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Maity AN, Chen JR, Ke SC. Exploring the mechanism of action of lysine 5,6-aminomutase using EPR and ENDOR spectroscopies. Methods Enzymol 2022; 669:197-228. [PMID: 35644172 DOI: 10.1016/bs.mie.2021.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Radical enzymes orchestrate challenging chemical transformations by devising strategies to tame the highly reactive radical intermediates. Electron paramagnetic resonance (EPR) spectroscopy is the most suitable technique to study various aspects of the radical enzymes. Lysine 5,6-aminomutase (5,6-LAM) is one such radical enzyme and employs coenzyme B12 and pyridoxal 5'-phosphate (PLP) to catalyze the 1,2-amino shift reaction through a radical mechanism. 5,6-LAM accepts either d-lysine or l-β-lysine as the substrate. EPR and electron nuclear double resonance (ENDOR) spectroscopies have played major roles in deciphering the mechanism of action of 5,6-LAM, while density functional theoretical (DFT) computation and synthetic isotopologues have played supporting roles. This comprehensive toolkit has revealed that 5,6-LAM undergoes large-scale conformational movement to bring PLP and coenzyme B12 close together, which allows the reaction to progress. The conformational change also closes the active site, which protects the radical intermediates and enables their transformation to product without unwanted side reactions. The substrate-related radical (S•), which is spin-coupled with Co2+ generated from homolysis of the CoC bond in coenzyme B12, was unequivocally characterized when a substrate analog, 4-thia-l-lysine, and isotopologues of it were reacted with 5,6-LAM. Studies with substrate analogs revealed a unique "odd-even" correlation with opening of the closed state. Moreover, mutagenesis studies identified the contributions that conserved residues in 5,6-LAM make toward binding of the substrate. Further studies with a cofactor analog, PLP-N-oxide, have shed light on various aspects of the mechanism of action of 5,6-LAM.
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Affiliation(s)
| | - Jun-Ru Chen
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Shyue-Chu Ke
- Department of Physics, National Dong Hwa University, Hualien, Taiwan.
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2
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Maity AN, Chen JR, Li QY, Ke SC. The Nitrogen Atom of Vitamin B 6 Is Essential for the Catalysis of Radical Aminomutases. Int J Mol Sci 2022; 23:ijms23095210. [PMID: 35563602 PMCID: PMC9105233 DOI: 10.3390/ijms23095210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Radical aminomutases are pyridoxal 5'-phosphate (PLP, a B6 vitamer)-dependent enzymes that require the generation of a 5'-deoxyadenosyl radical to initiate the catalytic cycle, to perform a 1,2 amino group shift reaction. The role of the nitrogen atom of PLP in radical aminomutases has not been investigated extensively yet. We report an alternative synthetic procedure to provide easy access to 1-deazaPLP (dAPLP), an isosteric analog of PLP which acts as a probe for studying the role of the nitrogen atom. Our results revealed that lysine 5,6-aminomutase (5,6-LAM), a radical aminomutase, reconstituted with dAPLP cannot turn over a substrate, demonstrating that the nitrogen atom is essential for radical aminomutases. In contrast, biochemical and spectroscopic studies on the S238A variant reconstituted with PLP revealed a minuscule loss of activity. This apparent anomaly can be explained by a water-mediated rescue of activity in S238A, as if mimicking the active site of lysine 2,3-aminomutase. This study leads to a better comprehension of how enzymes harness the optimum capability of PLP to realize catalysis.
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Chen JR, Ke TX, Frey PA, Ke SC. Electron Spin Echo Envelope Modulation Spectroscopy Reveals How Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase Positions the Radical Pair Intermediates and Modulates Their Stabilities for Efficient Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-Ru Chen
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Ting-Xi Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
| | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53726, United States
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 974301, Taiwan
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C-demethylation and 1, 2-amino shift in (E)-2-(1-(3-aminophenyl) ethylidene)hydrazinecarboxamide to (E)-2-(2-aminobenzylidene)hydrazinecarboxamide and their applications. Sci Rep 2020; 10:21913. [PMID: 33318572 PMCID: PMC7736590 DOI: 10.1038/s41598-020-79027-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/01/2020] [Indexed: 12/17/2022] Open
Abstract
A Novel (E)-2-(1-(3-aminophenyl)ethylidene)hydrazinecarboxamide 1 was synthesized by traditional method and converted to (E)-2-(2-aminobenzylidene)hydrazinecarboxamide 2 by single step in DMSO at room temperature. Synthesized compound 1 was analysed by spectroscopy (NMR and LC–MS) techniques and molecule 2 was characterized using single crystal X-ray diffraction and spectroscopy (NMR and GC–MS) techniques. These analytical technique results revealed that, C-demethylation and 1, 2 amino shift in phenyl ring of compound 1 gives molecule 2. DNA binding studies of compounds 1 and 2 was carried out by electronic absorption spectroscopy. This result revealed that, compounds 1 and 2 showed hyperchromism with bathochromic shift. Anticancer activity of compounds 1 and 2 is carried out by molecular docking with five receptors.Computer aided virtual screening demonstrated that the synthesized molecules possess ideal drug likeliness, pharmacokinetics features, toxicity profile for structure based drug discovery. The molecular docking studies revealed that the synthesized molecules are significant binding with the five selected cancer receptors with minimum binding energy (kcal/mol), number of hydrogen bonds, weak interaction, docking score and cluster RMS. The docking studies also suggested that the molecules showed interactions with DNA and the theoretical values of the binding are comparable with that of the experimental values. Hirshfeld surface analysis was used to analyze and quantify the intermolecular interactions in the crystal structure of compound 2.
