1
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Ali HS, de Visser SP. QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase. Chemistry 2024; 30:e202304172. [PMID: 38373118 DOI: 10.1002/chem.202304172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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2
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Song X, Liu J, Wang B. Emergence of Function from Nonheme Diiron Oxygenases: A Quantum Mechanical/Molecular Mechanical Study of Oxygen Activation and Organophosphonate Catabolism Mechanisms by PhnZ. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xitong Song
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Jia Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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3
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Cao X, Song H, Li XX, Zhao Y, Qiao Q, Wang Y. Which is the real oxidant in the competitive ligand self-hydroxylation and substrate oxidation, a biomimetic iron(II)-hydroperoxo species or an oxo-iron(IV)-hydroxy one? Dalton Trans 2022; 51:7571-7580. [DOI: 10.1039/d2dt00797e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nonheme iron(II)-hydroperoxo species (FeII-(η2-OOH)) 1 and the concomitant oxo-iron(IV)-hydroxyl one 2 are proposed as the key intermediates of a large class of 2-oxoglutarate dependent dioxygenases (e.g., isopenicillin N synthase). Extensive...
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4
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Liu J, Wu P, Yan S, Li Y, Cao Z, Wang B. Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOX. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Shengheng Yan
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuanyuan Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Zexing Cao
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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5
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Lu J, Wang B, Shaik S, Lai W. QM/MM Calculations Reveal the Important Role of α-Heteroatom Substituents in Controlling Selectivity of Mononuclear Nonheme HppE-Catalyzed Reactions. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jiarui Lu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Sason Shaik
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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6
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Song Z, Yue Y, Feng S, Sun H, Li Y, Xu F, Zhang Q, Wang W. Cysteine dioxygenase catalyzed C F bond cleavage: An in silico approach. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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7
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Yan J, Chen S. How To Produce Methane Precursor in the Upper Ocean by An Untypical Non‐Heme Fe‐Dependent Methylphosphonate Synthase? Chemphyschem 2020; 21:385-396. [DOI: 10.1002/cphc.202000025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ji‐Fan Yan
- Key Laboratory of Cluster Science of Ministry of Education School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
| | - Shi‐Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China
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8
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Lin Y, Stańczak A, Manchev Y, Straganz GD, Visser SP. Can a Mononuclear Iron(III)‐Superoxo Active Site Catalyze the Decarboxylation of Dodecanoic Acid in UndA to Produce Biofuels? Chemistry 2019; 26:2233-2242. [DOI: 10.1002/chem.201903783] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/24/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Yen‐Ting Lin
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical ScienceThe University of, Manchester 131 Princess Street Manchester M1 7DN UK
| | - Agnieszka Stańczak
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical ScienceThe University of, Manchester 131 Princess Street Manchester M1 7DN UK
- Faculty of ChemistrySilesian University of Technology ks. Marcina Strzody 9 44-100 Gliwice Poland
- Tunneling Group, Biotechnology CentreSilesian University of Technology ul. Krzywoustego 8 44–100 Gliwice Poland
| | - Yulian Manchev
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical ScienceThe University of, Manchester 131 Princess Street Manchester M1 7DN UK
| | - Grit D. Straganz
- Graz University of TechnologyInstitute of Biochemistry Petergasse 12 8010 Graz Austria
| | - Sam P. Visser
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical ScienceThe University of, Manchester 131 Princess Street Manchester M1 7DN UK
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9
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Singh W, Quinn D, Moody TS, Huang M. Reaction Mechanism of Histone Demethylation in αKG-dependent Non-Heme Iron Enzymes. J Phys Chem B 2019; 123:7801-7811. [PMID: 31469562 DOI: 10.1021/acs.jpcb.9b06064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Histone demethylases (KDMs) catalyze histone lysine demethylation, an important epigenetic process that controls gene expression in eukaryotes, and represent important cancer drug targets for cancer treatment. Demethylation of histone is comprised of sequential reaction steps including oxygen activation, decarboxylation, and demethylation. The initial oxygen binding and activation steps have been studied. However, the information on the complete catalytic reaction cycle is limited, which has impeded the structure-based design of inhibitors targeting KDMs. Here we report the mechanism of the complete reaction steps catalyzed by a representative nonheme iron αKG-dependent KDM, PHF8 using QM/MM approaches. The atomic-level understanding on the complete reaction mechanism of PHF8 would shed light on the structure-based design of selective inhibitors targeting KDMs to intervene in cancer epigenetics.
