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Brouwer B, Della-Felice F, Illies JH, Iglesias-Moncayo E, Roelfes G, Drienovská I. Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis. Chem Rev 2024; 124:10877-10923. [PMID: 39329413 PMCID: PMC11467907 DOI: 10.1021/acs.chemrev.4c00136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024]
Abstract
Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.
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Affiliation(s)
- Bart Brouwer
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Franco Della-Felice
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jan Hendrik Illies
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Emilia Iglesias-Moncayo
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Gerard Roelfes
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ivana Drienovská
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
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2
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Miller JR, Schnorrenberg EC, Aschenbrener C, Fox BG, Brunold TC. Kinetic and Spectroscopic Investigation of the Y157F and C93G/Y157F Variants of Cysteine Dioxygenase: Dissecting the Roles of the Second-Sphere Residues C93 and Y157. Biochemistry 2024; 63:1684-1696. [PMID: 38885352 PMCID: PMC11219262 DOI: 10.1021/acs.biochem.4c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
In mammals, l-cysteine (Cys) homeostasis is maintained by the mononuclear nonheme iron enzyme cysteine dioxygenase (CDO), which oxidizes Cys to cysteine sulfinic acid. CDO contains a rare post-translational modification, involving the formation of a thioether cross-link between a Cys residue at position 93 (Mus musculus CDO numbering) and a nearby tyrosine at position 157 (Cys-Tyr cross-link). As-isolated CDO contains both the cross-linked and non-cross-linked isoforms, and formation of the Cys-Tyr cross-link during repeated enzyme turnover increases CDO's catalytic efficiency by ∼10-fold. Interestingly, while the C93G CDO variant lacks the Cys-Tyr cross-link, it is similarly active as cross-linked wild-type (WT) CDO. Alternatively, the Y157F CDO variant, which also lacks the cross-link but maintains the free thiolate at position 93, exhibits a drastically reduced catalytic efficiency. These observations suggest that the untethered thiolate moiety of C93 is detrimental to CDO activity and/or that Y157 is essential for catalysis. To further assess the roles of residues C93 and Y157, we performed a spectroscopic and kinetic characterization of Y157F CDO and the newly designed C93G/Y157F CDO variant. Our results provide evidence that the non-cross-linked C93 thiolate stabilizes a water at the sixth coordination site of Cys-bound Y157F Fe(II)CDO. A water is also present, though more weakly coordinated, in Cys-bound C93G/Y157F Fe(II)CDO. The presence of a water molecule, which must be displaced by cosubstrate O2, likely makes a significant contribution to the ∼15-fold and ∼7-fold reduced catalytic efficiencies of the Y157F and C93G/Y157F CDO variants, respectively, relative to cross-linked WT CDO.
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Affiliation(s)
- Joshua R. Miller
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706, United States
| | | | - Cole Aschenbrener
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706, United States
| | - Brian G. Fox
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706, United States
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3
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Yuan F, Su B, Yu Y, Wang J. Study and design of amino acid-based radical enzymes using unnatural amino acids. RSC Chem Biol 2023; 4:431-446. [PMID: 37292061 PMCID: PMC10246556 DOI: 10.1039/d2cb00250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Radical enzymes harness the power of reactive radical species by placing them in a protein scaffold, and they are capable of catalysing many important reactions. New native radical enzymes, especially those with amino acid-based radicals, in the category of non-heme iron enzymes (including ribonucleotide reductases), heme enzymes, copper enzymes, and FAD-radical enzymes have been discovered and characterized. We discussed recent research efforts to discover new native amino acid-based radical enzymes, and to study the roles of radicals in processes such as enzyme catalysis and electron transfer. Furthermore, design of radical enzymes in a small and simple scaffold not only allows us to study the radical in a well-controlled system and test our understanding of the native enzymes, but also allows us to create powerful enzymes. In the study and design of amino acid-based radical enzymes, the use of unnatural amino acids allows precise control of pKa values and reduction potentials of the residue, as well as probing the location of the radical through spectroscopic methods, making it a powerful research tool. Our understanding of amino acid-based radical enzymes will allow us to tailor them to create powerful catalysts and better therapeutics.
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Affiliation(s)
- Feiyan Yuan
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Binbin Su
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Yang Yu
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 China
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4
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Ghosh AP, Toda MJ, Kozlowski PM. What Triggers the Cleavage of the Co–C 5′ Bond in Coenzyme B 12-Dependent Itaconyl-CoA Methylmalonyl-CoA Mutase? ACS Catal 2021. [DOI: 10.1021/acscatal.1c00291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Megan J. Toda
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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5
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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6
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Kunert R, Philouze C, Berthiol F, Jarjayes O, Storr T, Thomas F. Distorted copper(ii) radicals with sterically hindered salens: electronic structure and aerobic oxidation of alcohols. Dalton Trans 2020; 49:12990-13002. [PMID: 32909589 DOI: 10.1039/d0dt02524k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sterically hindered salen ligands featuring biphenyl and tetramethyl putrescine linkers were synthesized and chelated to copper. The resulting complexes CuLbp,tBu, CuLbp,OMe, CuLpu,tBu and CuLpu,OMe were structurally characterized, showing a significanty tetrahedrally distorted metal center. The complexes show two reversible oxidation waves in the range 0.2 to 0.8 V vs. Fc+/Fc. A further reduction wave is detected in the range -1.4 to -1.7 V vs. Fc+/Fc. It is reversible for CuLbp,tBu and CuLbp,OMe and assigned to the CuII/CuI redox couple. One-electron oxidation of CuLbp,OMe, CuLpu,tBu and CuLpu,OMe was performed chemically and electrochemically. It is accompanied by a quenching of the EPR resonances. Phenoxyl radical formation was established by X-Ray diffraction on the cations [CuLbp,OMe]+ and [CuLpu,OMe]+, whereby the coordination sphere is elongated upon oxidation with quinoidal distributions of bond distances. The cations exhibit a NIR band of moderate intensity in their optical spectrum, supporting their classification as class II mixed-valent radical species according to the Robin Day classification. The proposed electronic structures are supported by DFT calculations. The cations [CuLbp,OMe]+, [CuLpu,tBu]+ and [CuLpu,OMe]+ were active towards aerobic oxidation of the unactivated alcohol 2-phenylethanol, with TON numbers up to 58 within 3 h.