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Makins C, Whitelaw DA, McGregor M, Petit A, Mothersole RG, Prosser KE, Wolthers KR. Optimal electrostatic interactions between substrate and protein are essential for radical chemistry in ornithine 4,5-aminomutase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1077-1084. [DOI: 10.1016/j.bbapap.2017.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/11/2017] [Accepted: 05/15/2017] [Indexed: 11/17/2022]
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Murugan A, Vidyacharan S, Ghosh R, Sharada DS. Metal-Free Regioselective Dual C-H Functionalization in a Cascade Fashion: Access to Isocryptolepine Alkaloid Analogues. ChemistrySelect 2017. [DOI: 10.1002/slct.201700263] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Arumugavel Murugan
- Department of Chemistry; Indian Institute of Technology Hyderabad; Kandi Sangareddy-502 285, Telangana INDIA
| | - Shinde Vidyacharan
- Department of Chemistry; Indian Institute of Technology Hyderabad; Kandi Sangareddy-502 285, Telangana INDIA
| | - Ruma Ghosh
- Department of Chemistry; Indian Institute of Technology Hyderabad; Kandi Sangareddy-502 285, Telangana INDIA
| | - Duddu S. Sharada
- Department of Chemistry; Indian Institute of Technology Hyderabad; Kandi Sangareddy-502 285, Telangana INDIA
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Maity AN, Lin HH, Chiang HS, Lo HH, Ke SC. Reaction of Pyridoxal-5′-phosphate-N-oxide with Lysine 5,6-Aminomutase: Enzyme Flexibility toward Cofactor Analog. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00671] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Hsin-Hua Lin
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
| | | | - Hsin-Hsi Lo
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
| | - Shyue-Chu Ke
- Department
of Physics, National Dong Hwa University, Hualien, Taiwan 97401
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Maity AN, Ke SC. 4'-CyanoPLP presents better prospect for the experimental detection of elusive cyclic intermediate radical in the reaction of lysine 5,6-aminomutase. Biochem Biophys Res Commun 2015; 457:161-4. [PMID: 25542154 DOI: 10.1016/j.bbrc.2014.12.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/15/2014] [Indexed: 11/26/2022]
Abstract
The results of our calculations suggest that the reaction of 4'-cyanoPLP with lysine 5,6-aminomutase offers better prospect for the experimental detection of elusive cyclic azacyclopropylcarbinyl radical (I), which is proposed to be a key intermediate in the reaction of pyridoxal-5'-phosphate dependent radical aminomutases. We have calculated the corresponding hyperfine coupling constants (HFCCs) for (14)N and (13)C of cyano group using several basis sets to help the characterization of 4'-cyanoI.
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Affiliation(s)
| | - Shyue-Chu Ke
- Department of Physics, National Dong Hwa University, Hualien 97401, Taiwan.
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Makins C, Whitelaw DA, Mu C, Walsby CJ, Wolthers KR. Isotope effects for deuterium transfer and mutagenesis of Tyr187 provide insight into controlled radical chemistry in adenosylcobalamin-dependent ornithine 4,5-aminomutase. Biochemistry 2014; 53:5432-43. [PMID: 25100213 DOI: 10.1021/bi5006706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Adenosylcobalamin-dependent ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii utilizes pyridoxal 5'-phosphate (PLP) to interconvert d-ornithine to 2,4-diaminopentanoate via a multistep mechanism that involves two hydrogen transfer steps. Herein, we uncover features of the OAM catalytic mechanism that differentiate it from its homologue, the more catalytically promiscuous lysine 5,6-aminomutase. Kinetic isotope effects (KIEs) with dl-ornithine-3,3,4,4,5,5-d6 revealed a diminished (D)kcat/Km of 2.5 ± 0.4 relative to a (D)kcat of 7.6 ± 0.5, suggesting slow release of the substrate from the active site. In contrast, a KIE was not observed on the rate constant associated with Co-C bond homolysis as this step is likely "gated" by the formation of the external aldimine. The role of tyrosine 187, which lies planar to the PLP pyridine ring, was also investigated via site-directed mutagenesis. The 25- and 1260-fold reduced kcat values for Y187F and Y187A, respectively, are attributed to a slower rate of external aldimine formation and a diminution of adenosylcobalamin Co-C bond homolysis. Notably, electron paramagnetic resonance studies of Y187F suggest that the integrity of the active site is maintained as cob(II)alamin and the PLP organic radical (even at lower concentrations) remain tightly exchange-coupled. Modeling of d-lysine and l-β-lysine into the 5,6-LAM active site reveals interactions between the substrate and protein are weaker than those in OAM and fewer in number. The combined data suggest that the level of protein-substrate interactions in aminomutases not only influences substrate specificity, but also controls radical chemistry.
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Affiliation(s)
- Caitlyn Makins
- Department of Chemistry, University of British Columbia , 3333 University Way, Kelowna, BC V1V 1V7, Canada
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Pang J, Scrutton NS, Sutcliffe MJ. Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′-Phosphate in Ornithine 4,5-Aminomutase. Chemistry 2014; 20:11390-401. [DOI: 10.1002/chem.201402759] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Indexed: 02/02/2023]
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11
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Maity AN, Chen YH, Ke SC. Large-scale domain motions and pyridoxal-5'-phosphate assisted radical catalysis in coenzyme B12-dependent aminomutases. Int J Mol Sci 2014; 15:3064-87. [PMID: 24562332 PMCID: PMC3958899 DOI: 10.3390/ijms15023064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/25/2013] [Accepted: 01/22/2014] [Indexed: 12/31/2022] Open
Abstract
Lysine 5,6-aminomutase (5,6-LAM) and ornithine 4,5-aminomutase (4,5-OAM) are two of the rare enzymes that use assistance of two vitamins as cofactors. These enzymes employ radical generating capability of coenzyme B12 (5'-deoxyadenosylcobalamin, dAdoCbl) and ability of pyridoxal-5'-phosphate (PLP, vitamin B6) to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. In spite of all the similarities, these enzymes differ in substrate specificities. 4,5-OAM is highly specific for D-ornithine as a substrate while 5,6-LAM can accept D-lysine and L-β-lysine. This review focuses on recent computational, spectroscopic and structural studies of these enzymes and their implications on the related enzymes. Additionally, we also discuss the potential biosynthetic application of 5,6-LAM.