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Affiliation(s)
- Warispreet Singh
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom.,Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Derek Quinn
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Thomas S Moody
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom.,Arran Chemical Company Limited , Unit 1 Monksland Industrial Estate , Athlone , Co. Roscommon , Ireland
| | - Meilan Huang
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom
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10
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Wang B, Cao Z, Rovira C, Song J, Shaik S. Fenton-Derived OH Radicals Enable the MPnS Enzyme to Convert 2-Hydroxyethylphosphonate to Methylphosphonate: Insights from Ab Initio QM/MM MD Simulations. J Am Chem Soc 2019; 141:9284-9291. [PMID: 31132257 DOI: 10.1021/jacs.9b02659] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mechanism for dioxygen activation represents one of the core issues in metalloenzymes. In most cases, the activation of the O2 molecule requires additional electrons from an external reducant. However, nonheme hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are exceptional C-H oxygenases. Both enzymes do not utilize reductants, rather they employ directly iron(III)-superoxide species to initiate H-abstraction reactions and lead thereby to catalysis of the C-C cleavage in 2-hydroxyethylphosphonate (2-HEP). Using the recently characterized MPnS structure and QM(B3LYP)/MM-based metadynamics simulations, we deciphered the chemical mechanism for MPnS. Our simulations demonstrate O2 activation in MPnS is mediated by an adjacent Lysine residue (Lys28) in the active site, leading to an unusual H 2 O 2 intermediate in the reductant-independent nonheme MPnS enzyme. Furthermore, the so-generated H 2 O 2 intermediate is subsequently employed in a Fenton-type reaction, leading to a locked •OH radical that spontaneously attaches to the substrate carbonyl group. Meanwhile, the proton from the Fe(III)-OH is shuttled back to the deprotonated Lys28, affording the Fe(IV)-oxo species that is identified by experiment in HEPD. Thus, our calculations demonstrate an unusual proton-shuttle mechanism for O 2 activation in metalloenzymes.
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Affiliation(s)
- Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , P. R. China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , P. R. China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB , Universitat de Barcelona , Martí i Franquès 1 , 08028 Barcelona , Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluís Companys, 23 , 08020 Barcelona , Spain
| | - Jinshuai Song
- College of Chemistry and Molecular Engineering , Zhengzhou University , Zhengzhou 450001 , P. R. China
| | - Sason Shaik
- Institute of Chemistry , The Hebrew University of Jerusalem , 9190407 Jerusalem , Israel
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11
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Al-Jaber AS, Bani-Yaseen AD. On the encapsulation of Olsalazine by β-cyclodextrin: A DFT-based computational and spectroscopic investigations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 214:531-536. [PMID: 30818152 DOI: 10.1016/j.saa.2019.02.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 02/06/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
In this work, the supramolecular host-guest interaction of the prodrug Olsalazine (OLZ) and β-Cyclodextrin (β-CD) was examined experimentally and computationally. Experimentally, employing the UV-Vis spectroscopic method in aqueous media at various pH's, results obtained using the Benesi-Hilderbrand approach demonstrated that OLZ can form supramolecular inclusion complex with β-CD with stoichiometric ratio of 1:1. Furthermore, these results revealed that the formation of OLZ: β-CD complexes exhibited insignificant pH dependency in the range 5-8 with an average binding constant (Kb) of approximately 1×103M-1. Computationally, geometry optimization of 1:1 OLZ: β-CD complexes was performed employing the ONIOM (DFT((ωB97XB)/6-31+G(d)),SQM(PM3)) approach. Obtained results demonstrated that OLZ: β-CD complex is stabilized by the formation of intermolecular hydrogen bonds with an average length of approximately 1.8Å. Additionally, the stability of OLZ: β-CD complex was demonstrated employing ADMP molecular dynamic simulations over a timeframe of 500fs. The molecularity of the supramolecular host-guest interaction between OLZ and β-CD is presented and interpreted in the essence of TD-DFT and molecular orbitals analyses.
