1
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Kayrouz CM, Seyedsayamdost MR. Enzymatic strategies for selenium incorporation into biological molecules. Curr Opin Chem Biol 2024; 81:102495. [PMID: 38954947 DOI: 10.1016/j.cbpa.2024.102495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/09/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024]
Abstract
The trace element selenium (Se) is essential to the physiology of most organisms on the planet. The most well documented of Se's biological forms are selenoproteins, where selenocysteine often serves as the catalytic center for crucial redox processes. Se is also found in several other classes of biological molecules, including nucleic acids, sugars, and modified amino acids, although its role in the function of these metabolites is less understood. Despite its prevalence, only a small number of Se-specific biosynthetic pathways have been discovered. Around half of these were first characterized in the past three years, suggesting that the selenometabolome may be more diverse than previously appreciated. Here, we review the recent advances in our understanding of this intriguing biochemical space, and discuss prospects for future discovery efforts.
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Affiliation(s)
- Chase M Kayrouz
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States.
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2
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Chen L, Zhang L, Ye X, Deng Z, Zhao C. Ergothioneine and its congeners: anti-ageing mechanisms and pharmacophore biosynthesis. Protein Cell 2024; 15:191-206. [PMID: 37561026 PMCID: PMC10903977 DOI: 10.1093/procel/pwad048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/24/2023] [Indexed: 08/11/2023] Open
Abstract
Ergothioneine, Ovothiol, and Selenoneine are sulfur/selenium-containing histidine-derived natural products widely distributed across different organisms. They exhibit significant antioxidant properties, making them as potential lead compounds for promoting health. Increasing evidence suggests that Ergothioneine is positively correlated with healthy ageing and longevity. The mechanisms underlying Ergothioneine's regulation of the ageing process at cellular and molecular levels are beginning to be understood. In this review, we provide an in-depth and extensive coverage of the anti-ageing studies on Ergothioneine and discuss its possible intracellular targeting pathways. In addition, we highlight the recent efforts in elucidating the biosynthetic details for Ergothioneine, Ovothiol, and Selenoneine, with a particular focus on the study of their pharmacophore-forming enzymology.
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Affiliation(s)
- Li Chen
- Department of Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Liping Zhang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Xujun Ye
- Department of Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Zixin Deng
- Department of Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Changming Zhao
- Department of Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Ministry of Education, Wuhan University, Wuhan 430072, China
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3
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Liu M, Yang Y, Huang JW, Dai L, Zheng Y, Cheng S, He H, Chen CC, Guo RT. Structural insights into a novel nonheme iron-dependent oxygenase in selenoneine biosynthesis. Int J Biol Macromol 2024; 256:128428. [PMID: 38013086 DOI: 10.1016/j.ijbiomac.2023.128428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023]
Abstract
Selenoneine (SEN) is a natural histidine derivative with radical-scavenging activity and shows higher antioxidant potential than its sulfur-containing isolog ergothioneine (EGT). Recently, the SEN biosynthetic pathway in Variovorax paradoxus was reported. Resembling EGT biosynthesis, the committed step of SEN synthesis is catalyzed by a nonheme Fe-dependent oxygenase termed SenA. This enzyme catalyzes oxidative carbon‑selenium (C-Se) bond formation to conjugate N-α-trimethyl histidine (TMH) and selenosugar to yield selenoxide; the process parallels the EGT biosynthetic route, in which sulfoxide synthases known as EgtB members catalyze the conjugation of TMH and cysteine or γ-glutamylcysteine to afford sulfoxides. Here, we report the crystal structures of SenA and its complex with TMH and thioglucose (SGlc), an analog of selenoglucose (SeGlc) at high resolution. The overall structure of SenA adopts the archetypical fold of EgtB, which comprises a DinB-like domain and an FGE-like domain. While the TMH-binding site is highly conserved to that of EgtB, a various substrate-enzyme interaction network in the selenosugar-binding site of SenA features a number of water-mediated hydrogen bonds. The obtained structural information is beneficial for understanding the mechanism of SenA-mediated C-Se bond formation.