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Affiliation(s)
- R Kunert
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France.
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7
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Faria CB, de Castro FF, Martim DB, Abe CAL, Prates KV, de Oliveira MAS, Barbosa-Tessmann IP. Production of Galactose Oxidase Inside the Fusarium fujikuroi Species Complex and Recombinant Expression and Characterization of the Galactose Oxidase GaoA Protein from Fusarium subglutinans. Mol Biotechnol 2020; 61:633-649. [PMID: 31177409 DOI: 10.1007/s12033-019-00190-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Galactose oxidase catalyzes a two-electron oxidation, mainly from the C6 hydroxyl group of D-galactose, with the concomitant reduction of water to hydrogen peroxide. This enzyme is secreted by Fusarium species and has several biotechnological applications. In this study, a screening of galactose oxidase production among species of the Fusarium fujikuroi species complex demonstrated Fusarium subglutinans to be the main producer. The truncated F. subglutinans gaoA gene coding for the mature galactose oxidase was expressed from the prokaryotic vector pTrcHis2B in the E. coli Rosetta™ (DE3) strain. The purified recombinant enzyme presented temperature and pH optima of 30 °C and 7.0, respectively, KM of 132.6 ± 18.18 mM, Vmax of 3.2 ± 0.18 µmol of H2O2/min, kcat of 12,243 s-1, and a catalytic efficiency (kcat/KM) of 9.2 × 104 M-1 s-1. In the presence of 50% glycerol, the enzyme showed a T50 of 59.77 °C and was stable for several hours at pH 8.0 and 4 °C. Besides D-(+)-galactose, the purified enzyme also acted against D-(+)-raffinose, α-D-(+)-melibiose, and methyl-α-D-galactopyranoside, and was strongly inhibited by SDS. Although the F. subglutinans gaoA gene was successfully expressed in E. coli, its endogenous transcription was not confirmed by RT-PCR.
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Affiliation(s)
- Carla Bertechini Faria
- Department of Biochemistry, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, PR, 87020-900, Brazil
| | - Fausto Fernandes de Castro
- Department of Biochemistry, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, PR, 87020-900, Brazil
| | - Damaris Batistão Martim
- Department of Biochemistry, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, PR, 87020-900, Brazil
| | - Camila Agnes Lumi Abe
- Department of Biochemistry, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, PR, 87020-900, Brazil
| | - Kelly Valério Prates
- Department of Biochemistry, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, PR, 87020-900, Brazil
| | | | - Ione Parra Barbosa-Tessmann
- Department of Biochemistry, Universidade Estadual de Maringá, Av. Colombo, 5790, Maringá, PR, 87020-900, Brazil.
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8
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Forget SM, Xia F(R, Hein JE, Brumer H. Determination of biocatalytic parameters of a copper radical oxidase using real-time reaction progress monitoring. Org Biomol Chem 2020; 18:2076-2084. [DOI: 10.1039/c9ob02757b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
VTNA is applied to reaction progress curves to glean key kinetic and mechanistic details for a copper radical oxidase.
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Affiliation(s)
- Stephanie M. Forget
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
- Michael Smith Laboratories
| | - Fan (Roderick) Xia
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
- Michael Smith Laboratories
| | - Jason E. Hein
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Harry Brumer
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
- Michael Smith Laboratories
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9
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Paradisi A, Johnston EM, Tovborg M, Nicoll CR, Ciano L, Dowle A, McMaster J, Hancock Y, Davies GJ, Walton PH. Formation of a Copper(II)-Tyrosyl Complex at the Active Site of Lytic Polysaccharide Monooxygenases Following Oxidation by H 2O 2. J Am Chem Soc 2019; 141:18585-18599. [PMID: 31675221 PMCID: PMC7007232 DOI: 10.1021/jacs.9b09833] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Indexed: 01/14/2023]
Abstract
Hydrogen peroxide is a cosubstrate for the oxidative cleavage of saccharidic substrates by copper-containing lytic polysaccharide monooxygenases (LPMOs). The rate of reaction of LPMOs with hydrogen peroxide is high, but it is accompanied by rapid inactivation of the enzymes, presumably through protein oxidation. Herein, we use UV-vis, CD, XAS, EPR, VT/VH-MCD, and resonance Raman spectroscopies, augmented with mass spectrometry and DFT calculations, to show that the product of reaction of an AA9 LPMO with H2O2 at higher pHs is a singlet Cu(II)-tyrosyl radical species, which is inactive for the oxidation of saccharidic substrates. The Cu(II)-tyrosyl radical center entails the formation of significant Cu(II)-(●OTyr) overlap, which in turn requires that the plane of the d(x2-y2) SOMO of the Cu(II) is orientated toward the tyrosyl radical. We propose from the Marcus cross-relation that the active site tyrosine is part of a "hole-hopping" charge-transfer mechanism formed of a pathway of conserved tyrosine and tryptophan residues, which can protect the protein active site from inactivation during uncoupled turnover.
