1
|
Li J, Kumar A, Lewis JC. Non-native Intramolecular Radical Cyclization Catalyzed by a B 12 -Dependent Enzyme. Angew Chem Int Ed Engl 2023; 62:e202312893. [PMID: 37874184 DOI: 10.1002/anie.202312893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Despite the unique reactivity of vitamin B12 and its derivatives, B12 -dependent enzymes remain underutilized in biocatalysis. In this study, we repurposed the B12 -dependent transcription factor CarH to enable non-native radical cyclization reactions. An engineered variant of this enzyme, CarH*, catalyzes the formation γ- and δ-lactams through either redox-neutral or reductive ring closure with marked enhancement of reactivity and selectivity relative to the free B12 cofactor. CarH* also catalyzes an unusual spirocyclization by dearomatization of pendant arenes to produce bicyclic 1,3-diene products instead of 1,4-dienes provided by existing methods. These results and associated mechanistic studies highlight the importance of protein scaffolds for controlling the reactivity of B12 and expanding the synthetic utility of B12 -dependent enzymes.
Collapse
Affiliation(s)
- Jianbin Li
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Amardeep Kumar
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
2
|
Marques HM. The inorganic chemistry of the cobalt corrinoids - an update. J Inorg Biochem 2023; 242:112154. [PMID: 36871417 DOI: 10.1016/j.jinorgbio.2023.112154] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.
Collapse
Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| |
Collapse
|
3
|
Lee YH, Yeh YC, Fan PH, Zhong A, Ruszczycky MW, Liu HW. Changing Fates of the Substrate Radicals Generated in the Active Sites of the B 12-Dependent Radical SAM Enzymes OxsB and AlsB. J Am Chem Soc 2023; 145:3656-3664. [PMID: 36719327 PMCID: PMC9940012 DOI: 10.1021/jacs.2c12953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OxsB is a B12-dependent radical SAM enzyme that catalyzes the oxidative ring contraction of 2'-deoxyadenosine 5'-phosphate to the dehydrogenated, oxetane containing precursor of oxetanocin A phosphate. AlsB is a homologue of OxsB that participates in a similar reaction during the biosynthesis of albucidin. Herein, OxsB and AlsB are shown to also catalyze radical mediated, stereoselective C2'-methylation of 2'-deoxyadenosine monophosphate. This reaction proceeds with inversion of configuration such that the resulting product also possesses a C2' hydrogen atom available for abstraction. However, in contrast to methylation, subsequent rounds of catalysis result in C-C dehydrogenation of the newly added methyl group to yield a 2'-methylidene followed by radical addition of a 5'-deoxyadenosyl moiety to produce a heterodimer. These observations expand the scope of reactions catalyzed by B12-dependent radical SAM enzymes and emphasize the susceptibility of radical intermediates to bifurcation along different reaction pathways even within the highly organized active site of an enzyme.
Collapse
Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Po-Hsun Fan
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Aoshu Zhong
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Mark W. Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States; Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
4
|
Huang R, Zhi N, Yu L, Li Y, Wu X, He J, Zhu H, Qiao J, Liu X, Tian C, Wang J, Dong M. Genetically Encoded Photosensitizer Protein Reduces Iron–Sulfur Clusters of Radical SAM Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Rongrong Huang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Ning Zhi
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Yaoyang Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiangyu Wu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jiale He
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hongji Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaohong Liu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| |
Collapse
|
5
|
Gagsteiger J, Jahn S, Heidinger L, Gericke L, Andexer JN, Friedrich T, Loenarz C, Layer G. A Cobalamin-Dependent Radical SAM Enzyme Catalyzes the Unique C α -Methylation of Glutamine in Methyl-Coenzyme M Reductase. Angew Chem Int Ed Engl 2022; 61:e202204198. [PMID: 35638156 PMCID: PMC9401015 DOI: 10.1002/anie.202204198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 12/22/2022]
Abstract
Methyl‐coenzyme M reductase, which is responsible for the production of the greenhouse gas methane during biological methane formation, carries several unique posttranslational amino acid modifications, including a 2‐(S)‐methylglutamine. The enzyme responsible for the Cα‐methylation of this glutamine is not known. Herein, we identify and characterize a cobalamin‐dependent radical SAM enzyme as the glutamine C‐methyltransferase. The recombinant protein from Methanoculleus thermophilus binds cobalamin in a base‐off, His‐off conformation and contains a single [4Fe‐4S] cluster. The cobalamin cofactor cycles between the methyl‐cob(III)alamin, cob(II)alamin and cob(I)alamin states during catalysis and produces methylated substrate, 5′‐deoxyadenosine and S‐adenosyl‐l‐homocysteine in a 1 : 1 : 1 ratio. The newly identified glutamine C‐methyltransferase belongs to the class B radical SAM methyltransferases known to catalyze challenging methylation reactions of sp3‐hybridized carbon atoms.