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Affiliation(s)
| | - Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien 97401, Taiwan.
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien 97401, Taiwan.
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12
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El-Sherif AA, Aljahdali MS. Review: protonation, complex-formation equilibria, and metal–ligand interaction of salicylaldehyde Schiff bases. J COORD CHEM 2013. [DOI: 10.1080/00958972.2013.839027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ahmed A. El-Sherif
- Faculty of Science, Department of Chemistry, Cairo University, Cairo, Egypt
- Faculty of Arts and Science, Department of Chemistry, Northern Border University, Rafha, Saudi Arabia
| | - Mutlaq S. Aljahdali
- Faculty of Science, Department of Chemistry, King Abd Al-Aziz University, Jeddah, Saudi Arabia
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13
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Maity AN, Ke SC. 5-Fluorolysine as alternative substrate of lysine 5,6-aminomutase: A computational study. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Dowling DP, Croft AK, Drennan CL. Radical use of Rossmann and TIM barrel architectures for controlling coenzyme B12 chemistry. Annu Rev Biophys 2013; 41:403-27. [PMID: 22577824 DOI: 10.1146/annurev-biophys-050511-102225] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability of enzymes to harness free-radical chemistry allows for some of the most amazing transformations in nature, including reduction of ribonucleotides and carbon skeleton rearrangements. Enzyme cofactors involved in this chemistry can be large and complex, such as adenosylcobalamin (coenzyme B(12)), simpler, such as S-adenosylmethionine and an iron-sulfur cluster (i.e., poor man's B(12)), or very small, such as one nonheme iron atom coordinated by protein ligands. Although the chemistry catalyzed by these enzyme-bound cofactors is unparalleled, it does come at a price. The enzyme must be able to control these radical reactions, preventing unwanted chemistry and protecting the enzyme active site from damage. Here, we consider a set of radical folds: the (β/α)(8) or TIM barrel, combined with a Rossmann domain for coenzyme B(12)-dependent chemistry. Using specific enzyme examples, we consider how nature employs the common TIM barrel fold and its Rossmann domain partner for radical-based chemistry.
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Affiliation(s)
- Daniel P Dowling
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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15
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Chen YH, Maity AN, Frey PA, Ke SC. Mechanism-based Inhibition Reveals Transitions between Two Conformational States in the Action of Lysine 5,6-Aminomutase: A Combination of Electron Paramagnetic Resonance Spectroscopy, Electron Nuclear Double Resonance Spectroscopy, and Density Functional Theory Study. J Am Chem Soc 2012; 135:788-94. [DOI: 10.1021/ja309603a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien, Taiwan 97401
| | | | - Perry A. Frey
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
53726, United States
| | - Shyue-Chu Ke
- Physics Department, National Dong Hwa University, Hualien, Taiwan 97401
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16
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Condurso HL, Bruner SD. Structure guided approaches toward exploiting and manipulating nonribosomal peptide and polyketide biosynthetic pathways. Curr Opin Chem Biol 2012; 16:162-9. [DOI: 10.1016/j.cbpa.2012.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 01/31/2012] [Accepted: 02/02/2012] [Indexed: 11/28/2022]
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17
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Makins C, Miros FN, Scrutton NS, Wolthers KR. Role of histidine 225 in adenosylcobalamin-dependent ornithine 4,5-aminomutase. Bioorg Chem 2012; 40:39-47. [DOI: 10.1016/j.bioorg.2011.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/05/2011] [Accepted: 08/08/2011] [Indexed: 12/01/2022]
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18
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Pang J, Li X, Morokuma K, Scrutton NS, Sutcliffe MJ. Large-Scale Domain Conformational Change Is Coupled to the Activation of the Co–C Bond in the B12-Dependent Enzyme Ornithine 4,5-Aminomutase: A Computational Study. J Am Chem Soc 2012; 134:2367-77. [DOI: 10.1021/ja210417k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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Chen YH, Maity AN, Pan YC, Frey PA, Ke SC. Radical stabilization is crucial in the mechanism of action of lysine 5,6-aminomutase: role of tyrosine-263α as revealed by electron paramagnetic resonance spectroscopy. J Am Chem Soc 2011; 133:17152-5. [PMID: 21939264 DOI: 10.1021/ja207766c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenosylcobalamin- and pyridoxal-5'-phosphate-dependent lysine 5,6-aminomutase utilizes free radical intermediates to mediate 1,2-amino group rearrangement, during which an elusive high-energy aziridincarbinyl radical is proposed to be central in the mechanism of action. Understanding how the enzyme participates in stabilizing any of the radical intermediates is fundamentally significant. Y263F mutation abolished the enzymatic activity. With isotope-edited EPR methods, the roles of the Tyr263α residue in the putative active site are revealed. The Tyr263α residue stabilizes a radical intermediate, which most likely is the aziridincarbinyl radical, either by acting as a spin-relay device or serving as an anchor for the pyridine ring of pyridoxal-5'-phosphate through aromatic π-stacking interactions during spin transfer. The Tyr263α residue also protects the radical intermediate from interception by molecular oxygen. This study supports the proposed reaction mechanism, including the aziridincarbinyl radical, which has eluded detection for more than two decades.