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Affiliation(s)
- Alessandro Paradisi
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Esther M. Johnston
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | | | - Callum R. Nicoll
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Luisa Ciano
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Adam Dowle
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Jonathan McMaster
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Y. Hancock
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
- York
Cross-Disciplinary Centre for Systems Analysis, University of York, Heslington,
York YO10 5GE, United Kingdom
| | - Gideon J. Davies
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Paul H. Walton
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
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10
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Samanta D, Saha P, Ghosh P. Proton-Coupled Oxidation of Aldimines and Stabilization of H-Bonded Phenoxyl Radical-Phenol Skeletons. Inorg Chem 2019; 58:15060-15077. [DOI: 10.1021/acs.inorgchem.9b01568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debasish Samanta
- Department of Chemistry, R. K. Mission Residential College, Narendrapur, Kolkata 700103, India
| | - Pinaki Saha
- Department of Chemistry, R. K. Mission Residential College, Narendrapur, Kolkata 700103, India
| | - Prasanta Ghosh
- Department of Chemistry, R. K. Mission Residential College, Narendrapur, Kolkata 700103, India
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11
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Trammell R, Rajabimoghadam K, Garcia-Bosch I. Copper-Promoted Functionalization of Organic Molecules: from Biologically Relevant Cu/O 2 Model Systems to Organometallic Transformations. Chem Rev 2019; 119:2954-3031. [PMID: 30698952 DOI: 10.1021/acs.chemrev.8b00368] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Copper is one of the most abundant and less toxic transition metals. Nature takes advantage of the bioavailability and rich redox chemistry of Cu to carry out oxygenase and oxidase organic transformations using O2 (or H2O2) as oxidant. Inspired by the reactivity of these Cu-dependent metalloenzymes, chemists have developed synthetic protocols to functionalize organic molecules under enviormentally benign conditions. Copper also promotes other transformations usually catalyzed by 4d and 5d transition metals (Pd, Pt, Rh, etc.) such as nitrene insertions or C-C and C-heteroatom coupling reactions. In this review, we summarized the most relevant research in which copper promotes or catalyzes the functionalization of organic molecules, including biological catalysis, bioinspired model systems, and organometallic reactivity. The reaction mechanisms by which these processes take place are discussed in detail.
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Affiliation(s)
- Rachel Trammell
- Department of Chemistry , Southern Methodist University , Dallas , Texas 75275 , United States
| | | | - Isaac Garcia-Bosch
- Department of Chemistry , Southern Methodist University , Dallas , Texas 75275 , United States
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12
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Chen L, Naowarojna N, Chen B, Xu M, Quill M, Wang J, Deng Z, Zhao C, Liu P. Mechanistic Studies of a Nonheme Iron Enzyme OvoA in Ovothiol Biosynthesis Using a Tyrosine Analogue, 2-Amino-3-(4-hydroxy-3-(methoxyl) phenyl) Propanoic Acid (MeOTyr). ACS Catal 2018. [DOI: 10.1021/acscatal.8b03903] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Li Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Bin Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Meiling Xu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Melissa Quill
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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13
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Colomban C, Philouze C, Molton F, Leconte N, Thomas F. Copper(II) complexes of N3O ligands as models for galactose oxidase: Effect of variation of steric bulk of coordinated phenoxyl moiety on the radical stability and spectroscopy. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Chen L, Naowarojna N, Song H, Wang S, Wang J, Deng Z, Zhao C, Liu P. Use of a Tyrosine Analogue To Modulate the Two Activities of a Nonheme Iron Enzyme OvoA in Ovothiol Biosynthesis, Cysteine Oxidation versus Oxidative C-S Bond Formation. J Am Chem Soc 2018; 140:4604-4612. [PMID: 29544051 PMCID: PMC5884719 DOI: 10.1021/jacs.7b13628] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ovothiol is a histidine thiol derivative. The biosynthesis of ovothiol involves an extremely efficient trans-sulfuration strategy. The nonheme iron enzyme OvoA catalyzed oxidative coupling between cysteine and histidine is one of the key steps. Besides catalyzing the oxidative coupling between cysteine and histidine, OvoA also catalyzes the oxidation of cysteine to cysteine sulfinic acid (cysteine dioxygenase activity). Thus far, very little mechanistic information is available for OvoA-catalysis. In this report, we measured the kinetic isotope effect (KIE) in OvoA-catalysis using the isotopically sensitive branching method. In addition, by replacing an active site tyrosine (Tyr417) with 2-amino-3-(4-hydroxy-3-(methylthio)phenyl)propanoic acid (MtTyr) through the amber suppressor mediated unnatural amino acid incorporation method, the two OvoA activities (oxidative coupling between cysteine and histidine, and cysteine dioxygenase activity) can be modulated. These results suggest that the two OvoA activities branch out from a common intermediate and that the active site tyrosine residue plays some key roles in controlling the partitioning between these two pathways.