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Affiliation(s)
- Min Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yingyu Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shujing Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Hailin He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China; Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China; Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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4
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Paris JC, Hu S, Wen A, Weitz AC, Cheng R, Gee LB, Tang Y, Kim H, Vegas A, Chang WC, Elliott SJ, Liu P, Guo Y. An S=1 Iron(IV) Intermediate Revealed in a Non-Heme Iron Enzyme-Catalyzed Oxidative C-S Bond Formation. Angew Chem Int Ed Engl 2023; 62:e202309362. [PMID: 37640689 PMCID: PMC10592081 DOI: 10.1002/anie.202309362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/11/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Ergothioneine (ESH) and ovothiol A (OSHA) are two natural thiol-histidine derivatives. ESH has been implicated as a longevity vitamin and OSHA inhibits the proliferation of hepatocarcinoma. The key biosynthetic step of ESH and OSHA in the aerobic pathways is the O2 -dependent C-S bond formation catalyzed by non-heme iron enzymes (e.g., OvoA in ovothiol biosynthesis), but due to the lack of identification of key reactive intermediate the mechanism of this novel reaction is unresolved. In this study, we report the identification and characterization of a kinetically competent S=1 iron(IV) intermediate supported by a four-histidine ligand environment (three from the protein residues and one from the substrate) in enabling C-S bond formation in OvoA from Methyloversatilis thermotoleran, which represents the first experimentally observed intermediate spin iron(IV) species in non-heme iron enzymes. Results reported in this study thus set the stage to further dissect the mechanism of enzymatic oxidative C-S bond formation in the OSHA biosynthesis pathway. They also afford new opportunities to study the structure-function relationship of high-valent iron intermediates supported by a histidine rich ligand environment.
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Affiliation(s)
- Jared C Paris
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Sha Hu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Aiwen Wen
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Andrew C Weitz
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Ronghai Cheng
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Leland B Gee
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, CA 94025, USA
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Hyomin Kim
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Arturo Vegas
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Sean J Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA
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5
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Yan X, Xiao H, Song J, Li C. Unraveling the Pivotal Roles of Various Metal Ion Centers in the Catalysis of Quercetin 2,4-Dioxygenases. Molecules 2023; 28:6238. [PMID: 37687067 PMCID: PMC10488974 DOI: 10.3390/molecules28176238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Quercetin 2,4-dioxygenase (QueD) with various transition metal ion co-factors shows great differences, but the internal reasons have not been illustrated in detail. In order to explore the effects of metal ion centers on the catalytic reactivity of QueD, we calculated and compared the minimum energy crossing point (MECP) of dioxygen from the relatively stable triplet state to the active singlet state under different conditions by using the DFT method. It was found that the metal ions play a more important role in the activation of dioxygen compared with the substrate and the protein environment. Simultaneously, the catalytic reactions of the bacterial QueDs containing six different transition metal ions were studied by the QM/MM approach, and we finally obtained the reactivity sequence of metal ions, Ni2+ > Co2+ > Zn2+ > Mn2+ > Fe2+ > Cu2+, which is basically consistent with the previous experimental results. Our calculation results indicate that metal ions act as Lewis acids in the reaction to stabilize the substrate anion and the subsequent superoxo and peroxo species in the reaction, and promote the proton coupled electron transfer (PCET) process. Furthermore, the coordination tendencies of transition metal ion centers also have important effects on the catalytic cycle. These findings have general implications on metalloenzymes, which can expand our understanding on how various metal ions play their key role in modulating catalytic reactivity.
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Affiliation(s)
- Xueyuan Yan
- College of Chemistry & Chemical and Environmental Engineering, Weifang University, Weifang 261061, China
| | - Han Xiao
- State Key Laboratory of Structure of Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Jinshuai Song
- Institute of Green Catalysis, College of Chemistry, Zhengzhou University, Zhengzhou 450001, China;
| | - Chunsen Li
- State Key Laboratory of Structure of Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
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6
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Lu Y, Sen K, Yong C, Gunn DSD, Purton JA, Guan J, Desmoutier A, Abdul Nasir J, Zhang X, Zhu L, Hou Q, Jackson-Masters J, Watts S, Hanson R, Thomas HN, Jayawardena O, Logsdail AJ, Woodley SM, Senn HM, Sherwood P, Catlow CRA, Sokol AA, Keal TW. Multiscale QM/MM modelling of catalytic systems with ChemShell. Phys Chem Chem Phys 2023; 25:21816-21835. [PMID: 37097706 DOI: 10.1039/d3cp00648d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.
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Affiliation(s)
- You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - David S D Gunn
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - John A Purton
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Jingcheng Guan
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alec Desmoutier
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Jamal Abdul Nasir
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Xingfan Zhang
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Lei Zhu
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Qing Hou
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Joe Jackson-Masters
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Sam Watts
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Rowan Hanson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Harry N Thomas
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Omal Jayawardena
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Scott M Woodley
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hans M Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas W Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
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7
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Liu Y, Gao W, Yuan S, Ni M, Hao T, Zeng C, Xu X, Fu Y, Peng Y, Ding Q. One-pot synthesis of 11-sulfenyl dibenzodiazepines via tandem sulfenylation/cyclization of o-isocyanodiaryl amines and diaryl disulfides. Org Biomol Chem 2023; 21:4257-4263. [PMID: 37139575 DOI: 10.1039/d3ob00220a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A one-pot sulfenylation/cyclization of o-isocyanodiaryl amines has been described for the preparation of 11-sulfenyl dibenzodiazepines. This AgI-catalyzed reaction covers an unexplored tandem process to give seven-membered N-heterocycles. This transformation shows a broad range of substrate scope, simple operation, and moderate to good yields under aerobic conditions. Diphenyl diselenide can also be produced in an acceptable yield.