Collapse
Affiliation(s)
- Jana Gagsteiger
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
| | - Sören Jahn
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Lorenz Heidinger
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Lukas Gericke
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Jennifer N Andexer
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Christoph Loenarz
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Gunhild Layer
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
| |
Collapse
|
6
|
Esser AJ, Mukherjee S, Dereven‘kov IA, Makarov SV, Jacobsen DW, Spiekerkoetter U, Hannibal L. Versatile Enzymology and Heterogeneous Phenotypes in Cobalamin Complementation Type C Disease. iScience 2022; 25:104981. [PMID: 36105582 PMCID: PMC9464900 DOI: 10.1016/j.isci.2022.104981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nutritional deficiency and genetic errors that impair the transport, absorption, and utilization of vitamin B12 (B12) lead to hematological and neurological manifestations. The cblC disease (cobalamin complementation type C) is an autosomal recessive disorder caused by mutations and epi-mutations in the MMACHC gene and the most common inborn error of B12 metabolism. Pathogenic mutations in MMACHC disrupt enzymatic processing of B12, an indispensable step before micronutrient utilization by the two B12-dependent enzymes methionine synthase (MS) and methylmalonyl-CoA mutase (MUT). As a result, patients with cblC disease exhibit plasma elevation of homocysteine (Hcy, substrate of MS) and methylmalonic acid (MMA, degradation product of methylmalonyl-CoA, substrate of MUT). The cblC disorder manifests early in childhood or in late adulthood with heterogeneous multi-organ involvement. This review covers current knowledge on the cblC disease, structure–function relationships of the MMACHC protein, the genotypic and phenotypic spectra in humans, experimental disease models, and promising therapies.
Collapse
|
7
|
Dill Z, Li B, Bridwell-Rabb J. Purification and structural elucidation of a cobalamin-dependent radical SAM enzyme. Methods Enzymol 2022; 669:91-116. [PMID: 35644182 DOI: 10.1016/bs.mie.2021.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster, SAM, and Cbl to carry out remarkable catalytic feats in a large number of biosynthetic pathways. However, despite the abundance of annotated Cbl-dependent radical SAM enzymes, relatively few molecular details exist regarding how these enzymes function. Traditionally, challenges associated with purifying and reconstituting Cbl-dependent radical SAM enzymes have hindered biochemical studies aimed at elucidating the structures and mechanisms of these enzymes. Herein, we describe a bottom-up approach that was used to crystallize OxsB, learn about the overall architecture of a Cbl-dependent radical SAM enzyme, and facilitate mechanistic studies. We report lessons learned from the crystallization of different states of OxsB, including the apo-, selenomethionine (SeMet)-labeled, and fully reconstituted form of OxsB that has a [4Fe-4S] cluster, SAM, and Cbl bound. Further, we suggest that, when appropriate, this bottom-up method can be used to facilitate studies on enzymes in this class for which there are challenges associated with purifying and reconstituting the active enzyme.
Collapse
Affiliation(s)
- Zerick Dill
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI, United States
| | - Bin Li
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI, United States.
