent oxidoreductases, alpha/beta hydrolases, and alcohol dehydrogenases. The FAD-dependent hydroxynitrile lyases (FAD-HNLs) carry a flavin cofactor whose redox properties appear to be unimportant for catalysis. RESULTS We have determined the crystal structure of a 61 kDa hydroxynitrile lyase isoenzyme from Prunus amygdalus (PaHNL1) to 1.5 A resolution. Clear electron density originating from four glycosylation sites could be observed. As concerns the overall protein fold including the FAD cofactor, PaHNL1 belongs to the family of GMC oxidoreductases. The active site for the HNL reaction is probably at a very similar position as the active sites in homologous oxidases. CONCLUSIONS There is strong evidence from the structure and the reaction product that FAD-dependent hydroxynitrile lyases have evolved from an aryl alcohol oxidizing precursor. Since key residues implicated in oxidoreductase activity are also present in PaHNL1, it is not obvious why this enzyme shows no oxidase activity. Similarly, features proposed to be relevant for hydroxy-nitrile lyase activity in other hydroxynitrile lyases, i.e., a general base and a positive charge to stabilize the cyanide, are not obviously present in the putative active site of PaHNL1. Therefore, the reason for its HNL activity is far from being well understood at this point.
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Affiliation(s)
- I Dreveny
- Institut für Chemie, Karl-Franzens-Universität, Heinrichstrasse 28, Graz A-8010, Austria
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33
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Gruber K. Elucidation of the mode of substrate binding to hydroxynitrile lyase from Hevea brasiliensis. Proteins 2001; 44:26-31. [PMID: 11354003 DOI: 10.1002/prot.1068] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The hydroxynitrile lyase from Hevea brasiliensis (Hb-HNL) is used as a catalyst in enantiospecific syntheses of alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed reaction represents one of the few industrially relevant examples of enzyme mediated C-C coupling reactions. In this work, we modeled Hb-HNL substrate complexes that have as yet proven inaccessible to experimental structure determination and were able to identify two binding modes for the natural substrate acetone cyanohydrin in docking simulations. Discrimination of the two alternatives was achieved by modeling complexes with two different chiral cyanohydrins followed by an analysis of the respective relative binding energies from molecular mechanics and thermodynamic integration. Only for one of the alternative binding modes the experimentally established S-selectivity of the enzyme was correctly predicted. Our results yielded further support for an enzymatic mechanism involving the catalytic triad Ser80, His235, and Asp207 as a general acid/base. A pivotal role was ascribed to Lys236, which seems to be crucial for enzymatic activity at low pH values. In addition, the modeling calculations provided possible explanations for the observed substrate and enantioselectivity of the enzyme that rationalize available mutational data and will be the basis for future protein engineering efforts.
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Affiliation(s)
- K Gruber
- Institut für Chemie-Strukturbiologie, Universität Graz, Heinrichstrasse 28, A-8010 Graz, Austria.
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34
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Hanefeld U, Stranzl G, Straathof AJ, Heijnen JJ, Bergmann A, Mittelbach R, Glatter O, Kratky C. Electrospray ionization mass spectrometry, circular dichroism and SAXS studies of the (S)-hydroxynitrile lyase from Hevea brasiliensis. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1544:133-42. [PMID: 11341923 DOI: 10.1016/s0167-4838(00)00212-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report on experiments pertaining to solution properties of the (S)-hydroxynitrile lyase from Hevea brasiliensis (HbHNL). Small angle X-ray scattering unequivocally established the enzyme to occur in solution as a dimer, presumably of the same structure as in the crystal. The acid induced, irreversible deactivation of HbHNL was examined by electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD) and by measuring the enzyme activity. The deactivation is paralleled by an unfolding of the enzyme. ESI-MS of this 30000 Da per monomer heavy protein demonstrated that unfolding took place in several stages which are paralleled by a decrease in enzyme activity. Unfolding can also be observed by CD spectroscopy, and there is a clear correlation between enzyme activity and unfolding as detected by ESI-MS and CD.
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Affiliation(s)
- U Hanefeld
- Kluyverlaboratorium voor Biotecnologie, Techische Universiteit Delft, The Netherlands.
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35
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Dogru E, Warzecha H, Seibel F, Haebel S, Lottspeich F, Stöckigt J. The gene encoding polyneuridine aldehyde esterase of monoterpenoid indole alkaloid biosynthesis in plants is an ortholog of the alpha/betahydrolase super family. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:1397-406. [PMID: 10691977 DOI: 10.1046/j.1432-1327.2000.01136.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The biosynthesis of the anti-arrhythmic alkaloid ajmaline is catalysed by more than 10 specific enzymes. In this multistep process polyneuridine aldehyde esterase (PNAE) catalyses a central reaction by transforming polyneuridine aldehyde into epi-vellosimine, which is the immediate precursor for the synthesis of the ajmalane skeleton. PNAE was purified from cell suspension cultures of Rauvolfia serpentina. The N-terminal sequence and endoproteinase LysC fragments of the purified protein were used for primer design and for the amplification of specific PCR products leading to the isolation of PNAE-encoding cDNA from a R. serpentina library. The PNAE cDNA was fused with a C-terminal His-tag, expressed in Escherichia coli and purified to homogeneity using Ni-affinity chromatography. The pure enzyme shows extraordinary substrate specificity, completely different to other esterases. Sequence alignments indicate that PNAE is a new member of the alpha/beta hydrolase super family.
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Affiliation(s)
- E Dogru
- Lehrstuhl für Pharmazeutische Biologie, Institut für Pharmazie, Johannes Gutenberg-Universität Mainz
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36
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Abstract
Oxynitrilases for the preparation of (R)- or (S)-cyanohydrins are now readily available. The research efforts of a number of groups have established these enzymes as catalysts with significant potential for application to asymmetric synthesis. Advances made in molecular cloning and genetics have delivered information on the oxynitrilase mechanism of action and sufficient quantities of enzyme to satisfy industrial requirements.
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Affiliation(s)
- D V Johnson
- Spezialforschungsbereich Biokatalyse, Institut für Organische Chemie der Technischen Universität Graz, Graz, A-8010, Austria
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37
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Kazlauskas RJ. Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities. Curr Opin Chem Biol 2000; 4:81-8. [PMID: 10679382 DOI: 10.1016/s1367-5931(99)00056-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Rapid advances in structural biology have revealed the three-dimensional structures of many biocatalysts. Molecular modeling is the tool that links these structures with experimental observations. As a qualitative tool, current modeling methods are extremely useful. They can explain, on a molecular level, unusual features of reactions. They can predict how to increase the selectivity either by substrate modification or by site-directed mutagenesis. Quantitative predictions, for example the degree of enantioselectivity, are still not reliable, however. Modeling is limited also by the availability of three-dimensional structures. Most current modeling involves hydrolases, especially proteases and lipases, but structures for other types of enzymes are starting to appear.
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Affiliation(s)
- R J Kazlauskas
- Department of Chemistry, McGill University, Montréal, H3A 2K6, Canada.
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