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Affiliation(s)
- Yi Liu
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Wei Gao
- Jiangxi Academy of Forestry, Nanchang 330013, Jiangxi, China.
| | - Sitian Yuan
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Mengjia Ni
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Tianxin Hao
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Cuiying Zeng
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Xinyi Xu
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Yang Fu
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Yiyuan Peng
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
| | - Qiuping Ding
- National Engineering Research Center for Carbohydrate Synthesis, Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Key Laboratory for Green Chemistry of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, Jiangxi, China.
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8
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Yi H, Fu C, Diao K, Li Z, Cui X, Xiao W. Characterization and genomic analysis of a novel halovirus infecting Chromohalobacter beijerinckii. Front Microbiol 2022; 13:1041471. [PMID: 36569053 PMCID: PMC9769972 DOI: 10.3389/fmicb.2022.1041471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Bacteriophages function as a regulator of host communities and metabolism. Many phages have been isolated and sequenced in environments such as the ocean, but very little is known about hypersaline environments. Phages infecting members of the genus Chromohalobacter remain poorly understood, and no Chromohalobacter phage genome has been reported. In this study, a halovirus infecting Chromohalobacter sp. F3, YPCBV-1, was isolated from Yipinglang salt mine. YPCBV-1 could only infect host strain F3 with burst size of 6.3 PFU/cell. It could produce progeny in 5%-20% (w/v) NaCl with an optimal concentration of 10% (w/v), but the optimal adsorption NaCl concentration was 5%-8% (w/v). YPCBV-1 is sensitive to pure water and depends on NaCl or KCl solutions to survive. YPCBV-1 stability increased with increasing salinity but decreased in NaCl saturated solutions, and it has a broader salinity adaptation than the host. YPCBV-1 has a double-stranded DNA of 36,002 bp with a G + C content of 67.09% and contains a total of 55 predicted ORFs and no tRNA genes. Phylogenetic analysis and genomic network analysis suggested that YPCBV-1 is a novel Mu-like phage under the class Caudoviricetes. Auxiliary metabolic gene, SUMF1/EgtB/PvdO family non-heme iron enzyme, with possible roles in antioxidant was found in YPCBV-1. Moreover, DGR-associated genes were predicted in YPCBV-1 genome, which potentially produce hypervariable phage tail fiber. These findings shed light on the halovirus-host interaction in hypersaline environments.
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9
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Fu Y, Wang B, Cao Z. Biodegradation of 2,5-Dihydroxypyridine by 2,5-Dihydroxypyridine Dioxygenase and Its Mutants: Insights into O–O Bond Activation and Flexible Reaction Mechanisms from QM/MM Simulations. Inorg Chem 2022; 61:20501-20512. [DOI: 10.1021/acs.inorgchem.2c03229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yuzhuang Fu
- 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, 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, 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 361005, China
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10
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Wu P, Gu Y, Liao L, Wu Y, Jin J, Wang Z, Zhou J, Shaik S, Wang B. Coordination Switch Drives Selective C−S Bond Formation by the Non‐Heme Sulfoxide Synthases**. Angew Chem Int Ed Engl 2022; 61:e202214235. [DOI: 10.1002/anie.202214235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Peng Wu
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering School of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
- 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 Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
| | - Yang Gu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Langxing Liao
- 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 Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
| | - Yanfei Wu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Jiaoyu Jin
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhanfeng Wang
- Center for Advanced Materials Research Beijing Normal University Zhuhai 519087 China
| | - Jiahai Zhou
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicine Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Jerusalem 9190401 Israel
| | - 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 Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen University Xiamen 361005 China
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11
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Cordell GA, Lamahewage SNS. Ergothioneine, Ovothiol A, and Selenoneine-Histidine-Derived, Biologically Significant, Trace Global Alkaloids. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092673. [PMID: 35566030 PMCID: PMC9103826 DOI: 10.3390/molecules27092673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 11/16/2022]
Abstract
The history, chemistry, biology, and biosynthesis of the globally occurring histidine-derived alkaloids ergothioneine (10), ovothiol A (11), and selenoneine (12) are reviewed comparatively and their significance to human well-being is discussed.