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Affiliation(s)
- Li Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Heng Song
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Shu Wang
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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15
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Erxleben A. Transition metal salen complexes in bioinorganic and medicinal chemistry. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.06.060] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Chaplin AK, Bernini C, Sinicropi A, Basosi R, Worrall JAR, Svistunenko DA. Tyrosine or Tryptophan? Modifying a Metalloradical Catalytic Site by Removal of the Cys-Tyr Cross-Link in the Galactose 6-Oxidase Homologue GlxA. Angew Chem Int Ed Engl 2017; 56:6502-6506. [DOI: 10.1002/anie.201701270] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 03/13/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Amanda K. Chaplin
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
| | - Caterina Bernini
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Jonathan A. R. Worrall
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
| | - Dimitri A. Svistunenko
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
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17
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Chaplin AK, Bernini C, Sinicropi A, Basosi R, Worrall JAR, Svistunenko DA. Tyrosine or Tryptophan? Modifying a Metalloradical Catalytic Site by Removal of the Cys-Tyr Cross-Link in the Galactose 6-Oxidase Homologue GlxA. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Amanda K. Chaplin
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
| | - Caterina Bernini
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Jonathan A. R. Worrall
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
| | - Dimitri A. Svistunenko
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
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18
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Active-site maturation and activity of the copper-radical oxidase GlxA are governed by a tryptophan residue. Biochem J 2017; 474:809-825. [DOI: 10.1042/bcj20160968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/02/2017] [Accepted: 01/13/2017] [Indexed: 11/17/2022]
Abstract
GlxA from Streptomyces lividans is a mononuclear copper-radical oxidase and a member of the auxiliary activity family 5 (AA5). Its domain organisation and low sequence homology make it a distinct member of the AA5 family in which the fungal galactose 6-oxidase (Gox) is the best characterised. GlxA is a key cuproenzyme in the copper-dependent morphological development of S. lividans with a function that is linked to the processing of an extracytoplasmic glycan. The catalytic sites in GlxA and Gox contain two distinct one-electron acceptors comprising the copper ion and a 3′-(S-cysteinyl) tyrosine. The latter is formed post-translationally through a covalent bond between a cysteine and a copper-co-ordinating tyrosine ligand and houses a radical. In GlxA and Gox, a second co-ordination sphere tryptophan residue (Trp288 in GlxA) is present, but the orientation of the indole ring differs between the two enzymes, creating a marked difference in the π–π stacking interaction of the benzyl ring with the 3′-(S-cysteinyl) tyrosine. Differences in the spectroscopic and enzymatic activity have been reported between GlxA and Gox with the indole orientation suggested as a reason. Here, we report a series of in vivo and in vitro studies using the W288F and W288A variants of GlxA to assess the role of Trp288 on the morphology, maturation, spectroscopic and enzymatic properties. Our findings point towards a salient role for Trp288 in the kinetics of copper loading and maturation of GlxA, with its presence essential for stabilising the metalloradical site required for coupling catalytic activity and morphological development.
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19
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Hayes EC, Porter TR, Barrows CJ, Kaminsky W, Mayer JM, Stoll S. Electronic Structure of a Cu(II)-Alkoxide Complex Modeling Intermediates in Copper-Catalyzed Alcohol Oxidations. J Am Chem Soc 2016; 138:4132-45. [PMID: 26907976 PMCID: PMC4988936 DOI: 10.1021/jacs.5b13088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In the copper-catalyzed oxidation of alcohols to aldehydes, a Cu(II)-alkoxide (Cu(II)-OR) intermediate is believed to modulate the αC-H bond strength of the deprotonated substrate to facilitate the oxidation. As a structural model for these intermediates, we characterized the electronic structure of the stable compound Tp(tBu)Cu(II)(OCH2CF3) (Tp(tBu) = hydro-tris(3-tert-butyl-pyrazolyl)borate) and investigated the influence of the trifluoroethoxide ligand on the electronic structure of the complex. The compound exhibits an electron paramagnetic resonance (EPR) spectrum with an unusually large gzz value of 2.44 and a small copper hyperfine coupling Azz of 40 × 10(-4) cm(-1) (120 MHz). Single-crystal electron nuclear double resonance (ENDOR) spectra show that the unpaired spin population is highly localized on the copper ion (≈68%), with no more than 15% on the ethoxide oxygen. Electronic absorption and magnetic circular dichroism (MCD) spectra show weak ligand-field transitions between 5000 and 12,000 cm(-1) and an intense ethoxide-to-copper charge transfer (LMCT) transition at 24,000 cm(-1), resulting in the red color of this complex. Resonance Raman (rR) spectroscopy reveals a Cu-O stretch mode at 592 cm(-1). Quantum chemical calculations support the interpretation and assignment of the experimental data. Compared to known Cu(II)-thiolate and Cu(II)-alkylperoxo complexes from the literature, we found an increased σ interaction in the Cu(II)-OR bond that results in the spectroscopic features. These insights lay the basis for further elucidating the mechanism of copper-catalyzed alcohol oxidations.