| |
Collapse
|
8
|
Gagsteiger J, Jahn S, Heidinger L, Gericke L, Andexer JN, Friedrich T, Loenarz C, Layer G. A Cobalamin‐Dependent Radical SAM Enzyme Catalyzes the Unique Cα‐Methylation of Glutamine in Methyl‐Coenzyme M Reductase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jana Gagsteiger
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie GERMANY
| | - Sören Jahn
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Lorenz Heidinger
- Albert-Ludwigs-Universität Freiburg Institut für Biochemie GERMANY
| | - Lukas Gericke
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Jennifer N. Andexer
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Biochemie GERMANY
| | - Christoph Loenarz
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie Stefan-Meier-Str. 19 79104 Freiburg GERMANY
| |
Collapse
|
9
|
Sinner E, Marous DR, Townsend CA. Evolution of Methods for the Study of Cobalamin-Dependent Radical SAM Enzymes. ACS BIO & MED CHEM AU 2022; 2:4-10. [PMID: 35341020 PMCID: PMC8950095 DOI: 10.1021/acsbiomedchemau.1c00032] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While bioinformatic evidence of cobalamin-dependent radical S-adenosylmethionine (SAM) enzymes has existed since the naming of the radical SAM superfamily in 2001, none were biochemically characterized until 2011. In the past decade, the field has flourished as methodological advances have facilitated study of the subfamily. Because of the ingenuity and perseverance of researchers in this field, we now have functional, mechanistic, and structural insight into how this class of enzymes harnesses the power of both the cobalamin and radical SAM cofactors to achieve catalysis. All of the early characterized enzymes in this subfamily were methylases, but the activity of these enzymes has recently been expanded beyond methylation. We anticipate that the characterized functions of these enzymes will become both better understood and increasingly diverse with continued study.
Collapse
Affiliation(s)
- Erica
K. Sinner
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
| | - Daniel R. Marous
- Department
of Chemistry, Wittenberg University, 200 W Ward St., Springfield, Ohio 45504, United States
| | - Craig A. Townsend
- Department
of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
| |
Collapse
|
10
|
Martini MA, Rüdiger O, Breuer N, Nöring B, DeBeer S, Rodríguez-Maciá P, Birrell JA. The Nonphysiological Reductant Sodium Dithionite and [FeFe] Hydrogenase: Influence on the Enzyme Mechanism. J Am Chem Soc 2021; 143:18159-18171. [PMID: 34668697 PMCID: PMC8569811 DOI: 10.1021/jacs.1c07322] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[FeFe] hydrogenases are highly active enzymes for interconverting protons and electrons with hydrogen (H2). Their active site H-cluster is formed of a canonical [4Fe-4S] cluster ([4Fe-4S]H) covalently attached to a unique [2Fe] subcluster ([2Fe]H), where both sites are redox active. Heterolytic splitting and formation of H2 takes place at [2Fe]H, while [4Fe-4S]H stores electrons. The detailed catalytic mechanism of these enzymes is under intense investigation, with two dominant models existing in the literature. In one model, an alternative form of the active oxidized state Hox, named HoxH, which forms at low pH in the presence of the nonphysiological reductant sodium dithionite (NaDT), is believed to play a crucial role. HoxH was previously suggested to have a protonated [4Fe-4S]H. Here, we show that HoxH forms by simple addition of sodium sulfite (Na2SO3, the dominant oxidation product of NaDT) at low pH. The low pH requirement indicates that sulfur dioxide (SO2) is the species involved. Spectroscopy supports binding at or near [4Fe-4S]H, causing its redox potential to increase by ∼60 mV. This potential shift detunes the redox potentials of the subclusters of the H-cluster, lowering activity, as shown in protein film electrochemistry (PFE). Together, these results indicate that HoxH and its one-electron reduced counterpart Hred'H are artifacts of using a nonphysiological reductant, and not crucial catalytic intermediates. We propose renaming these states as the "dithionite (DT) inhibited" states Hox-DTi and Hred-DTi. The broader potential implications of using a nonphysiological reductant in spectroscopic and mechanistic studies of enzymes are highlighted.
Collapse
Affiliation(s)
- Maria Alessandra Martini
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Nina Breuer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Birgit Nöring
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Patricia Rodríguez-Maciá
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, U.K
| | - James A Birrell
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
11
|
Lehene M, Plesa D, Ionescu-Zinca S, Iancu SD, Leopold N, Makarov SV, Brânzanic AMV, Silaghi-Dumitrescu R. Adduct of Aquacobalamin with Hydrogen Peroxide. Inorg Chem 2021; 60:12681-12684. [PMID: 34382784 DOI: 10.1021/acs.inorgchem.1c01483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aquacobalamin binds hydrogen peroxide reversibly to form a cobalt(III) hydroperoxo adduct with a 0.25 mM dissociation constant, as evidenced by UV-vis absorption spectroscopy and corroborated by NMR, Raman spectroscopy, stopped-flow UV-vis measurements, and density functional theory calculations.