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Affiliation(s)
- Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL 60202, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Correspondence:
| | - Sujeewa N. S. Lamahewage
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA;
- Department of Chemistry, University of Ruhuna, Matara 81000, Sri Lanka
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12
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Cheng R, Weitz AC, Paris J, Tang Y, Zhang J, Song H, Naowarojna N, Li K, Qiao L, Lopez J, Grinstaff MW, Zhang L, Guo Y, Elliott S, Liu P. OvoA Mtht from Methyloversatilis thermotolerans ovothiol biosynthesis is a bifunction enzyme: thiol oxygenase and sulfoxide synthase activities. Chem Sci 2022; 13:3589-3598. [PMID: 35432880 PMCID: PMC8943887 DOI: 10.1039/d1sc05479a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/24/2022] [Indexed: 01/03/2023] Open
Abstract
Mononuclear non-heme iron enzymes are a large class of enzymes catalyzing a wide-range of reactions. In this work, we report that a non-heme iron enzyme in Methyloversatilis thermotolerans, OvoAMtht, has two different activities, as a thiol oxygenase and a sulfoxide synthase. When cysteine is presented as the only substrate, OvoAMtht is a thiol oxygenase. In the presence of both histidine and cysteine as substrates, OvoAMtht catalyzes the oxidative coupling between histidine and cysteine (a sulfoxide synthase). Additionally, we demonstrate that both substrates and the active site iron's secondary coordination shell residues exert exquisite control over the dual activities of OvoAMtht (sulfoxide synthase vs. thiol oxygenase activities). OvoAMtht is an excellent system for future detailed mechanistic investigation on how metal ligands and secondary coordination shell residues fine-tune the iron-center electronic properties to achieve different reactivities. Modulation of OvoAMtht's dual activities: sulfoxide synthase and thiol oxygenase.![]()
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Affiliation(s)
- Ronghai Cheng
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Andrew C Weitz
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Jared Paris
- Department of Chemistry, Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 1521 USA
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 1521 USA
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology 130 Meilong Rd Shanghai 200237 China
| | - Heng Song
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Kelin Li
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Lu Qiao
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Juan Lopez
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Mark W Grinstaff
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology 130 Meilong Rd Shanghai 200237 China
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 1521 USA
| | - Sean Elliott
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
| | - Pinghua Liu
- Department of Chemistry, Boston University 590 Commonwealth Ave. Boston MA 02215 USA
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13
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Zhang S, Li X, Wang Y, Wei J, Zhang X, Liu Y. Computational Study of the Peroxygenase Mechanism Catalyzed by Hemoglobin Dehaloperoxidase Involved in the Degradation of Chlorophenols. Inorg Chem 2022; 61:2628-2639. [PMID: 35080380 DOI: 10.1021/acs.inorgchem.1c03721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biochemical evidence showed that hemoglobin dehaloperoxidase (DHP B) from Amphitrite Ornata is a multifunctional hemoprotein that catalyzes both dehalogenation and hydroxylation of halophenols via the peroxidase and peroxygenase mechanism, respectively, which sets the basis for the degradation of halophenols. In the peroxygenase mechanism, the reaction was previously suggested to be triggered either by the hydrogen atom abstraction by the Fe═O center or by the proton abstraction by His55. To illuminate the peroxygenase mechanism of DHP B at the atomistic level, on the basis of the high-resolution crystal structure, computational models were constructed, and a series of quantum mechanical/molecular mechanical calculations have been performed. According to the calculation results, the pathway (Path a) initiated by the H-abstraction by the Fe═O center is feasible. In another pathway (Path b), His55 can abstract the proton from the hydroxyl group of the substrate (4-Cl-o-cresol) to initiate the reaction; however, its feasibility depends on the prior electron transfer from the substrate to the porphyrin group. The rate-limiting step of Path a is the OH-rebound, which corresponds to an energy barrier of 14.7 kcal/mol at the quartet state. His55 acts as an acid-base catalyst and directly involves in the catalysis. Our mutant study indicates that His55 can be replaced by other titratable residues. These findings may provide useful information for further understanding of the catalytic reaction of DHP B and for the design of enzymes in the degradation of pollutants, in particular, halophenols.