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Affiliation(s)
- Amina S Al-Jaber
- Department of Chemistry & Earth Sciences, College of Arts & Science, Qatar University, Doha, P.O. Box 2713, State of Qatar
| | - Abdulilah Dawoud Bani-Yaseen
- Department of Chemistry & Earth Sciences, College of Arts & Science, Qatar University, Doha, P.O. Box 2713, State of Qatar.
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12
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Lu J, Lai W. Mechanistic Insights into a Stibene Cleavage Oxygenase NOV1 from Quantum Mechanical/Molecular Mechanical Calculations. ChemistryOpen 2019; 8:228-235. [PMID: 30828510 PMCID: PMC6382310 DOI: 10.1002/open.201800259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/30/2019] [Indexed: 12/03/2022] Open
Abstract
NOV1, a stilbene cleavage oxygenase, catalyzes the cleavage of the central double bond of stilbenes to two phenolic aldehydes, using a 4-His Fe(II) center and dioxygen. Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the reaction mechanism of the central double bond cleavage of phytoalexin resveratrol by NOV1. Our results showed that the oxygen molecule prefers to bind to the iron center in a side-on fashion, as suggested from the experiment. The quintet Fe-O2 complex with the side-on superoxo antiferromagnetic coupled to the resveratrol radical is identified as the reactive oxygen species. The QM/MM results support the dioxygenase mechanism involving a dioxetane intermediate with a rate-limiting barrier of 10.0 kcal mol-1. The alternative pathway through an epoxide intermediate is ruled out due to a larger rate-limiting barrier (26.8 kcal mol-1). These findings provide important insight into the catalytic mechanism of carotenoid cleavage oxygenases and also the dioxygen activation of non-heme enzymes.
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Affiliation(s)
- Jiarui Lu
- Department of ChemistryRenmin University of ChinaNo. 59 Zhongguancun Street, Haidian DistrictBeijing100872P. R. China
| | - Wenzhen Lai
- Department of ChemistryRenmin University of ChinaNo. 59 Zhongguancun Street, Haidian DistrictBeijing100872P. R. China
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13
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Li S, Lu J, Lai W. Mechanistic insights into ring cleavage of hydroquinone by PnpCD from quantum mechanical/molecular mechanical calculations. Org Biomol Chem 2019; 17:8194-8205. [DOI: 10.1039/c9ob01084j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM calculations for ring cleavage of hydroquinone by PnpCD show that Asn258 loses coordination to the iron when the reaction begins. The first-sphere Glu262 can act as an acid–base catalyst to lower the rate-limiting barrier.
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Affiliation(s)
- Senzhi Li
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Jiarui Lu
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Wenzhen Lai
- Department of Chemistry
- Renmin University of China
- Beijing
- China
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14
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de Visser SP. Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases. CHEM REC 2018; 18:1501-1516. [PMID: 29878456 DOI: 10.1002/tcr.201800033] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/05/2023]
Abstract
Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO2 . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase.