Collapse
Affiliation(s)
- Maria Lehene
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| | - Diana Plesa
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| | - Stefania Ionescu-Zinca
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| | - Stefania D Iancu
- Faculty of Physics, Babes-Bolyai University (BBU), Str. Kogalniceanu 1, RO-400084 Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babes-Bolyai University (BBU), Str. Kogalniceanu 1, RO-400084 Cluj-Napoca, Romania
| | - Sergei V Makarov
- Ivanovo State University of Chemistry and Technology, Sheremetevskiy Str. 7, 153000 Ivanovo, Russia
| | - Adrian M V Brânzanic
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| |
Collapse
|
12
|
Salnikov DS, Makarov SV, Koifman OI. The radical versus ionic mechanisms of reduced cobalamin inactivation by tert-butyl hydroperoxide and hydrogen peroxide in aqueous solution. NEW J CHEM 2021. [DOI: 10.1039/d0nj04231e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
It was demonstrated that antioxidants cannot protect reduced cobalamin against its modification by hydrogen peroxide.
Collapse
Affiliation(s)
| | | | - Oscar I. Koifman
- Ivanovo State University of Chemistry and Technology
- Ivanovo
- Russia
| |
Collapse
|
13
|
Dereven’kov IA, Makarov SV. Catalytic effect of tetrasulfonated cobalt phthalocyanine on selenite reduction by dithionite. REACTION KINETICS MECHANISMS AND CATALYSIS 2019. [DOI: 10.1007/s11144-019-01687-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
14
|
Wang SC. Cobalamin-dependent radical S-adenosyl-l-methionine enzymes in natural product biosynthesis. Nat Prod Rep 2019; 35:707-720. [PMID: 30079906 DOI: 10.1039/c7np00059f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covering: 2011 to 2018 This highlight summarizes the investigation of cobalamin (Cbl)- and radical S-adenosyl-l-methionine (SAM)-dependent enzymes found in natural product biosynthesis to date and suggests some possibilities for the future. Though some mechanistic aspects are apparently shared, the overall diversity of this family's functions and abilities is significant and may be tailored to the specific substrate and/or reaction being catalyzed. A little over a year ago, the first crystal structure of a Cbl- and radical SAM-dependent enzyme was solved, providing the first insight into what may be the shared scaffolding of these enzymes.
Collapse
Affiliation(s)
- Susan C Wang
- Case Western Reserve University School of Medicine, Department of Biochemistry, USA.
| |
Collapse
|
15
|
Blaszczyk AJ, Knox HL, Booker SJ. Understanding the role of electron donors in the reaction catalyzed by Tsrm, a cobalamin-dependent radical S-adenosylmethionine methylase. J Biol Inorg Chem 2019; 24:831-839. [PMID: 31350635 DOI: 10.1007/s00775-019-01689-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023]
Abstract
The cobalamin-dependent radical S-adenosylmethionine (SAM) enzyme TsrM catalyzes the methylation of C2 of L-tryptophan to form 2-methyltryptophan during the biosynthesis of thiostrepton A. Although TsrM is a member of the radical SAM superfamily, unlike all other annotated members, it does not catalyze a reductive cleavage of SAM to a 5'-deoxyadenosyl 5'-radical intermediate. In fact, it has been proposed that TsrM catalyzes its reaction through two polar nucleophilic displacements, with its cobalamin cofactor cycling directly between methylcobalamin (MeCbl) and cob(I)alamin. Nevertheless, the enzyme has been stated to require the action of a reductant, which can be satisfied by dithiothreitol. By contrast, all other annotated RS enzymes require a reductant that exhibits a much lower reduction potential, which is necessary for the reductive cleavage of SAM. Herein, we show that TsrM can catalyze multiple turnovers in the absence of any reducing agent, but only when it is pre-loaded with MeCbl. When hydroxocobalamin (OHCbl) or cob(II)alamin is bound to TsrM, a reductant is required to convert it to cob(I)alamin, which can acquire a methyl group directly from SAM. Our studies suggest that TsrM uses an external reductant to prime its reaction by converting bound OHCbl or cob(II)alamin to MeCbl, and to regenerate the MeCbl form of the cofactor upon adventitious oxidation of the cob(I)alamin intermediate to cob(II)alamin.