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Affiliation(s)
- Shiqing Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xue Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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14
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Wei J, Wang Y, Li X, Zhang X, Liu Y. Mechanistic Insights into Pyridine Ring Degradation Catalyzed by 2,5-Dihydroxypyridine Dioxygenase NicX. Inorg Chem 2022; 61:2517-2529. [DOI: 10.1021/acs.inorgchem.1c03370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xue Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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15
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Zhang S, Li X, Wang Y, Yan L, Wei J, Liu Y. Computational Study of the C5-Hydroxylation Mechanism Catalyzed by the Diiron Monooxygenase PtmU3 as Part of the Platensimycin Biosynthesis. Inorg Chem 2021; 60:17783-17796. [PMID: 34762413 DOI: 10.1021/acs.inorgchem.1c02407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PtmU3 is a newly identified nonheme diiron monooxygenase, which installs a C-5 β-hydroxyl group into the C-19 CoA-ester intermediate involved in the biosynthesis of unique diterpene-derived scaffolds of platensimycin and platencin. PtmU3 possesses a noncanonical diiron active site architecture of a saturated six-coordinate iron center and lacks the μ-oxo bridge. Although the hydroxylation process is a simple reaction for nonheme mononuclear iron-dependent enzymes, how PtmU3 employs the diiron center to catalyze the H-abstraction and OH-rebound is still unknown. In particular, the electronic characteristic of diiron is also unclear. To understand the catalytic mechanism of PtmU3, we constructed two reactant models in which both the Fe1II-Fe2III-superoxo and Fe1II-Fe2IV═O are considered to trigger the H-abstraction and performed a series of quantum mechanics/molecular mechanics calculations. Our calculation results reveal that PtmU3 is a special monooxygenase, that is, both atoms of the dioxygen molecule can be incorporated into two molecules of the substrate by the successive reactions. In the first-round reaction, PtmU3 uses the Fe1II-Fe2III-superoxo to install a hydroxyl group into the substrate, generating the high-reactive Fe1II-Fe2IV═O complex. In the second-round reaction, the Fe1II-Fe2IV═O species is responsible for the hydroxylation of another molecule of the substrate. In the diiron center, Fe2 adopts the high spin state (S = 5/2) during the catalysis, whereas for Fe1, in addition to its structural role, it may also play an assistant role for Fe1 catalysis. In the two successive OH-installing steps, the H-abstraction is always the rate-liming step. E241 and D308 not only act as bridging ligands to connect two Fe ions but also take part in the electron reorganization. Owing to the high reactivity of Fe1II-Fe2IV═O compared to Fe1II-Fe2III-superoxo, besides the C5-hydroxylation, the C3- or C18-hydroxylation was also calculated to be feasible.
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Affiliation(s)
- Shiqing Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
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16
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Kang H, Zheng M. Influence of the quantum mechanical region size in QM/MM modelling: A case study of fluoroacetate dehalogenase catalyzed C F bond cleavage. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Wang Y, Yan L, Li X, Zhang S, Wei J, Liu Y. Formation Mechanism of Cofactor Cys-Tyr in the Cysteine Dioxygenases (CDO and F 2-CDO) and Its Influence on Catalysis: A QM/MM Study. Inorg Chem 2021; 60:7844-7856. [PMID: 34008401 DOI: 10.1021/acs.inorgchem.1c00340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cysteine dioxygenase (CDO) is a nonheme mononuclear iron enzyme, which catalyzes the oxidation of cysteine to cysteine sulfinic acid. Crystal structure studies of mammalian CDO showed that there is a cross-linked cysteine-tyrosine (Cys-Tyr) cofactor in its active site. Moreover, the formation of the Cys-Tyr cofactor requires the metal cofactor (Fe2+) and O2, and it was previously considered to substantially enhance the catalytic efficiency and half-life of CDO. Recently, a pure human CDO (F2-CDO) without including the Cys-Tyr cofactor was crystalized by the site-directed mutagenesis approach in the anaerobic condition. In this work, to gain insights into the formation mechanism of the Cys-Tyr cofactor and whether it can really promote the catalytic reactivity of CDO, a series of computational models have been constructed, and quantum mechanical/molecular mechanical (QM/MM) calculations have been performed. Our calculation results reveal that WT-CDO and F2-CDO follow different mechanisms for the formation of the Cys-Tyr cofactor. In F2-CDO, the cofactor formation contains the H-abstraction, C-S bond formation, intramolecular F migration, and aromatization of the residue F2Y157, in which the Fe-coordinate dioxygen can be recovered after the formation cofactor; however, in the WT-CDO, the cofactor formation shows some differences. During the reaction, hydrogen peroxide is generated, and the final aromatization requires the assistance of one water molecule. Furthermore, the overall barriers of cofactor formation are always higher than l-cysteine oxidation for both WT-CDO and F2-CDO irrespective of the absence or presence of the cofactor. Thus, we can theoretically confirm that the Cys-Tyr cofactor is not essential for the oxidation activity of CDO, and cofactor formation is just an accompanying reaction but not a prerequisite for the oxidation reaction. These results may provide useful information for understanding the catalysis of CDO.