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Affiliation(s)
- Yung-Han Chen
- Physics Department, National Dong Hwa University, Hualien, Taiwan 97401
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Wu B, Szymański W, Heberling MM, Feringa BL, Janssen DB. Aminomutases: mechanistic diversity, biotechnological applications and future perspectives. Trends Biotechnol 2011; 29:352-62. [PMID: 21477876 DOI: 10.1016/j.tibtech.2011.02.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 02/22/2011] [Accepted: 02/23/2011] [Indexed: 11/26/2022]
Abstract
Aminomutases carry out the chemically challenging exchange of a hydrogen atom and an amine substituent present on neighboring carbon atoms. In recent years, aminomutases have been intensively investigated for their biophysical, structural and mechanistic characteristics. The reactions catalyzed by these enzymes have considerable potential for biotechnological applications. Here, we present an overview of this diverse group of enzymes, with a focus on enzymatic mechanisms and recent developments in their use in applied biocatalysis.
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Affiliation(s)
- Bian Wu
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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Frey PA, Reed GH. Pyridoxal-5'-phosphate as the catalyst for radical isomerization in reactions of PLP-dependent aminomutases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1548-57. [PMID: 21435400 DOI: 10.1016/j.bbapap.2011.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
Abstract
PLP catalyzes the 1,2 shifts of amino groups in free radical-intermediates at the active sites of amino acid aminomutases. Free radical forms of the substrates are created upon H atom abstractions carried out by the 5'-deoxyadenosyl radical. In most of these enzymes, the 5'-deoxyadenosyl radical is generated by an iron-sulfur cluster-mediated reductive cleavage of S-adenosyl-(S)-methionine. However, in lysine 5,6-aminomutase and ornithine 4,5-aminomutase, the radical is generated by homolytic cleavage of the cobalt-carbon bond of adenosylcobalamin. The imine linkages in the initial radical forms of the external aldimines undergo radical addition to form azacyclopropylcarbinyl radicals as central intermediates in the catalytic cycles. In the case of lysine 2,3-aminomutase, the multistep catalytic mechanism is corroborated by direct spectroscopic observation and characterization of a product radical trapped during steady-state turnover. Analogues of the substrate-related radical having substituents adjacent to the radical center to stabilize the unpaired electron are also observed and characterized spectroscopically. A functional allylic analogue of the 5'-deoxyadenosyl radical is observed spectroscopically. A high-resolution crystal structure fully supports the mechanistic proposals. Evidence for a similar free radical mediated amino group transfer in the adenosylcobalamin-dependent lysine 5,6-aminomutase is provided by spectroscopic detection and characterization of radicals generated from the 4-thia analogues of the lysine substrates. This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology.
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Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Wisconsin-Madison, 1710 University Avenue, Madison, WI 53726, USA.
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22
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Sandala GM, Smith DM, Radom L. Modeling the reactions catalyzed by coenzyme B12-dependent enzymes. Acc Chem Res 2010; 43:642-51. [PMID: 20136160 DOI: 10.1021/ar900260c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes accelerate chemical reactions with an exceptional selectivity that makes life itself possible. Understanding the factors responsible for this efficient catalysis is of utmost importance in our quest to harness the tremendous power of enzymes. Computational chemistry has emerged as an important adjunct to experimental chemistry and biochemistry in this regard, because it provides detailed insights into the relationship between structure and function in a systematic and straightforward manner. In this Account, we highlight our recent high-level theoretical investigations toward this end in studying the radical-based reactions catalyzed by enzymes dependent on coenzyme B(12) (or adenosylcobalamin, AdoCbl). In addition to their fundamental position in biology, the AdoCbl-dependent enzymes represent a valuable framework within which to understand Nature's method of efficiently handling high-energy species to execute very specific reactions. The AdoCbl-mediated reactions are characterized by the interchange of a hydrogen atom and a functional group on adjacent carbon atoms. Our calculations are consistent with the conclusion that the main role of AdoCbl is to provide a source of radicals, thus moving the 1,2-rearrangements onto the radical potential energy surface. Our studies also show that the radical rearrangement step is facilitated by partial proton transfer involving the substrate. Specifically, we observe that the energy requirements for radical rearrangement are reduced dramatically with appropriate partial protonation or partial deprotonation or sometimes (synergistically) both. Such interactions are particularly relevant to enzyme catalysis, because it is likely that the local amino acid environment in the active site of an enzyme can function in this capacity through hydrogen bonding. Finally, our calculations indicate that the intervention of a very stable radical along the reaction pathway may inactivate the enzyme, demonstrating that sustained catalysis depends on a delicate energy balance. Radical-based enzyme reactions are often difficult to probe experimentally, so theoretical investigations have a particularly valuable role to play in their study. Our research demonstrates that a small-model approach can provide important and revealing insights into the mechanism of action of AdoCbl-dependent enzymes.
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Affiliation(s)
- Gregory M. Sandala
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - David M. Smith
- Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
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Lei LW, Jiang YZ, Zou Y. Hexaaquamanganese(II) bis{[ N-(3-methoxy-2-oxidobenzylidene)glycylglycinato]copper(II)} hexahydrate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:m520-1. [PMID: 21579016 PMCID: PMC2979099 DOI: 10.1107/s1600536810013061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 04/08/2010] [Indexed: 11/10/2022]
Abstract
The ligand N-(2-hydroxy-3-methoxybenzylidene)glycylglycine (H3L), a Schiff base derived from glycylglycine and 3-methoxysalicylaldehyde, was used in the synthesis of a new organic–inorganic coordination complex, [Mn(H2O)6][Cu(C12H11N2O5)]2·6H2O. The MnII atom is located on an inversion center and is coordinated to six water molecules in a slightly distorted octahedral geometry. The CuII atom is chelated by the tetradentate Schiff base ligand in a distorted CuN2O2 square-planar coordination. In the crystal structure, the complex [Mn(H2O)6]2+ cations and the [CuL]− anions are arranged in columns parallel to the a axis and are held together by O—H⋯O hydrogen bonding. Additional hydrogen bonds of the same type further link the columns into a three-dimensional network.
