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Li RN, Chen SL. Mechanism for the Halogenation and Azidation of Lysine Catalyzed by Non-heme Iron BesD Enzyme. Chem Asian J 2022; 17:e202200438. [PMID: 35763338 DOI: 10.1002/asia.202200438] [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: 04/26/2022] [Revised: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Selective halogenation is important in synthetic chemistry. BesD, a new member of the non-heme Fe(II)/α-ketoglutarate (αKG)-dependent halogenase family, can activate the sp3 C-H bond and halogenate lysine, in particular without a carrier protein. Using the density functional calculations, a chlorination mechanism in BesD has been proposed, mainly including the formation of Cl-Fe(IV)=O through the αKG decarboxylation, the isomerization of Cl-Fe(IV)=O, the substrate hydrogen abstraction by Fe(IV)=O, and the rebound of chloro to the substrate carbon radical. The hydrogen abstraction is rate-limiting. The isomerization of Cl-Fe(IV)=O is essential for the hydrogen abstraction and the chiral selectivity. The BesD-catalyzed bromination and azidation of lysine adopt the same mechanism as the chlorination. The hardly-changed overall barriers indicate that the introduced ligands (X) do not affect the reaction rate significantly, implying that the X-introduced reactions catalyzed by BesD may be extended to other X anions.
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Affiliation(s)
- Rui-Ning Li
- Beijing Institute of Technology, School of Chemistry and Chemical Engineering, 100081, Beijing, CHINA
| | - Shi-Lu Chen
- Beijing Institute of Technology, School of Chemistry and Chemical Engineering, 5th, ZhongGuanCun South Street, 100081, Beijing, CHINA
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2
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Banerjee A, Li J, Molenda MA, Opalade AA, Adhikary A, Brennessel WW, Malkhasian AYS, Jackson TA, Chavez FA. Probing the Mechanism for 2,4'-Dihydroxyacetophenone Dioxygenase Using Biomimetic Iron Complexes. Inorg Chem 2021; 60:7168-7179. [PMID: 33900072 DOI: 10.1021/acs.inorgchem.1c00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we report the synthesis and characterization of [Fe(T1Et4iPrIP)(2-OH-AP)(OTf)](OTf) (2), [Fe(T1Et4iPrIP)(2-O-AP)](OTf) (3), and [Fe(T1Et4iPrIP)(DMF)3](OTf)3 (4) (T1Et4iPrIP = tris(1-ethyl-4-isopropyl-imidazolyl)phosphine; 2-OH-AP = 2-hydroxyacetophenone, and 2-O-AP- = monodeprotonated 2-hydroxyacetophenone). Both 2 and 3 serve as model complexes for the enzyme-substrate adduct for the nonheme enzyme 2,4'-dihydroacetophenone (DHAP) dioxygenase or DAD, while 4 serves as a model for the ferric form of DAD. Complexes 2-4 have been characterized by X-ray crystallography which reveals T1Et4iPrIP to bind iron in a tridentate fashion. Complex 2 additionally contains a bidentate 2-OH-AP ligand and a monodentate triflate ligand yielding distorted octahedral geometry, while 3 possesses a bidentate 2-O-AP- ligand and exhibits distorted trigonal bipyramidal geometry (τ = 0.56). Complex 4 displays distorted octahedral geometry with 3 DMF ligands completing the ligand set. The UV-vis spectrum of 2 matches more closely to the DAD-substrate spectrum than 3, and therefore, it is believed that the substrate for DAD is bound in the protonated form. TD-DFT studies indicate that visible absorption bands for 2 and 3 are due to MLCT bands. Complexes 2 and 3 are capable of oxidizing the coordinated substrate mimics in a stoichiometric and catalytic fashion in the presence of O2. Complex 4 does not convert 2-OH-AP to products under the same catalytic conditions; however, it becomes anaerobically reduced in the presence of 2 equiv 2-OH-AP to 2.
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Affiliation(s)
- Atanu Banerjee
- Dr. K. C. Patel R & D Centre, Charotar University of Science and Technology (CHARUSAT), P D Patel Institute of Applied Sciences, 388421 Anand, Gujrat, India
| | - Jia Li
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - Monika A Molenda
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - Adedamola A Opalade
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - William W Brennessel
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | | | - Timothy A Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Ferman A Chavez
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
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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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Santatiwongchai J, Gleeson D, Gleeson MP. Theoretical Evaluation of the Reaction Mechanism of Serine Hydroxymethyltransferase. J Phys Chem B 2019; 123:407-418. [PMID: 30522268 DOI: 10.1021/acs.jpcb.8b10196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene THF. SHMT is a folate pathway enzyme and is therefore of considerable medical interest due to its role as an important intervention point for antimalarial, anticancer, and antibacterial treatments. Despite considerable experimental effort, the precise reaction mechanism of SHMT remains unclear. In this study, we explore the mechanism of SHMT to determine the roles of active site residues and the nature and the sequence of chemical steps. Molecular dynamics (MD) methods were employed to generate a suitable starting structure which then underwent analysis using hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. The QM region consisted of 12 key residues, two substrates, and explicit solvent. Our results show that the catalytic reaction proceeds according to a retro-aldol synthetic process with His129 acting as the general base in the reaction. The rate-determining step involves the cleavage of the PLP-serine aldimine Cα-Cβ bond and the formation of formaldehyde in line with experimental evidence. The pyridyl ring of the PLP-serine aldimine substrate exists in deprotonated form, being stabilized directly by Asp208 via a strong H-bond, as well as through interactions with Arg371, Lys237, and His211, and with the surrounding protein which was electrostatically embedded. This knowledge has the potential to impact the design and development of new inhibitors.
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Affiliation(s)
- Jirapat Santatiwongchai
- Department of Chemistry, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
| | - Duangkamol Gleeson
- Department of Chemistry, Faculty of Science , King Mongkut's Institute of Technology Ladkrabang , Bangkok 10520 , Thailand
| | - M Paul Gleeson
- Department of Chemistry, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand.,Department of Biomedical Engineering, Faculty of Engineering , King Mongkut's Institute of Technology Ladkrabang , Bangkok 10520 , Thailand
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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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Manna RN, Malakar T, Jana B, Paul A. Unraveling the Crucial Role of Single Active Water Molecule in the Oxidative Cleavage of Aliphatic C–C Bond of 2,4′-Dihydroxyacetophenone Catalyzed by 2,4′-Dihydroxyacetophenone Dioxygenase Enzyme: A Quantum Mechanics/Molecular Mechanics Investigation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03201] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rabindra Nath Manna
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tanmay Malakar
- Raman Center for Atomic, Molecular, and Optical Science, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Ankan Paul
- Raman Center for Atomic, Molecular, and Optical Science, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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