Collapse
Affiliation(s)
- Anthony J Blaszczyk
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hayley L Knox
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
16
|
Pugina RA, Denisova EA, Ivlev PA, Salnikov DS, Makarov SV. Synthesis of vitamin B12 derivatives with sodium hydroxymethanesulfinate. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s1088424618501092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The reaction of cyanocobalamin (CNCbl) with sodium hydroxymethanesulfinate (HMS) was studied over a wide range of pH (4–11) under aerobic conditions. CNCbl is destroyed in the presence of HMS in aqueous solution to form uncolored substances. The accumulation of stable yellow corrinoids (SYCs) preceded these changes at pH [Formula: see text] 8. The major stable yellow corrinoid is (15R)-Co[Formula: see text], Coß — dicyano-13-dehydro-15-hydro-l5-hydroxycob(III)alamin. The yield of this SYC is 25%, and the stability of this compound decreases significantly with increasing concentrations of HMS, pH and temperature.
Collapse
Affiliation(s)
- Raida A. Pugina
- Department of Food Chemistry, State University of Chemistry and Technology, Sheremetevskiy str. 7, Ivanovo, 153000, Russia
| | - Elena A. Denisova
- Department of Food Chemistry, State University of Chemistry and Technology, Sheremetevskiy str. 7, Ivanovo, 153000, Russia
| | - Pavel A. Ivlev
- Department of Food Chemistry, State University of Chemistry and Technology, Sheremetevskiy str. 7, Ivanovo, 153000, Russia
| | - Denis S. Salnikov
- Department of Food Chemistry, State University of Chemistry and Technology, Sheremetevskiy str. 7, Ivanovo, 153000, Russia
| | - Sergei V. Makarov
- Department of Food Chemistry, State University of Chemistry and Technology, Sheremetevskiy str. 7, Ivanovo, 153000, Russia
| |
Collapse
|
17
|
Dereven'kov IA, Makarov SV, Bui Thi TT, Makarova AS, Koifman OI. Studies on the Reduction of Dehydroascorbic Acid by Glutathione in the Presence of Aquahydroxocobinamide. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ilia A. Dereven'kov
- Ivanovo State University of Chemistry and Technology; Sheremetevskiy str. 7 153000 Ivanovo Russia
| | - Sergei V. Makarov
- Ivanovo State University of Chemistry and Technology; Sheremetevskiy str. 7 153000 Ivanovo Russia
| | - Thu Thuy Bui Thi
- Faculty of Chemical Engineering; Industrial University of Ho Chi Minh city; 12 Nguyen Van Bao, ward 4, Go Vap district 727010 Ho Chi Minh City Vietnam
| | - Anna S. Makarova
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences; Academicheskaya str. 1 153045 Ivanovo Russian Federation
| | - Oskar I. Koifman
- Ivanovo State University of Chemistry and Technology; Sheremetevskiy str. 7 153000 Ivanovo Russia
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences; Academicheskaya str. 1 153045 Ivanovo Russian Federation
| |
Collapse
|
18
|
Salnikov DS, Makarov SV, Ivlev PA. Comparative Study of Redox Reactions of Aqua- and Thiocyanatocobalamin. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s1070363218050201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
19
|
Dereven'kov IA, Polyakova AY, Makarov SV. Kinetic and Mechanistic Studies on the Reaction between Aquacobalamin and Selenocysteine. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ilia A. Dereven'kov
- Department of Food Chemistry; Ivanovo State University of Chemistry and Technology; Sheremetevskiy str. 7 153000 Ivanovo Russia
| | - Anastasiya Yu. Polyakova
- Department of Food Chemistry; Ivanovo State University of Chemistry and Technology; Sheremetevskiy str. 7 153000 Ivanovo Russia
| | - Sergei V. Makarov
- Department of Food Chemistry; Ivanovo State University of Chemistry and Technology; Sheremetevskiy str. 7 153000 Ivanovo Russia
| |
Collapse
|
20
|
Dereven'kov IA, Ivlev PA, Bischin C, Salnikov DS, Silaghi-Dumitrescu R, Makarov SV, Koifman OI. Comparative studies of reaction of cobalamin (II) and cobinamide (II) with sulfur dioxide. J Biol Inorg Chem 2017; 22:969-975. [PMID: 28620693 DOI: 10.1007/s00775-017-1474-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/07/2017] [Indexed: 12/20/2022]
Abstract
The kinetics of reactions of cobalamin (II) and cobinamide (II) with sulfur dioxide was studied by UV-visible (UV-vis) spectroscopy. Reaction results in oxidation of Co(II) center and involves two aquated SO2 moieties. The final product is suggested to be complex Co(III)-S2O 4•- . The absence of corrin ring modifications during the reactions was proved.