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Wolthers KR, Levy C, Scrutton NS, Leys D. Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase. J Biol Chem 2010; 285:13942-50. [PMID: 20106986 PMCID: PMC2859556 DOI: 10.1074/jbc.m109.068908] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 11/16/2009] [Indexed: 11/06/2022] Open
Abstract
D-ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin (AdoCbl) to a pyridoxal 5'-phosphate (PLP) cofactor. We have solved OAM crystal structures in different catalytic states that together demonstrate unusual stability of the AdoCbl Co-C bond and that radical catalysis is coupled to large-scale domain motion. The 2.0-A substrate-free enzyme crystal structure reveals the Rossmann domain, harboring the intact AdoCbl cofactor, is tilted toward the edge of the PLP binding triose-phosphate isomerase barrel domain. The PLP forms an internal aldimine link to the Rossmann domain through Lys(629), effectively locking the enzyme in this "open" pre-catalytic conformation. The distance between PLP and 5'-deoxyadenosyl group is 23 A, and large-scale domain movement is thus required prior to radical catalysis. The OAM crystals contain two Rossmann domains within the asymmetric unit that are unconstrained by the crystal lattice. Surprisingly, the binding of various ligands to OAM crystals (in an oxygen-free environment) leads to transimination in the absence of significant reorientation of the Rossmann domains. In contrast, when performed under aerobic conditions, this leads to extreme disorder in the latter domains correlated with the loss of the 5'-deoxyadenosyl group. Our data indicate turnover and hence formation of the "closed" conformation is occurring within OAM crystals, but that the equilibrium is poised toward the open conformation. We propose that substrate binding induces large-scale domain motion concomitant with a reconfiguration of the 5'-deoxyadenosyl group, triggering radical catalysis in OAM.
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Affiliation(s)
- Kirsten R. Wolthers
- From the Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin Levy
- From the Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- From the Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David Leys
- From the Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Zhou WJ, Jiang YZ, Zou Y. (2-{[2-Carboxyl-ato-1-(4-chloro-phen-yl)eth-yl]imino-meth-yl}phenolato-κO,N,O')(1H-imidazole-κN)copper(II) monohydrate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:m579-80. [PMID: 21579059 PMCID: PMC2979152 DOI: 10.1107/s1600536810014765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 04/22/2010] [Indexed: 11/30/2022]
Abstract
The CuII atom of the title complex, [Cu(C16H12ClNO3)(C3H4N2)]·H2O, has a distorted square-planar coordination geometry formed by a tridentate Schiff base dianion and an imidazole ligand. The imidazole is nearly coplanar with the coordination plane, the dihedral angle between the planes being 3.73 (12)°. In the Schiff base ligand, the two benzene rings are oriented at a dihedral angle of 75.87 (12)°. O—H⋯O and N—H⋯O hydrogen bonding is present in the crystal structure. One H atom of the uncoordinated water molecule is disordered equally over two sites.
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Affiliation(s)
- Wen-Jun Zhou
- Chemistry Department, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
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26
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Zou Y. Tetra-aqua-bis[μ-N-(5-nitro-2-oxido-benzyl-idene)glycylglycinato]manganese(II)dinickel(II) tetra-hydrate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:m471-2. [PMID: 21580554 PMCID: PMC2983766 DOI: 10.1107/s1600536810011293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 03/25/2010] [Indexed: 11/10/2022]
Abstract
The two unique Ni(II) atoms of the title complex, [MnNi(2)(C(11)H(8)N(3)O(6))(2)(H(2)O)(4)]·4H(2)O, have a slightly distorted square-planar coordination environment with a tetra-dentate N-(5-nitro-2-oxidobenzyl-idene)glycylglycinate Schiff base trianion. The Ni(II) atoms are coordinated by one phenolate O atom, one imine N atom, one amido N atom and one carboxyl-ate O atom. The Mn(II )atom is connected via the carboxyl-ate groups, forming a hetero-trinuclear Ni(II)-Mn(II)-Ni(II) system. The Mn(II) atom is six-coordinated in an octa-hedral geometry by four O atoms from two carboxyl-ate groups and four water mol-ecules. The Ni(II)-Mn(II)-Ni(II) hetero-trinuclear mol-ecules are stacked in the crystal and cross-linked through O-H⋯O hydrogen bonds.
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Affiliation(s)
- Yang Zou
- Chemistry Department, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
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27
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Zou Y, Jiang YZ, Wang WZ. Diaqua[N-(5-nitro-2-oxidobenzylidene)glycinato]copper(II) dihydrate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:m455. [PMID: 21580541 PMCID: PMC2983767 DOI: 10.1107/s1600536810010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 03/22/2010] [Indexed: 11/11/2022]
Abstract
In the title complex, [Cu(C9H6N2O5)(H2O)2]·2H2O, the CuII atom has a square-pyramidal coordination environment with a tridentate N-(5-nitro-2-oxidobenzylidene)glycinate Schiff base ligand and a water molecule in the basal plane. The apical site is occupied by an O atom from another coordinated water molecule. The crystal structure is stabilized by O—H⋯O hydrogen bonds, building a two-dimensional network parallel to (100).
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28
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Marsh ENG, Patterson DP, Li L. Adenosyl radical: reagent and catalyst in enzyme reactions. Chembiochem 2010; 11:604-21. [PMID: 20191656 PMCID: PMC3011887 DOI: 10.1002/cbic.200900777] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 12/17/2022]
Abstract
Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.