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Affiliation(s)
- Ellen C. Hayes
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195
| | | | - Charles J. Barrows
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195
| | - Werner Kaminsky
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195
| | | | - Stefan Stoll
- Department of Chemistry, Box 351700, University of Washington, Seattle, WA 98195
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20
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Kruft BI, Magliozzo RS, Jarzęcki AA. Density Functional Theory Insights into the Role of the Methionine–Tyrosine–Tryptophan Adduct Radical in the KatG Catalase Reaction: O2 Release from the Oxyheme Intermediate. J Phys Chem A 2015; 119:6850-66. [DOI: 10.1021/jp511358p] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bonnie I. Kruft
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Andrzej A. Jarzęcki
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
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21
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GlxA is a new structural member of the radical copper oxidase family and is required for glycan deposition at hyphal tips and morphogenesis of Streptomyces lividans. Biochem J 2015. [PMID: 26205496 DOI: 10.1042/bj20150190] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Streptomyces lividans displays a distinct dependence on copper to fully initiate morphological development. Evidence has accumulated to implicate the participation of an extracytoplasmic cuproenzyme in morphogenesis. In the present study, we show that GlxA fulfils all criteria to be that cuproenzyme. GlxA is membrane associated and has an active site consisting of a mononuclear copper and a cross-linked Y-C cofactor. The domain organization of the tertiary structure defines GlxA as a new structural member of the mono-copper oxidase family, with copper co-ordination geometry similar to, but spectroscopically distinct from fungal galactose oxidase (Gox). EPR spectroscopy reveals that the oxidation of cupric GlxA generates a protein radical residing on the Y-C cross-link. A variety of canonical Gox substrates (including D-galactose) were tested but none were readily turned over by GlxA. A glxA null-mutant leads to loss of glycan accumulation at hyphal tips and consequently a drastically changed morphology both on solid substrates and in liquid-grown environments, a scenario similarly observed in the absence of the neighbouring glycan synthase CslA (cellulase synthase-like protein). In addition the glxA mutant has lost the stimulation of development by copper, supporting a model whereby the enzymatic action of GlxA on the glycan is required for development and morphology. From a biotechnology perspective, the open mycelium morphology observed with the glxA mutant in submerged culture has implications for use as an enzyme production host.
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22
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Yang Y, Zhou Q, Wang L, Liu X, Zhang W, Hu M, Dong J, Li J, Xiaoxuan L, Ouyang H, Li H, Gao F, Gong W, Lu Y, Wang J. Significant Improvement of Oxidase Activity through the Genetic Incorporation of a Redox-active Unnatural Amino Acid. Chem Sci 2015; 6:3881-3885. [PMID: 26417427 PMCID: PMC4583198 DOI: 10.1039/c5sc01126d] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 04/13/2015] [Indexed: 12/19/2022] Open
Abstract
Incorporation of 3-methoxytyrosine boosts the oxidase activity of the myoglobin model of oxidase, stressing the importance of the redox potential tuning of tyrosine.
While nature employs various covalent and non-covalent strategies to modulate tyrosine (Y) redox potential and pKa in order to optimize enzyme activities, such approaches have not been systematically applied for the design of functional metalloproteins. Through the genetic incorporation of 3-methoxytyrosine (OMeY) into myoglobin, we replicated important features of cytochrome c oxidase (CcO) in this small soluble protein, which exhibits selective O2 reduction activity while generating a small amount of reactive oxygen species (ROS). These results demonstrate that the electron donating ability of a tyrosine residue in the active site is important for CcO function. Moreover, we elucidated the structural basis for the genetic incorporation of OMeY into proteins by solving the X-ray structure of OMeY specific aminoacyl-tRNA synthetase complexed with OMeY.
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Affiliation(s)
- Yu Yang
- Center of Biophysics and Computational Biology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Qing Zhou
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Li Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China ; Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Xiaohong Liu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Wei Zhang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Meirong Hu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jianshu Dong
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jiasong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China ; Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Lv Xiaoxuan
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Hanlin Ouyang
- Center of Biophysics and Computational Biology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Han Li
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Feng Gao
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Weimin Gong
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Yi Lu
- Center of Biophysics and Computational Biology and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
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23
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Catalytic performance and mechanism of Cu(II)-hydrazone complexes as models of galactose oxidase. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.06.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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McMillan AW, Kier BL, Shu I, Byrne A, Andersen NH, Parson WW. Fluorescence of tryptophan in designed hairpin and Trp-cage miniproteins: measurements of fluorescence yields and calculations by quantum mechanical molecular dynamics simulations. J Phys Chem B 2013; 117:1790-809. [PMID: 23330783 PMCID: PMC3581364 DOI: 10.1021/jp3097378] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The quantum yield of tryptophan (Trp) fluorescence was measured in 30 designed miniproteins (17 β-hairpins and 13 Trp-cage peptides), each containing a single Trp residue. Measurements were made in D(2)O and H(2)O to distinguish between fluorescence quenching mechanisms involving electron and proton transfer in the hairpin peptides, and at two temperatures to check for effects of partial unfolding of the Trp-cage peptides. The extent of folding of all the peptides also was measured by NMR. The fluorescence yields ranged from 0.01 in some of the Trp-cage peptides to 0.27 in some hairpins. Fluorescence quenching was found to occur by electron transfer from the excited indole ring of the Trp to a backbone amide group or the protonated side chain of a nearby histidine, glutamate, aspartate, tyrosine, or cysteine residue. Ionized tyrosine side chains quenched strongly by resonance energy transfer or electron transfer to the excited indole ring. Hybrid classical/quantum mechanical molecular dynamics simulations were performed by a method that optimized induced electric dipoles separately for the ground and excited states in multiple π-π* and charge-transfer (CT) excitations. Twenty 0.5 ns trajectories in the tryptophan's lowest excited singlet π-π* state were run for each peptide, beginning by projections from trajectories in the ground state. Fluorescence quenching was correlated with the availability of a CT or exciton state that was strongly coupled to the π-π* state and that matched or fell below the π-π* state in energy. The fluorescence yields predicted by summing the calculated rates of charge and energy transfer are in good accord with the measured yields.