Collapse
Affiliation(s)
- Ilia A Dereven'kov
- Institute of Macroheterocyclic Compounds, Ivanovo State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000, Ivanovo, Russia
| | - Pavel A Ivlev
- Institute of Macroheterocyclic Compounds, Ivanovo State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000, Ivanovo, Russia
| | - Cristina Bischin
- Department of Chemistry and Chemical Engineering, "Babes-Bolyai" University, Str. Arany Janos Nr. 11, 400028, Cluj-Napoca, Romania
| | - Denis S Salnikov
- Institute of Macroheterocyclic Compounds, Ivanovo State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000, Ivanovo, Russia.
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry and Chemical Engineering, "Babes-Bolyai" University, Str. Arany Janos Nr. 11, 400028, Cluj-Napoca, Romania
| | - Sergei V Makarov
- Institute of Macroheterocyclic Compounds, Ivanovo State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000, Ivanovo, Russia
| | - Oscar I Koifman
- Institute of Macroheterocyclic Compounds, Ivanovo State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000, Ivanovo, Russia
| |
Collapse
|
21
|
Wang Y, Schnell B, Baumann S, Müller R, Begley TP. Biosynthesis of Branched Alkoxy Groups: Iterative Methyl Group Alkylation by a Cobalamin-Dependent Radical SAM Enzyme. J Am Chem Soc 2017; 139:1742-1745. [PMID: 28040895 PMCID: PMC6078419 DOI: 10.1021/jacs.6b10901] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biosynthesis of branched alkoxy groups, such as the unique t-butyl group found in a variety of natural products, is still poorly understood. Recently, cystobactamids were isolated and identified from Cystobacter sp as novel antibacterials. These metabolites contain an isopropyl group proposed to be formed using CysS, a cobalamin-dependent radical S-adenosylmethionine (SAM) methyltransferase. Here, we reconstitute the CysS-catalyzed reaction, on p-aminobenzoate thioester substrates, and demonstrate that it not only catalyzes sequential methylations of a methyl group to form ethyl and isopropyl groups but remarkably also sec-butyl and t-butyl groups. To our knowledge, this is the first in vitro reconstitution of a cobalamin-dependent radical SAM enzyme catalyzing the conversion of a methyl group to a t-butyl group.
Collapse
Affiliation(s)
- Yuanyou Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Bastien Schnell
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, Universitätscampus E8.1, D-66123 Saarbrücken, Germany
| | - Sascha Baumann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, Universitätscampus E8.1, D-66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, Universitätscampus E8.1, D-66123 Saarbrücken, Germany
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
22
|
Li N, Zheng Y, Jiang X, Zhang R, Chen W. Generation of reactive cobalt oxo oxamate radical species for biomimetic oxidation of contaminants. RSC Adv 2017. [DOI: 10.1039/c7ra08317c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bio-inspired formation of [CoIVO˙]− species: cobalt oxo radical intermediate was directly observed in ESI-MS.