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Affiliation(s)
- Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Shiqing Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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18
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Naowarojna N, Cheng R, Lopez J, Wong C, Qiao L, Liu P. Chemical modifications of proteins and their applications in metalloenzyme studies. Synth Syst Biotechnol 2021; 6:32-49. [PMID: 33665390 PMCID: PMC7897936 DOI: 10.1016/j.synbio.2021.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/14/2020] [Accepted: 01/03/2021] [Indexed: 12/21/2022] Open
Abstract
Protein chemical modifications are important tools for elucidating chemical and biological functions of proteins. Several strategies have been developed to implement these modifications, including enzymatic tailoring reactions, unnatural amino acid incorporation using the expanded genetic codes, and recognition-driven transformations. These technologies have been applied in metalloenzyme studies, specifically in dissecting their mechanisms, improving their enzymatic activities, and creating artificial enzymes with non-natural activities. Herein, we summarize some of the recent efforts in these areas with an emphasis on a few metalloenzyme case studies.
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Affiliation(s)
| | | | - Juan Lopez
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Christina Wong
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Lu Qiao
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
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19
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Ekanayake DM, Fischer AA, Elwood ME, Guzek AM, Lindeman SV, Popescu CV, Fiedler AT. Nonheme iron-thiolate complexes as structural models of sulfoxide synthase active sites. Dalton Trans 2020; 49:17745-17757. [PMID: 33241840 PMCID: PMC7781232 DOI: 10.1039/d0dt03403g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two mononuclear iron(ii)-thiolate complexes have been prepared that represent structural models of the nonheme iron enzymes EgtB and OvoA, which catalyze the O2-dependent formation of carbon-sulfur bonds in the biosynthesis of thiohistidine compounds. The series of Fe(ii) complexes reported here feature tripodal N4 chelates (LA and LB) that contain both pyridyl and imidazolyl donors (LA = (1H-imidazol-4-yl)-N,N-bis((pyridin-2-yl)methyl)methanamine; LB = N,N-bis((1-methylimidazol-2-yl)methyl)-2-pyridylmethylamine). Further coordination with monodentate aromatic or aliphatic thiolate ligands yielded the five-coordinate, high-spin Fe(ii) complexes [FeII(LA)(SMes)]BPh4 (1) and [FeII(LB)(SCy)]BPh4 (2), where SMes = 2,4,6-trimethylthiophenolate and SCy = cyclohexanethiolate. X-ray crystal structures revealed that 1 and 2 possess trigonal bipyramidal geometries formed by the N4S ligand set. In each case, the thiolate ligand is positioned cis to an imidazole donor, replicating the arrangement of Cys- and His-based substrates in the active site of EgtB. The geometric and electronic structures of 1 and 2 were analyzed with UV-vis absorption and Mössbauer spectroscopies in tandem with density functional theory (DFT) calculations. Exposure of 1 and 2 to nitric oxide (NO) yielded six-coordinate FeNO adducts that were characterized with infrared and electron paramagnetic resonance (EPR) spectroscopies, confirming that these complexes are capable of binding diatomic molecules. Reaction of 1 and 2 with O2 causes oxidation of the thiolate ligands to disulfide products. The implications of these results for the development of functional models of EgtB and OvoA are discussed.
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20
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Structural basis of ergothioneine biosynthesis. Curr Opin Struct Biol 2020; 65:1-8. [DOI: 10.1016/j.sbi.2020.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/05/2020] [Indexed: 02/04/2023]
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21
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The catalytic mechanism of sulfoxide synthases. Curr Opin Chem Biol 2020; 59:111-118. [PMID: 32726707 DOI: 10.1016/j.cbpa.2020.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/09/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
Sulfoxide synthases are non-heme iron enzymes that catalyze oxidative carbonsulfur bond formation in the biosynthesis of thiohistidines such as ergothioneine and ovothiol. The catalytic mechanism of these enzymes has been studied by protein crystallography, steady-state kinetics, non-natural amino acid incorporation and computational modeling. This review discusses the current status of this research and also highlights similarities between the CS bond forming activity of sulfoxide synthases with that of synthetic coordination compounds.