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Affiliation(s)
- Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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15
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Ulrich EC, Kamat SS, Hove-Jensen B, Zechel DL. Methylphosphonic Acid Biosynthesis and Catabolism in Pelagic Archaea and Bacteria. Methods Enzymol 2018; 605:351-426. [DOI: 10.1016/bs.mie.2018.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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Faponle AS, Seebeck FP, de Visser SP. Sulfoxide Synthase versus Cysteine Dioxygenase Reactivity in a Nonheme Iron Enzyme. J Am Chem Soc 2017; 139:9259-9270. [PMID: 28602090 DOI: 10.1021/jacs.7b04251] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sulfoxide synthase EgtB represents a unique family of nonheme iron enzymes that catalyze the formation of a C-S bond between N-α-trimethyl histidine and γ-glutamyl cysteine, which is the key step in the biosynthesis of ergothioneine, an important amino acid related to aging. A controversy has arisen regarding its catalytic mechanism related to the function of the active-site Tyr377 residue. The biosynthesis of ergothioneine in EgtB shows structural similarities to cysteine dioxygenase which transfers two oxygen atoms to the thiolate group of cysteine. The question, therefore, is how do EgtB enzymes catalyze the C-S bond-formation reaction, while also preventing a dioxygenation of its cysteinate substrate? In this work we present a quantum mechanics/molecular mechanics study into the mechanism of sulfoxide synthase enzymes as compared to cysteine dioxygenase enzymes and present pathways for both reaction channels in EgtB. We show that EgtB contains a conserved tyrosine residue that reacts via proton-coupled electron transfer with the iron(III)-superoxo species and creates an iron(III)-hydroperoxo intermediate, thereby preventing the possible thiolate dioxygenation side reaction. The nucleophilic C-S bond-formation step happens subsequently concomitant to relay of the proton of the iron(II)-hydroperoxo back to Tyr377. This is the rate-determining step in the reaction cycle and is followed by hydrogen-atom transfer from the CE1-H group of trimethyl histidine substrate to iron(II)-superoxo. In the final step, a quick and almost barrierless sulfoxidation leads to the sulfoxide product complexes. The work highlights a unique machinery and active-site setup of the enzyme that drives the sulfoxide synthase reaction.
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Affiliation(s)
- Abayomi S Faponle
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Florian P Seebeck
- Department for Chemistry, University of Basel , St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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17
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Zhao C, Chen H. Mechanism of Organophosphonate Catabolism by Diiron Oxygenase PhnZ: A Third Iron-Mediated O–O Activation Scenario in Nature. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chongyang Zhao
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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18
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Peck SC, Wang C, Dassama LMK, Zhang B, Guo Y, Rajakovich LJ, Bollinger JM, Krebs C, van der Donk WA. O-H Activation by an Unexpected Ferryl Intermediate during Catalysis by 2-Hydroxyethylphosphonate Dioxygenase. J Am Chem Soc 2017; 139:2045-2052. [PMID: 28092705 PMCID: PMC5302023 DOI: 10.1021/jacs.6b12147] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Activation
of O–H bonds by inorganic metal-oxo complexes
has been documented, but no cognate enzymatic process is known. Our
mechanistic analysis of 2-hydroxyethylphosphonate dioxygenase
(HEPD), which cleaves the C1–C2 bond of its substrate to afford
hydroxymethylphosphonate on the biosynthetic pathway to
the commercial herbicide phosphinothricin, uncovered an example
of such an O–H-bond-cleavage event. Stopped-flow UV–visible
absorption and freeze-quench Mössbauer experiments identified
a transient iron(IV)-oxo (ferryl) complex. Maximal accumulation of
the intermediate required both the presence of deuterium in the substrate
and, importantly, the use of 2H2O as solvent.
The ferryl complex forms and decays rapidly enough to be on the catalytic
pathway. To account for these unanticipated results, a new mechanism
that involves activation of an O–H bond by the ferryl complex
is proposed. This mechanism accommodates all available data on the
HEPD reaction.
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Affiliation(s)
- Spencer C Peck
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Chen Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Laura M K Dassama
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Yisong Guo
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Lauren J Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States.,Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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19
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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20
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Peck SC, van der Donk WA. Go it alone: four-electron oxidations by mononuclear non-heme iron enzymes. J Biol Inorg Chem 2016; 22:381-394. [PMID: 27783267 DOI: 10.1007/s00775-016-1399-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
Abstract
This review discusses the current mechanistic understanding of a group of mononuclear non-heme iron-dependent enzymes that catalyze four-electron oxidation of their organic substrates without the use of any cofactors or cosubstrates. One set of enzymes acts on α-ketoacid-containing substrates, coupling decarboxylation to oxygen activation. This group includes 4-hydroxyphenylpyruvate dioxygenase, 4-hydroxymandelate synthase, and CloR involved in clorobiocin biosynthesis. A second set of enzymes acts on substrates containing a thiol group that coordinates to the iron. This group is comprised of isopenicillin N synthase, thiol dioxygenases, and enzymes involved in the biosynthesis of ergothioneine and ovothiol. The final group of enzymes includes HEPD and MPnS that both carry out the oxidative cleavage of the carbon-carbon bond of 2-hydroxyethylphosphonate but generate different products. Commonalities amongst many of these enzymes are discussed and include the initial substrate oxidation by a ferric-superoxo-intermediate and a second oxidation by a ferryl species.