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Affiliation(s)
- Andrew W. McMillan
- Department of Biochemistry, Structure and Design, University of Washington, Seattle, WA 98195
- Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
| | - Brandon L. Kier
- Department of Chemistry, Structure and Design, University of Washington, Seattle, WA 98195
- Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
| | - Irene Shu
- Department of Chemistry, Structure and Design, University of Washington, Seattle, WA 98195
| | - Aimee Byrne
- Department of Chemistry, Structure and Design, University of Washington, Seattle, WA 98195
| | - Niels H. Andersen
- Department of Chemistry, Structure and Design, University of Washington, Seattle, WA 98195
- Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
| | - William W. Parson
- Department of Biochemistry, Structure and Design, University of Washington, Seattle, WA 98195
- Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98195
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25
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Lyons CT, Stack TDP. Recent advances in phenoxyl radical complexes of salen-type ligands as mixed-valent galactose oxidase models. Coord Chem Rev 2013; 257:528-540. [PMID: 23264696 PMCID: PMC3524984 DOI: 10.1016/j.ccr.2012.06.003] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The interplay between redox-active transition metal ions and redox-active ligands in metalloenzyme sites is an area of considerable research interest. Galactose oxidase (GO) is the archetypical example, catalyzing the aerobic oxidation of primary alcohols to aldehydes via two one-electron cofactors: a copper atom and a cysteine-modified tyrosine residue. The electronic structure of the oxidized form of the enzyme (GO(ox)) has been investigated extensively through small molecule analogues including metal-salen phenoxyl radical complexes. Similar to GO(ox), one-electron oxidized metal-salen complexes are mixed-valent species, in which molecular orbitals (MOs) with predominantly phenolate and phenoxyl π-character act as redox-active centers bridged by mixing with metal d-orbitals. A detailed evaluation of the electronic distribution in these odd electron species using a variety of spectroscopic, electrochemical, and theoretical techniques has led to keen insights into the electronic structure of GO(ox).
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Affiliation(s)
| | - T. Daniel P. Stack
- Department of Chemistry, Stanford University, Sanford, CA 94305, United States
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26
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Butsch K, Günther T, Klein A, Stirnat K, Berkessel A, Neudörfl J. Redox chemistry of copper complexes with various salen type ligands. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2012.08.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Zhou Q, Hu M, Zhang W, Jiang L, Perrett S, Zhou J, Wang J. Probing the function of the Tyr-Cys cross-link in metalloenzymes by the genetic incorporation of 3-methylthiotyrosine. Angew Chem Int Ed Engl 2012. [PMID: 23197358 DOI: 10.1002/anie.201207229] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qing Zhou
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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28
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Zhou Q, Hu M, Zhang W, Jiang L, Perrett S, Zhou J, Wang J. Probing the Function of the Tyr-Cys Cross-Link in Metalloenzymes by the Genetic Incorporation of 3-Methylthiotyrosine. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Ruszczycky MW, Ogasawara Y, Liu HW. Radical SAM enzymes in the biosynthesis of sugar-containing natural products. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:1231-44. [PMID: 22172915 PMCID: PMC3438383 DOI: 10.1016/j.bbapap.2011.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 11/28/2011] [Indexed: 11/24/2022]
Abstract
Carbohydrates play a key role in the biological activity of numerous natural products. In many instances their biosynthesis requires radical mediated rearrangements, some of which are catalyzed by radical SAM enzymes. BtrN is one such enzyme responsible for the dehydrogenation of a secondary alcohol in the biosynthesis of 2-deoxystreptamine. DesII is another example that catalyzes a deamination reaction necessary for the net C4 deoxygenation of a glucose derivative en route to desosamine formation. BtrN and DesII represent the two most extensively characterized radical SAM enzymes involved in carbohydrate biosynthesis. In this review, we summarize the biosynthetic roles of these two enzymes, their mechanisms of catalysis, the questions that have arisen during these investigations and the insight they can offer for furthering our understanding of radical SAM enzymology. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Mark W. Ruszczycky
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yasushi Ogasawara
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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30
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Butsch K, Klein A, Nitsche S, Stirnat K, Hawkett JR, McInnes EJL, Bauer M. Generation and characterisation of the phenoxyl-radical containing Cu(II) complex [Cu(triaz)2]+ (triaz- = O,N chelating triazole-phenolate). Dalton Trans 2012; 41:11464-75. [PMID: 22895494 DOI: 10.1039/c2dt31369c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The new copper complex [Cu(triaz)(2)] (Htriaz = 2,4-di-(tert-butyl)-6-(5-chloro-2H-benzo[d][1,2,3]triazol-2-yl)phenol) was investigated in detail by single crystal XRD, EPR-, UV/Vis-absorption-, CV-, and spectroelectrochemistry. The oxidised species [Cu(triaz)(2)](+) was characterised by UV/Vis spectroelectrochemistry and contains a phenoxyl-radical bound to Cu(II). This quite stable species was chemically generated by two different methods: aerial oxidation of a Cu(I) precursor in the presence of Htriaz (and base) or from [Cu(triaz)(2)] by adding a Cu(II) salt (disproportionation). The efficiency for the latter reaction has been studied by UV/Vis spectroscopy, XAS and catalytic test reactions (oxidation of benzyl alcohol).