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22
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Zhang S, Liu Y. Mechanical Insights into the Enzymatic Cleavage of Double C-C Bond in Poly( cis-1,4-isoprene) by the Latex Clearing Protein. Inorg Chem 2020; 59:9627-9637. [PMID: 32644783 DOI: 10.1021/acs.inorgchem.0c00726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The b-type cytochrome LcpK30 is a latex clearing protein (Lcp), which acts as an endotype dioxygenase to catalyze the extracellular cleavage of the chemically inert aliphatic polymer poly(cis-1,4-isoprene), producing oligo-isoprenoids with different terminal carbonyl groups (aldehyde and ketone, -CH2-CHO and -CH2-COCH3). On the basis of the fact that the muteins of E148A, E148Q, and E148H have substantially reduced reactivity, and the E148-initiated reaction mechanism has been previously proposed, in which a cyclic dioxetane intermediate or an epoxide intermediate may be involved, however, open questions still remain. In this paper, on the basis of the crystal structure of LcpK30, the enzyme-substrate reactant model was constructed, and the cleavage mechanism of the central double bond of poly(cis-1,4-isoprene) was elucidated by performing quantum mechanics/molecular mechanics calculations. Our calculation results revealed that the oxidative cleavage reaction is triggered by the addition of the heme-bound dioxygen to the double bond of the polymer, and E148 does not act as the catalytic base to extract the allylic proton to assist the reaction as previously suggested. Of the two considered pathways, the pathway that involves the dioxetane intermediate was calculated to be more favorable. During the catalysis, the distal oxygen first adds to the double bond of the substrate to form a radical intermediate, and then the Fe-O1 (proximal oxygen) bond cleaves to generate the dioxetane intermediate, which can easily collapse affording the final ketone and aldehyde products. In general, the cleavage mechanism of double C-C bond catalyzed by LcpK30 is similar to those of indoleamine 2,3-dioxygenase, tryptophan 2,3-dioxygenase, and the nonheme stilbene cleavage oxygenase NOV1 that all depend on the iron-bound dioxygen to initiate the cleavage reaction.
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Affiliation(s)
- Shiqing Zhang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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23
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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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24
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Goncharenko KV, Flückiger S, Liao C, Lim D, Stampfli AR, Seebeck FP. Selenocysteine as a Substrate, an Inhibitor and a Mechanistic Probe for Bacterial and Fungal Iron-Dependent Sulfoxide Synthases. Chemistry 2020; 26:1328-1334. [PMID: 31545545 DOI: 10.1002/chem.201903898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Indexed: 01/03/2023]
Abstract
Sulfoxide synthases are non-heme iron enzymes that participate in the biosynthesis of thiohistidines, such as ergothioneine and ovothiol A. The sulfoxide synthase EgtB from Chloracidobacterium thermophilum (CthEgtB) catalyzes oxidative coupling between the side chains of N-α-trimethyl histidine (TMH) and cysteine (Cys) in a reaction that entails complete reduction of molecular oxygen, carbon-sulfur (C-S) and sulfur-oxygen (S-O) bond formation as well as carbon-hydrogen (C-H) bond cleavage. In this report, we show that CthEgtB and other bacterial sulfoxide synthases cannot efficiently accept selenocysteine (SeCys) as a substrate in place of cysteine. In contrast, the sulfoxide synthase from the filamentous fungus Chaetomium thermophilum (CthEgt1) catalyzes C-S and C-Se bond formation at almost equal efficiency. We discuss evidence suggesting that this functional difference between bacterial and fungal sulfoxide synthases emerges from different modes of oxygen activation.
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Affiliation(s)
- Kristina V Goncharenko
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Sebastian Flückiger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Cangsong Liao
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - David Lim
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Anja R Stampfli
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
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25
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Song H, Naowarojna N, Cheng R, Lopez J, Liu P. Non-heme iron enzyme-catalyzed complex transformations: Endoperoxidation, cyclopropanation, orthoester, oxidative C-C and C-S bond formation reactions in natural product biosynthesis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 117:1-61. [PMID: 31564305 DOI: 10.1016/bs.apcsb.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Non-heme iron enzymes catalyze a wide range of chemical transformations, serving as one of the key types of tailoring enzymes in the biosynthesis of natural products. Hydroxylation reaction is the most common type of reactions catalyzed by these enzymes and hydroxylation reactions have been extensively investigated mechanistically. However, the mechanistic details for other types of transformations remain largely unknown or unexplored. In this paper, we present some of the most recently discovered transformations, including endoperoxidation, orthoester formation, cyclopropanation, oxidative C-C and C-S bond formation reactions. In addition, many of them are multi-functional enzymes, which further complicate their mechanistic investigations. In this work, we summarize their biosynthetic pathways, with special emphasis on the mechanistic details available for these newly discovered enzymes.