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Affiliation(s)
- Spencer C Peck
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA. .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA.
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21
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Protein effects in non-heme iron enzyme catalysis: insights from multiscale models. J Biol Inorg Chem 2016; 21:645-57. [DOI: 10.1007/s00775-016-1374-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/20/2016] [Indexed: 01/09/2023]
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22
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Mono- and binuclear non-heme iron chemistry from a theoretical perspective. J Biol Inorg Chem 2016; 21:619-44. [DOI: 10.1007/s00775-016-1357-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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23
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Moreira C, Ramos MJ, Fernandes PA. Reaction Mechanism ofMycobacterium TuberculosisGlutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations. Chemistry 2016; 22:9218-25. [DOI: 10.1002/chem.201600305] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Cátia Moreira
- UCIBIO, REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; 4169-007 Porto Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; 4169-007 Porto Portugal
| | - Pedro Alexandrino Fernandes
- UCIBIO, REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; 4169-007 Porto Portugal
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24
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Quesne MG, Borowski T, de Visser SP. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs. Chemistry 2015; 22:2562-81. [PMID: 26696271 DOI: 10.1002/chem.201503802] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/08/2022]
Abstract
Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
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Affiliation(s)
- Matthew G Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland. .,Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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25
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Khavani M, Izadyar M. Implicit and explicit solvent effects on the selectivity of the cycloaddition reaction of cyclopentadiene and methyl acrylate; a theoretical study. PROGRESS IN REACTION KINETICS AND MECHANISM 2015. [DOI: 10.3184/146867815x14297104685269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The product selectivity of the Diels–Alder reaction between cyclopentadiene and methyl acrylate has been studied through a solvent effect analysis by implicit and explicit solvent models. Two paths for this reaction have been proposed and thermodynamic and kinetic parameters for each path were calculated by the B3LYP functional with 6-311++G(d,p) basis set at 298.15 K. In the explicit solvent model, hydrogen bonds were investigated by the QM/MM method. According to the results, the proportion of the exo product in the gas phase is more than for the endo one, which is in contrast to the solvent phase. HOMO–LUMO analyses in the gas phase and different solvents have been done and solvent effects on the energies of the HOMO–LUMO orbitals were investigated. According to the results, the band gap of the TSs was increased in the presence of the solvents. Finally, natural population analysis has been performed to calculate the electronic charges of some atoms that are involved in the centre of the reaction. The data obtained showed that different solvents, including polar and nonpolar solvents, have different effects on the electronic charges of the atoms. Topological analysis of the structures during the reaction by the quantum theory of atoms in molecules (QTAIM) method in the gas phase and different solvents confirmed a cyclic structure for the transition state.
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Affiliation(s)
- Mohammad Khavani
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Izadyar
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
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26
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 760] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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27
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Pabis A, Geronimo I, York DM, Paneth P. Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field. J Chem Theory Comput 2014; 10:2246-2254. [PMID: 24955078 PMCID: PMC4059247 DOI: 10.1021/ct500205z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Indexed: 12/03/2022]
Abstract
Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron-sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein-water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance.