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Affiliation(s)
- Katharina Butsch
- Universität zu Köln, Department für Chemie, Institut für Anorganische Chemie, Greinstrasse 6, D-50939 Köln, Germany
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31
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Pratt RC, Lyons CT, Wasinger EC, Stack TDP. Electrochemical and spectroscopic effects of mixed substituents in bis(phenolate)-copper(II) galactose oxidase model complexes. J Am Chem Soc 2012; 134:7367-77. [PMID: 22471355 PMCID: PMC3343640 DOI: 10.1021/ja211247f] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonsymmetric substitution of salen (1(R(1),R(2))) and reduced salen (2(R(1),R(2))) Cu(II)-phenoxyl complexes with a combination of -(t)Bu, -S(i)Pr, and -OMe substituents leads to dramatic differences in their redox and spectroscopic properties, providing insight into the influence of the cysteine-modified tyrosine cofactor in the enzyme galactose oxidase (GO). Using a modified Marcus-Hush analysis, the oxidized copper complexes are characterized as Class II mixed-valent due to the electronic differentiation between the two substituted phenolates. Sulfur K-edge X-ray absorption spectroscopy (XAS) assesses the degree of radical delocalization onto the single sulfur atom of nonsymmetric [1((t)Bu,SMe)](+) at 7%, consistent with other spectroscopic and electrochemical results that suggest preferential oxidation of the -SMe bearing phenolate. Estimates of the thermodynamic free-energy difference between the two localized states (ΔG(o)) and reorganizational energies (λ(R(1)R(2))) of [1(R(1),R(2))](+) and [2(R(1),R(2))](+) lead to accurate predictions of the spectroscopically observed IVCT transition energies. Application of the modified Marcus-Hush analysis to GO using parameters determined for [2(R(1),R(2))](+) predicts a ν(max) of ∼13600 cm(-1), well within the energy range of the broad Vis-NIR band displayed by the enzyme.
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Affiliation(s)
- Russell C. Pratt
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Christopher T. Lyons
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Erik C. Wasinger
- Department of Chemistry, California State University, Chico, Chico, California 95929, United States
| | - T. Daniel. P. Stack
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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32
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Kumar N, Liu S, Kozlowski PM. Charge Separation Propensity of the Coenzyme B12-Tyrosine Complex in Adenosylcobalamin-Dependent Methylmalonyl-CoA Mutase Enzyme. J Phys Chem Lett 2012; 3:1035-1038. [PMID: 26286568 DOI: 10.1021/jz300102s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report the electrophilic Fukui function analysis based on density functional reactivity theory (DFRT) to demonstrate the feasibility of the proton-coupled electron transfer (PCET) mechanism. To characterize the charge propensity of an electron-transfer site other than the proton-acceptor site of the coenzyme B12-tyrosine complex, several structural models (ranging from minimal to actual enzyme scaffolds) have been employed at DFT and QM/MM computations. It is shown, based on the methylmalonyl-CoA mutase (MCM) enzyme that substrate binding plays a significant role in displacing the phenoxyl proton of the tyrosine (Y89), which initiates the electron transfer from Y89 to coenzyme B12. PCET-based enzymatic reaction implies that one electron-reduced form of the AdoCbl cofactor induces the cleavage of the Co-C bond, as an alternative to its neutral analogue, which can assist in understanding the origin of the observed trillion-fold rate enhancement in MCM enzyme.
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Affiliation(s)
- Neeraj Kumar
- †Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Shubin Liu
- ‡Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
| | - Pawel M Kozlowski
- †Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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Rokhsana D, Howells AE, Dooley DM, Szilagyi RK. Role of the Tyr-Cys Cross-link to the Active Site Properties of Galactose Oxidase. Inorg Chem 2012; 51:3513-24. [DOI: 10.1021/ic2022769] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dalia Rokhsana
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United
States
| | - Alta E. Howells
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United
States
| | - David M. Dooley
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United
States
| | - Robert K. Szilagyi
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United
States
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Sulfanyl stabilization of copper-bonded phenoxyls in model complexes and galactose oxidase. Proc Natl Acad Sci U S A 2011; 108:18600-5. [PMID: 22065750 DOI: 10.1073/pnas.1109931108] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Integrating sulfanyl substituents into copper-bonded phenoxyls significantly alters their optical and redox properties and provides insight into the influence of cysteine modification of the tyrosine cofactor in the enzyme galactose oxidase. The model complexes [1(SR2)](+) are class II mixed-valent Cu(II)-phenoxyl-phenolate species that exhibit intervalence charge transfer bands and intense visible sulfur-aryl π → π* transitions in the energy range, which provides a greater spectroscopic fidelity to oxidized galactose oxidase than non-sulfur-bearing analogs. The potentials for phenolate-based oxidations of the sulfanyl-substituted 1(SR2) are lower than the alkyl-substituted analogs by up to ca. 150 mV and decrease following the steric trend: -S(t)Bu > -S(i) Pr > -SMe. Density functional theory calculations suggest that reducing the steric demands of the sulfanyl substituent accommodates an in-plane conformation of the alkylsulfanyl group with the aromatic ring, which stabilizes the phenoxyl hole by ca. 8 kcal mol(-1) (1 kcal = 4.18 kJ; 350 mV) through delocalization onto the sulfur atom. Sulfur K-edge X-ray absorption spectroscopy clearly indicates a contribution of ca. 8-13% to the hole from the sulfur atoms in [1(SR2)](+). The electrochemical results for the model complexes corroborate the ca. 350 mV (density functional theory) contribution of hole delocalization on to the cysteine-tyrosine cross-link to the stability of the phenoxyl radical in the enzyme, while highlighting the importance of the in-plane conformation observed in all crystal structures of the enzyme.