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Affiliation(s)
- E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Dustin P. Patterson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University – Purdue University Indianapolis, Indianapolis, IN 46202, USA
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Fernández I, Cossío FP, Sierra MA. Dyotropic Reactions: Mechanisms and Synthetic Applications. Chem Rev 2009; 109:6687-711. [DOI: 10.1021/cr900209c] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Israel Fernández
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
| | - Fernando P. Cossío
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
| | - Miguel A. Sierra
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
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30
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Structure and chemistry of 4-methylideneimidazole-5-one containing enzymes. Curr Opin Chem Biol 2009; 13:460-8. [PMID: 19620019 DOI: 10.1016/j.cbpa.2009.06.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Accepted: 06/12/2009] [Indexed: 11/21/2022]
Abstract
The prosthetic group 4-methylideneimidazole-5-one (MIO) is the catalytic component of the ammonia lyase class of enzymes. This family is responsible for the processing of amino acids in a variety of metabolic pathways through the elimination of ammonia to form unsaturated products. Recently, new chemistry has been attributed to this family with the discovery of MIO-based aminomutases. The mechanism of electrophilic chemistry catalyzed by MIO-based enzymes has been investigated for several decades. Recent X-ray crystal structures of members of the family have provided novel insight into the molecular basis for catalysis and substrate recognition. In addition, the inclusion of aminomutases in natural product biosynthetic pathways has spurned recent advances toward rational engineering and chemoenzymatic applications.
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Abstract
This chapter reviews the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyl transfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations.
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Affiliation(s)
- Rowena G Matthews
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor MI 48109-2216, USA
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32
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Wolthers KR, Rigby SEJ, Scrutton NS. Mechanism of radical-based catalysis in the reaction catalyzed by adenosylcobalamin-dependent ornithine 4,5-aminomutase. J Biol Chem 2008; 283:34615-25. [PMID: 18948256 DOI: 10.1074/jbc.m807911200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report an analysis of the reaction mechanism of ornithine 4,5-aminomutase, an adenosylcobalamin (AdoCbl)- and pyridoxal L-phosphate (PLP)-dependent enzyme that catalyzes the 1,2-rearrangement of the terminal amino group of D-ornithine to generate (2R,4S)-2,4-diaminopentanoic acid. We show by stopped-flow absorbance studies that binding of the substrate D-ornithine or the substrate analogue D-2,4-diaminobutryic acid (DAB) induces rapid homolysis of the AdoCbl Co-C bond (781 s(-1), D-ornithine; 513 s(-1), DAB). However, only DAB results in the stable formation of a cob(II)alamin species. EPR spectra of DAB and [2,4,4-(2)H(3)]DAB bound to holo-ornithine 4,5-aminomutase suggests strong electronic coupling between cob(II)alamin and a radical form of the substrate analog. Loading of substrate/analogue onto PLP (i.e. formation of an external aldimine) is also rapid (532 s(-1), D-ornithine; 488 s(-1), DAB). In AdoCbl-depleted enzyme, formation of the external aldimine occurs over long time scales (approximately 50 s) and occurs in three resolvable kinetic phases, identifying four distinct spectral intermediates (termed A-D). We infer that these represent the internal aldimine (lambda(max) 416 nm; A), two different unliganded PLP states of the enzyme (lambda(max) at 409 nm; B and C), and the external aldimine (lambda(max) 426 nm; D). An imine linkage with d-ornithine and DAB generates both tautomeric forms of the external aldimine, but with D-ornithine the equilibrium is shifted toward the ketoimine state. The influence of this equilibrium distribution of prototropic isomers in driving homolysis and stabilizing radical intermediate states is discussed. Our work provides the first detailed analysis of radical-based catalysis in this Class III AdoCbl-dependent enzyme.
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Affiliation(s)
- Kirsten R Wolthers
- Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess St., Manchester M1 7DN, United Kingdom.
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33
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Liao RZ, Ding WJ, Yu JG, Fang WH, Liu RZ. Theoretical studies on pyridoxal 5′-phosphate-dependent transamination of α-amino acids. J Comput Chem 2008; 29:1919-29. [DOI: 10.1002/jcc.20958] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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34
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Lee MH, Kim BR, Kim HT. Investigation of the active site at the deuterated Schiff-base complex formed between the coenzyme vitamin B6 and the primary amine. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.05.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Patwardhan A, Marsh ENG. Changes in the free energy profile of glutamate mutase imparted by the mutation of an active site arginine residue to lysine. Arch Biochem Biophys 2007; 461:194-9. [PMID: 17306212 PMCID: PMC1995565 DOI: 10.1016/j.abb.2007.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 01/04/2007] [Indexed: 11/23/2022]
Abstract
Arginine 100 plays an important role in substrate recognition in adenosylcobalamin-dependent glutamate mutase. We have examined how the mutation of this residue to lysine affects the partitioning of tritium, incorporated at the exchangeable position of the coenzyme, between substrate and product. We find that partitioning of tritium back to the substrate predominates in the mutant enzyme, regardless of whether the reaction is run in the forward or reverse direction. This contrasts with the behavior of the wild-type enzyme in which tritium partitions equally between substrate and product, independent of the direction of the reaction. From this we conclude that the mutation significantly impairs the ability of the enzyme to catalyze the rearrangement of substrate radical to product radical. The results illustrate the importance of electrostatic interactions in stabilizing free radical intermediates in this class of enzymes.