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Affiliation(s)
- Anna Pabis
- Institute
of Applied Radiation Chemistry, Lodz University
of Technology, Zeromskiego
116, 90-924 Lodz, Poland
- Department
of Chemistry and Chemical Biology, Center for Integrative Proteomics
Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Inacrist Geronimo
- Institute
of Applied Radiation Chemistry, Lodz University
of Technology, Zeromskiego
116, 90-924 Lodz, Poland
| | - Darrin M. York
- Department
of Chemistry and Chemical Biology, Center for Integrative Proteomics
Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Lodz University
of Technology, Zeromskiego
116, 90-924 Lodz, Poland
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28
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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29
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 441] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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30
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Kellie JL, Wilson KA, Wetmore SD. Standard role for a conserved aspartate or more direct involvement in deglycosylation? An ONIOM and MD investigation of adenine-DNA glycosylase. Biochemistry 2013; 52:8753-65. [PMID: 24168684 DOI: 10.1021/bi401310w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
8-Oxoguanine (OG) is one of the most frequently occurring forms of DNA damage and is particularly deleterious since it forms a stable Hoogsteen base pair with adenine (A). The repair of an OG:A mispair is initiated by adenine-DNA glycosylase (MutY), which hydrolyzes the sugar-nucleobase bond of the adenine residue before the lesion is processed by other proteins. MutY has been proposed to use a two-part chemical step involving protonation of the adenine nucleobase, followed by SN1 hydrolysis of the glycosidic bond. However, differences between a recent (fluorine recognition complex, denoted as the FLRC) crystal structure and the structure on which most mechanistic conclusions have been based to date (namely, the lesion recognition complex or LRC) raise questions regarding the mechanism used by MutY and the discrete role of various active-site residues. The present work uses both molecular dynamics (MD) and quantum mechanical (ONIOM) models to compare the active-site conformational dynamics in the two crystal structures, which suggests that only the understudied FLRC leads to a catalytically competent reactant. Indeed, all previous computational studies on MutY have been initiated from the LRC structure. Subsequently, for the first time, various mechanisms are examined with detailed ONIOM(M06-2X:PM6) reaction potential energy surfaces (PES) based on the FLRC structure, which significantly extends the mechanistic picture. Specifically, our work reveals that the reaction proceeds through a different route than the commonly accepted mechanism and the catalytic function of various active-site residues (Geobacillus stearothermophilus numbering). Specifically, contrary to proposals based on the LRC, E43 is determined to solely be involved in the initial adenine protonation step and not the deglycosylation reaction as the general base. Additionally, a novel catalytic role is proposed for Y126, whereby this residue plays a significant role in stabilizing the highly charged active site, primarily through interactions with E43. More importantly, D144 is found to explicitly catalyze the nucleobase dissociation step through partial nucleophilic attack. Although this is a more direct role than previously proposed for any other DNA glycosylase, comparison to previous work on other glycosylases justifies the larger contribution in the case of MutY and allows us to propose a unified role for the conserved Asp/Glu in the DNA glycosylases, as well as other enzymes that catalyze nucleotide deglycosylation reactions.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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31
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32
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Zhang Y, Yan S, Yao L. A Mechanistic Study of Trichoderma reesei Cel7B Catalyzed Glycosidic Bond Cleavage. J Phys Chem B 2013; 117:8714-22. [DOI: 10.1021/jp403999s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yu Zhang
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Shihai Yan
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Lishan Yao
- Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
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33
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Du L, Gao J, Liu Y, Liu C. Water-Dependent Reaction Pathways: An Essential Factor for the Catalysis in HEPD Enzyme. J Phys Chem B 2012; 116:11837-44. [DOI: 10.1021/jp305454m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Likai Du
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Jun Gao
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
| | - Chengbu Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
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34
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McSorley FR, Wyatt PB, Martinez A, DeLong EF, Hove-Jensen B, Zechel DL. PhnY and PhnZ Comprise a New Oxidative Pathway for Enzymatic Cleavage of a Carbon–Phosphorus Bond. J Am Chem Soc 2012; 134:8364-7. [DOI: 10.1021/ja302072f] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fern R. McSorley
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, Canada K7L 3N6
| | - Peter B. Wyatt
- School
of Biological and Chemical
Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - Asuncion Martinez
- Division of Biological Engineering,
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Edward F. DeLong
- Division of Biological Engineering,
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,
Massachusetts 02139, United States
| | - Bjarne Hove-Jensen
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, Canada K7L 3N6
| | - David L. Zechel
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, Canada K7L 3N6
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35
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Chen H, Cho KB, Lai W, Nam W, Shaik S. Dioxygen Activation by a Non-Heme Iron(II) Complex: Theoretical Study toward Understanding Ferric–Superoxo Complexes. J Chem Theory Comput 2012; 8:915-26. [DOI: 10.1021/ct300015y] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hui Chen
- Beijing National Laboratory for Molecular
Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Kyung-Bin Cho
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Wenzhen Lai
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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