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Affiliation(s)
- Heng Song
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, People's Republic of China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA, United States
| | - Juan Lopez
- Department of Chemistry, Boston University, Boston, MA, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA, United States
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26
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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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27
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Xue J, Lu J, Lai W. Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation. Phys Chem Chem Phys 2019; 21:9957-9968. [PMID: 31041955 DOI: 10.1039/c9cp00794f] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.
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Affiliation(s)
- Junqin Xue
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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28
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Stampfli AR, Goncharenko KV, Meury M, Dubey BN, Schirmer T, Seebeck FP. An Alternative Active Site Architecture for O 2 Activation in the Ergothioneine Biosynthetic EgtB from Chloracidobacterium thermophilum. J Am Chem Soc 2019; 141:5275-5285. [PMID: 30883103 DOI: 10.1021/jacs.8b13023] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sulfoxide synthases are nonheme iron enzymes that catalyze oxidative carbon-sulfur bond formation between cysteine derivatives and N-α-trimethylhistidine as a key step in the biosynthesis of thiohistidines. The complex catalytic mechanism of this enzyme reaction has emerged as the controversial subject of several biochemical and computational studies. These studies all used the structure of the γ-glutamyl cysteine utilizing sulfoxide synthase, MthEgtB from Mycobacterium thermophilum (EC 1.14.99.50), as a structural basis. To provide an alternative model system, we have solved the crystal structure of CthEgtB from Chloracidobacterium thermophilum (EC 1.14.99.51) that utilizes cysteine as a sulfur donor. This structure reveals a completely different configuration of active site residues that are involved in oxygen binding and activation. Furthermore, comparison of the two EgtB structures enables a classification of all ergothioneine biosynthetic EgtBs into five subtypes, each characterized by unique active-site features. This active site diversity provides an excellent platform to examine the catalytic mechanism of sulfoxide synthases by comparative enzymology, but also raises the question as to why so many different solutions to the same biosynthetic problem have emerged.
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Affiliation(s)
- Anja R Stampfli
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland.,Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Kristina V Goncharenko
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| | - Marcel Meury
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| | - Badri N Dubey
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Florian P Seebeck
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
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29
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Zhang Y, Zhang H, Zheng Q. How Chorismatases Regulate Distinct Reaction Channels in a Single Conserved Active Pocket: Mechanistic Analysis with QM/MM (ONIOM) Investigations. Chemistry 2019; 25:1326-1336. [PMID: 30395358 DOI: 10.1002/chem.201804622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Indexed: 01/12/2023]
Abstract
The FkbO and Hyg5 subfamilies of chorismatases share the same active-site architectures, but perform distinct reaction mechanisms, that is, FkbO employs a hydrolysis reaction whereas Hyg5 proceeds through an intramolecular mechanism. Despite extensive research efforts, the detailed mechanism of the product selectivity in chorismatases need to be further unmasked. In this study, the effects of the A/G residue group (A244FkbO /G240Hyg5 ) and the V/Q residue group (V209FkbO /Q201Hyg5 ) on the catalytic mechanisms are investigated by employing molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of the two wild-type models (FkbO/CHO and Hyg5/CHO; CHO=chorismate) and four mutants models (A244G-FkbO/CHO and G240A-Hyg5/CHO; V209Q-FkbO/CHO and Q201V-Hyg5/CHO). Our results showed that the A/G residue group mentioned by previous works would cause changes in the binding states of the substrate and the orientation of the catalytic glutamate, but only these changes affect the product selectivity in chorismatases limitedly. Interestingly, the distal V/Q residue group, which determines the internal water self-regulating ability at the active site, has significant impact on the selectivity of the catalytic mechanisms. The V/Q residue group is suggested to be an important factor to control the catalytic activities in chorismatases. The results are consistent with biochemical and structural experiments, providing novel insight into the mechanism of product selectivity in chorismatases.
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Affiliation(s)
- Yulai Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China
| | - Hongxing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry, of Education, Jilin University, Changchun, 130023, P.R. China
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30
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Bai J, Hou Q, Zhu W, Liu Y. Mechanical insights into the oxidative cleavage of resveratrol catalyzed by dioxygenase NOV1 from Novosphingobium aromaticivorans: confirmation of dioxygenase mechanism by QM/MM calculations. Catal Sci Technol 2019. [DOI: 10.1039/c8cy01885e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM calculations confirm that the oxidative cleavage of resveratrol catalyzed by dioxygenase NOV1 follows the dioxygenase mechanism.
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Affiliation(s)
- Jie Bai
- Key Lab of Colloid and Interface Chemistry, Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Qianqian Hou
- Shandong Non-metallic Materials Institute
- Jinan
- China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering
- Xuzhou Institute of Technology
- Xuzhou
- China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
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31
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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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32
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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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