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36
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Zou Y, Liu WL, Xie JL, Ni CL, Ni ZP, Li YZ, Meng QJ, Yao YG. Synthesis and crystal structure of metal complexes of Schiff bases derived from Glycylglycine and Salicylaldehyde [Ni(H2O)6(Ml)2]·nH2O (M = Cu, Ni; L = C11H9N2O4). J COORD CHEM 2006. [DOI: 10.1080/00958970410001689067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Yang Zou
- a Coordination Chemistry Institute , State Key Laboratory of Coordination Chemistry, Nanjing University , Nanjing, 210093, P.R. China
| | - Wen-Long Liu
- a Coordination Chemistry Institute , State Key Laboratory of Coordination Chemistry, Nanjing University , Nanjing, 210093, P.R. China
| | - Jing-Li Xie
- a Coordination Chemistry Institute , State Key Laboratory of Coordination Chemistry, Nanjing University , Nanjing, 210093, P.R. China
| | - Chun-Lin Ni
- a Coordination Chemistry Institute , State Key Laboratory of Coordination Chemistry, Nanjing University , Nanjing, 210093, P.R. China
| | - Zhao-Ping Ni
- a Coordination Chemistry Institute , State Key Laboratory of Coordination Chemistry, Nanjing University , Nanjing, 210093, P.R. China
| | - Yi-Zhi Li
- a Coordination Chemistry Institute , State Key Laboratory of Coordination Chemistry, Nanjing University , Nanjing, 210093, P.R. China
| | - Qing-Jin Meng
- a Coordination Chemistry Institute , State Key Laboratory of Coordination Chemistry, Nanjing University , Nanjing, 210093, P.R. China
| | - Yuan-Gen Yao
- b State Key Laboratory of Structure Chemistry , Fujian Institute of Research on the Structure of Matter , Fujian 350002, P.R. China
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Zhu D, Su Z, Mu Z, Qiu Y, Wang Y. Synthesis, crystal structures and properties of five-coordinate Schiff-base Zn(II) complexes. J COORD CHEM 2006. [DOI: 10.1080/00958970500270877] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- D. Zhu
- a Department of Chemistry , Institute of Functional Materials, Northeast Normal University , Changchun, Jilin, 130024, PR China
| | - Z. Su
- a Department of Chemistry , Institute of Functional Materials, Northeast Normal University , Changchun, Jilin, 130024, PR China
| | - Z. Mu
- a Department of Chemistry , Institute of Functional Materials, Northeast Normal University , Changchun, Jilin, 130024, PR China
| | - Y. Qiu
- a Department of Chemistry , Institute of Functional Materials, Northeast Normal University , Changchun, Jilin, 130024, PR China
| | - Y. Wang
- a Department of Chemistry , Institute of Functional Materials, Northeast Normal University , Changchun, Jilin, 130024, PR China
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Investigation of Fragmentation Patterns in Pyridoxal-primary Amine Complexes by Electrospray Ionization Mass Spectrometry. B KOREAN CHEM SOC 2006. [DOI: 10.5012/bkcs.2006.27.6.947] [Citation(s) in RCA: 3] [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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39
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Kaminaga Y, Schnepp J, Peel G, Kish CM, Ben-Nissan G, Weiss D, Orlova I, Lavie O, Rhodes D, Wood K, Porterfield DM, Cooper AJL, Schloss JV, Pichersky E, Vainstein A, Dudareva N. Plant phenylacetaldehyde synthase is a bifunctional homotetrameric enzyme that catalyzes phenylalanine decarboxylation and oxidation. J Biol Chem 2006; 281:23357-66. [PMID: 16766535 DOI: 10.1074/jbc.m602708200] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have isolated and characterized Petunia hybrida cv. Mitchell phenylacetaldehyde synthase (PAAS), which catalyzes the formation of phenylacetaldehyde, a constituent of floral scent. PAAS is a cytosolic homotetrameric enzyme that belongs to group II pyridoxal 5'-phosphate-dependent amino-acid decarboxylases and shares extensive amino acid identity (approximately 65%) with plant L-tyrosine/3,4-dihydroxy-L-phenylalanine and L-tryptophan decarboxylases. It displays a strict specificity for phenylalanine with an apparent Km of 1.2 mM. PAAS is a bifunctional enzyme that catalyzes the unprecedented efficient coupling of phenylalanine decarboxylation to oxidation, generating phenylacetaldehyde, CO2, ammonia, and hydrogen peroxide in stoichiometric amounts.
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Affiliation(s)
- Yasuhisa Kaminaga
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907-2010, USA
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Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL. A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc Natl Acad Sci U S A 2004; 101:15870-5. [PMID: 15514022 PMCID: PMC528771 DOI: 10.1073/pnas.0407074101] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5'-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, approximately 25 A from the active site. In this mode of pyridoxal-5'-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5'-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.