Collapse
Affiliation(s)
- Nan Li
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Yun Zheng
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Xuemei Jiang
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Ran Zhang
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| | - Wenxing Chen
- National Engineering Lab for Textile Fiber Materials & Processing Technology (Zhejiang)
- Zhejiang Sci-Tech University
- Hangzhou 310018
- China
| |
Collapse
|
23
|
Sen Gupta KK, Bhattacharjee N, Pal B. Oxidative Cleavage of S-S Bond During the Reduction of Tris(pyridine-2-carboxylato)manganese(III) by Dithionite in Sodium Picolinate-Picolinic Acid Buffer Medium. INT J CHEM KINET 2016. [DOI: 10.1002/kin.21022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Biswajit Pal
- Department of Chemistry; St. Paul's C. M. College; Kolkata 700 009 India
| |
Collapse
|
24
|
Blaszczyk AJ, Silakov A, Zhang B, Maiocco SJ, Lanz ND, Kelly WL, Elliott SJ, Krebs C, Booker SJ. Spectroscopic and Electrochemical Characterization of the Iron-Sulfur and Cobalamin Cofactors of TsrM, an Unusual Radical S-Adenosylmethionine Methylase. J Am Chem Soc 2016; 138:3416-26. [PMID: 26841310 DOI: 10.1021/jacs.5b12592] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
TsrM, an annotated radical S-adenosylmethionine (SAM) enzyme, catalyzes the methylation of carbon 2 of the indole ring of L-tryptophan. Its reaction is the first step in the biosynthesis of the unique quinaldic acid moiety of thiostrepton A, a thiopeptide antibiotic. The appended methyl group derives from SAM; however, the enzyme also requires cobalamin and iron-sulfur cluster cofactors for turnover. In this work we report the overproduction and purification of TsrM and the characterization of its metallocofactors by UV-visible, electron paramagnetic resonance, hyperfine sublevel correlation (HYSCORE), and Mössbauer spectroscopies as well as protein-film electrochemistry (PFE). The enzyme contains 1 equiv of its cobalamin cofactor in its as-isolated state and can be reconstituted with iron and sulfide to contain one [4Fe-4S] cluster with a site-differentiated Fe(2+)/Fe(3+) pair. Our spectroscopic studies suggest that TsrM binds cobalamin in an uncharacteristic five-coordinate base-off/His-off conformation, whereby the dimethylbenzimidazole group is replaced by a non-nitrogenous ligand, which is likely a water molecule. Electrochemical analysis of the protein by PFE indicates a one-electron redox feature with a midpoint potential of -550 mV, which is assigned to a [4Fe-4S](2+)/[4Fe-4S](+) redox couple. Analysis of TsrM by Mössbauer and HYSCORE spectroscopies suggests that SAM does not bind to the unique iron site of the cluster in the same manner as in other radical SAM (RS) enzymes, yet its binding still perturbs the electronic configuration of both the Fe/S cluster and the cob(II)alamin cofactors. These biophysical studies suggest that TsrM is an atypical RS enzyme, consistent with its reported inability to catalyze formation of a 5'-deoxyadenosyl 5'-radical.
Collapse
Affiliation(s)
| | | | | | - Stephanie J Maiocco
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | | | - Wendy L Kelly
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Sean J Elliott
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | | | | |
Collapse
|
25
|
Dereven’kov IA, Thi TTB, Salnikov DS, Makarov SV. Effect of amino acids on the interaction between cobalamin(II) and dehydroascorbic acid. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416030080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
26
|
|
27
|
Allen KD, Wang SC. Spectroscopic characterization and mechanistic investigation of P-methyl transfer by a radical SAM enzyme from the marine bacterium Shewanella denitrificans OS217. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2135-44. [PMID: 25224746 DOI: 10.1016/j.bbapap.2014.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 09/05/2014] [Accepted: 09/07/2014] [Indexed: 10/24/2022]
Abstract
Natural products containing carbon-phosphorus bonds elicit important bioactivity in many organisms. l-Phosphinothricin contains the only known naturally-occurring carbon-phosphorus-carbon bond linkage. In actinomycetes, the cobalamin-dependent radical S-adenosyl-l-methionine (SAM) methyltransferase PhpK catalyzes the formation of the second C-P bond to generate the complete C-P-C linkage in phosphinothricin. Here we use electron paramagnetic resonance and nuclear magnetic resonance spectroscopies to characterize and demonstrate the activity of a cobalamin-dependent radical SAM methyltransferase denoted SD_1168 from Shewanella denitrificans OS217, a marine bacterium that has not been reported to synthesize phosphinothricin. Recombinant, refolded, and reconstituted SD_1168 binds a four-iron, four-sulfur cluster that interacts with SAM and cobalamin. In the presence of SAM, a reductant, and methylcobalamin, SD_1168 surprisingly catalyzes the P-methylation of N-acetyl-demethylphosphinothricin and demethylphosphinothricin to produce N-acetyl-phosphinothricin and phosphinothricin, respectively. In addition, this enzyme is active in the absence of methylcobalamin if the strong reductant titanium (III) citrate and hydroxocobalamin are provided. When incubated with [methyl-(13)C] cobalamin and titanium citrate, both [methyl-(13)C] and unlabeled N-acetylphosphinothricin are produced. Our results suggest that SD_1168 catalyzes P-methylation using radical SAM-dependent chemistry with cobalamin as a coenzyme. In light of recent genomic information, the discovery of this P-methyltransferase suggests that S. denitrificans produces a phosphinate natural product.