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Aparecido Cordeiro F, Bertechini Faria C, Parra Barbosa-Tessmann I. Identification of new galactose oxidase genes in Fusarium spp. J Basic Microbiol 2011; 50:527-37. [PMID: 21077113 DOI: 10.1002/jobm.201000078] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Galactose oxidase (GO) converts galactose to an aldehyde and has several biotechnological applications, including cancer diagnosis. It is mainly produced by Fusarium austroamericanum but is also produced by Fusarium acuminatum and by isolates of the Fusarium graminearum and Gibberella fujikuroi complexes. The F. austroamericanum GO gaoA gene has been cloned, but the GO genes from other secreting species have not been characterized. Problems associated with the F. austroamericanum GO such as high pI and low catalytic efficiency and thermostability, and the difficult purification process makes the search for homologous genes attractive. In this work, the GO genes from Fusarium verticillioides and Fusarium subglutinans, two species of the G. fujikuroi complex, were cloned, sequenced, and analyzed. New GO genes were found in databases and were used to construct a phylogenetic tree, which revealed the existence of three orthologous lineages of GO genes in Fusarium spp. In addition, RT-PCR analyses revealed that the new GO cloned gene may be endogenously expressed in F. subglutinans but not in F. verticillioides, in the used culture conditions.
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Safaei E, Kabir MM, Wojtczak A, Jagličić Z, Kozakiewicz A, Lee YI. Synthesis, crystal structure, magnetic and redox properties of copper(II) complexes of N-alkyl(aryl) tBu-salicylaldimines. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2010.11.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kozlowski PM, Kamachi T, Kumar M, Nakayama T, Yoshizawa K. Theoretical Analysis of the Diradical Nature of Adenosylcobalamin Cofactor−Tyrosine Complex in B12-Dependent Mutases: Inspiring PCET-Driven Enzymatic Catalysis. J Phys Chem B 2010; 114:5928-39. [DOI: 10.1021/jp100573b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takashi Kamachi
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Manoj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tomonori Nakayama
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
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Seyedsayamdost MR, Argirević T, Minnihan EC, Stubbe J, Bennati M. Structural examination of the transient 3-aminotyrosyl radical on the PCET pathway of E. coli ribonucleotide reductase by multifrequency EPR spectroscopy. J Am Chem Soc 2009; 131:15729-38. [PMID: 19821570 PMCID: PMC4703294 DOI: 10.1021/ja903879w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Indexed: 11/28/2022]
Abstract
E. coli ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to deoxynucleotides, a process that requires long-range radical transfer over 35 A from a tyrosyl radical (Y(122)*) within the beta2 subunit to a cysteine residue (C(439)) within the alpha2 subunit. The radical transfer step is proposed to occur by proton-coupled electron transfer via a specific pathway consisting of Y(122) --> W(48) --> Y(356) in beta2, across the subunit interface to Y(731) --> Y(730) --> C(439) in alpha2. Using the suppressor tRNA/aminoacyl-tRNA synthetase (RS) methodology, 3-aminotyrosine has been incorporated into position 730 in alpha2. Incubation of this mutant with beta2, substrate, and allosteric effector resulted in loss of the Y(122)* and formation of a new radical, previously proposed to be a 3-aminotyrosyl radical (NH(2)Y*). In the current study [(15)N]- and [(14)N]-NH(2)Y(730)* have been generated in H(2)O and D(2)O and characterized by continuous wave 9 GHz EPR and pulsed EPR spectroscopies at 9, 94, and 180 GHz. The data give insight into the electronic and molecular structure of NH(2)Y(730)*. The g tensor (g(x) = 2.0052, g(y) = 2.0042, g(z) = 2.0022), the orientation of the beta-protons, the hybridization of the amine nitrogen, and the orientation of the amino protons relative to the plane of the aromatic ring were determined. The hyperfine coupling constants and geometry of the NH(2) moiety are consistent with an intramolecular hydrogen bond within NH(2)Y(730)*. This analysis is an essential first step in using the detailed structure of NH(2)Y(730)* to formulate a model for a PCET mechanism within alpha2 and for use of NH(2)Y in other systems where transient Y*s participate in catalysis.
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Affiliation(s)
- Mohammad R Seyedsayamdost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
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