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Affiliation(s)
- Frederick Berkovitch
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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42
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Liu WL, Zou Y, Ni CL, Ni ZP, Li YZ, Yao YG, Meng QJ. Synthesis and characterization of copper(II) Schiff base complexes derived from salicylaldehyde and glycylglycylglycine. Polyhedron 2004. [DOI: 10.1016/j.poly.2003.11.049] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Tang KH, Casarez AD, Wu W, Frey PA. Kinetic and biochemical analysis of the mechanism of action of lysine 5,6-aminomutase. Arch Biochem Biophys 2003; 418:49-54. [PMID: 13679082 DOI: 10.1016/s0003-9861(03)00346-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Lysine 5,6-aminomutase (5,6-LAM) catalyzes the reversible and nearly isoenergetic transformations of D-lysine into 2,5-diaminohexanoate (2,5-DAH) and of L-beta-lysine into 3,5-diaminohexanoate (3,5-DAH). The activity of 5,6-LAM depends on pyridoxal-5(')-phosphate (PLP) and adenosylcobalamin. The currently postulated multistep mechanism involves at least 12 steps, two of which involve hydrogen transfer. The deuterium kinetic isotope effects on k(cat) and k(cat)/K(m) have been found to be 10.4+/-0.3 and 8.3+/-1.9, respectively, in the reaction of DL-lysine-3,3,4,4,5,5,6,6-d(8). The corresponding isotope effects for reaction of DL-lysine-4,4,5,5-d(4) are 8.5+/-0.7 and 7.1+/-1.2, respectively. Neither cob(II)alamin nor a free radical can be detected in the steady state by UV-Vis spectrophotometry or electron paramagnetic resonance (EPR) spectroscopy. Therefore, hydrogen abstraction from carbon-5 of the substrate side chain is rate limiting in the mechanism. DL-4-Oxalysine is an alternative substrate for 5,6-LAM. DL-4-Oxalysine reacts irreversibly because the product breaks down into ammonia, acetaldehyde, and DL-serine. The value of K(m) for the reaction of DL-4-oxalysine is lower than that for DL-lysine and that of k(cat) for DL-4-oxalysine is slightly lower than that for DL-lysine. As measured by values of k(cat)/K(m), 5,6-LAM uses DL-4-oxalysine essentially as efficiently as the best substrates, D-lysine and L-beta-lysine, and more efficiently than DL-lysine. DL-4-Oxalysine induces the same suicide inactivation by electron transfer as do the biological substrates. The putative substrate-related radical intermediate is not sufficiently stabilized by the nonbonding 4-oxa electrons to be detectable by EPR spectroscopy.
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Affiliation(s)
- Kuo-Hsiang Tang
- Department of Biochemistry, University of Wisconsin-Madison, 53726, USA
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44
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Affiliation(s)
- Fahmi Himo
- Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden
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45
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Khoroshun DV, Warncke K, Ke SC, Musaev DG, Morokuma K. Internal degrees of freedom, structural motifs, and conformational energetics of the 5'-deoxyadenosyl radical: implications for function in adenosylcobalamin-dependent enzymes. A computational study. J Am Chem Soc 2003; 125:570-9. [PMID: 12517173 DOI: 10.1021/ja028393k] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential energy surface of the free 5'-deoxyadenosyl radical in the gas phase is explored using density functional and second-order Møller-Plesset perturbation theories with 6-31G(d) and 6-31++G(d,p) basis sets and interpreted in terms of attractive and repulsive interactions. The 5',8-cyclization is found to be exothermic by approximately 20 kcal/mol but kinetically unfavorable; the lowest cyclization transition state (TS) lies about 7 kcal/mol higher than the highest TS for conversion between most of the open isomers. In open isomers, the two energetically most important attractive interactions are the hydrogen bonds (a) between the 2'-OH group and the N3 adenine center and (b) between the 2'-OH and 3'-OH groups. The relative ribose-adenine rotation about the C1'-N9 glycosyl bond in a certain range changes the energy by as much as 10-15 kcal/mol, the origin being (i) the repulsive 2'-H.H-C8 and O1'.N3 and (ii) the attractive 2'-OH.N3 ribose-adenine interactions. The hypothetical synergy between the glycosyl rotation and the Co-C bond scission may contribute to the experimentally established labilization of the Co-C bond in enzyme-bound adenosylcobalamin. The computational results are not inconsistent with the rotation about the C1'-N9 glycosyl bond being the principal coordinate for long-range radical migration in coenzyme B(12)-dependent enzymes. The effect of the protein environment on the model system results reported here remains an open question.
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Affiliation(s)
- Dmitry V Khoroshun
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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Zipse H. Charge distribution and charge separation in radical rearrangement reactions. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2003. [DOI: 10.1016/s0065-3160(03)38003-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Abstract
The crystal structure of glutamate mutase with bound coenzyme B(12) suggests a radical shuttling mechanism within the active site of the enzyme. Quantum chemical calculations of the rearrangement in combination with kinetic and mutational studies suggest the catalytic mechanism of this enzyme to proceed via a fragmentation/recombination sequence with intermediates stabilized by partial protonation/deprotonation. Crucial residues in the active site have been identified. Solution structure studies indicate the mechanism of B(12) binding to the apoenzyme.
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Affiliation(s)
- Karl Gruber
- Institut für Chemie, Universität Graz, Heinrichstrasse 28, Austria.
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48
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Semialjac M, Schwarz H. Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation. J Am Chem Soc 2002; 124:8974-83. [PMID: 12137553 DOI: 10.1021/ja020101s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ) are used to investigate several possible mechanisms involving free radical intermediates as well as their protonated forms for processes related to the coenzyme B(12)-dependent rearrangement catalyzed by ethanolamine ammonia lyase. Two major types of rearrangements are discussed in detail, intramolecular migration and dissociation of the amine/ammonia groups, for both of which several scenarios are considered. According to the calculations, the complete dissociation of the migrating group and its subsequent association constitute an unlikely route for both the protonated and the unprotonated reactant because of the high-energy barriers (more than 23 kcal/mol) involved in these steps. Direct migration of the protonated amine group is far more favorable (10.4 kcal/mol) and therefore presents the most likely candidate for the actual enzymatic reaction. The calculations further imply that the direct loss of an ammonium cation (10.6 kcal/mol) represents a feasible pathway as well. Comparing the rearrangements for the aminoethanol radical and its protonated counterpart, in line with previous findings reported by Golding, Radom, and co-workers, we find that the migration of a protonated group is in general associated with lower energy barriers, suggesting that the actual enzyme substrate quite likely corresponds to (partially) protonated aminoethanol. As the extent of the substrate protonation/deprotonation by the active site of the enzyme may vary, the actual energy barriers are expected to range between the values calculated for the two extreme cases of a substrate, that is, the aminoethanol radical 2 and its fully protonated form 6.
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Affiliation(s)
- Marija Semialjac
- Institut für Chemie der Technischen Universität Berlin, D-10623 Berlin, Germany.
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