Collapse
Affiliation(s)
- Kylie D Allen
- School of Molecular Biosciences, College of Veterinary Medicine, PO Box 647520, Washington State University, Pullman, WA 99164-7520, USA.
| | - Susan C Wang
- School of Molecular Biosciences, College of Veterinary Medicine, PO Box 647520, Washington State University, Pullman, WA 99164-7520, USA.
| |
Collapse
|
28
|
Salnikov DS, Makarov SV, van Eldik R, Kucherenko PN, Boss GR. Kinetics and mechanism of the reaction of hydrogen sulfide with diaquacobinamide in aqueous solution. Eur J Inorg Chem 2014; 2014:4123-4133. [PMID: 25580081 PMCID: PMC4286256 DOI: 10.1002/ejic.201402082] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Indexed: 11/09/2022]
Abstract
We conducted a detailed kinetic study of the reaction of the vitamin B12 analog diaquacobinamide ((H2O)2Cbi(III)) with hydrogen sulfide in water from pH 3 to 11. The reaction proceeds in three steps: (i) formation of three different complexes between cobinamide and hydrogen sulfide, viz. (HO-)(HS-)Cbi(III), (H2O)(HS-)Cbi(III), and (HS-)2Cbi(III); (ii) inner-sphere electron transfer (ISET) in the two complexes with one coordinated HS- to form the reduced cobinamide complex [(H)S]Cbi(II); and (iii) addition of a second molecule of hydrogen sulfide to the reduced cobinamide. ISET does not proceed in the (HS-)2Cbi(III) complex. The final products of the reaction between cobinamide and hydrogen sulfide were found to be independent of pH, with the main product being a complex of cobinamide(II) with the anion-radical SSH2-.
Collapse
Affiliation(s)
- Denis S. Salnikov
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000 Ivanovo, Russia
- Department of Chemistry and Pharmacy, University of Erlangen – Nuremberg, Egerland strasse 1, 91058 Erlangen, Germany
| | - Sergei V. Makarov
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000 Ivanovo, Russia
| | - Rudi van Eldik
- Department of Chemistry and Pharmacy, University of Erlangen – Nuremberg, Egerland strasse 1, 91058 Erlangen, Germany
| | - Polina N. Kucherenko
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000 Ivanovo, Russia
| | - Gerry R. Boss
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0652, United States
| |
Collapse
|
29
|
Surducan M, Makarov SV, Silaghi-Dumitrescu R. Redox and linkage isomerism with ligands relevant to oxidative and nitrosative stress in cobalamin. Polyhedron 2014. [DOI: 10.1016/j.poly.2014.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
30
|
Dereven'kov IA, Salnikov DS, Makarov SV, Boss GR, Koifman OI. Kinetics and mechanism of oxidation of super-reduced cobalamin and cobinamide species by thiosulfate, sulfite and dithionite. Dalton Trans 2014; 42:15307-16. [PMID: 23999614 DOI: 10.1039/c3dt51714d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We studied the kinetics of reactions of cob(I)alamin and cob(I)inamide with thiosulfate, sulfite, and dithionite by UV-Visible (UV-Vis) and stopped-flow spectroscopy. We found that the two Co(I) species were oxidized by these sulfur-containing compounds to Co(II) forms: oxidation by excess thiosulfate leads to penta-coordinate complexes and oxidation by excess sulfite or dithionite leads to hexa-coordinate Co(II)-SO2(-) complexes. The net scheme involves transfer of three electrons in the case of oxidation by thiosulfate and one electron for oxidation by sulfite and dithionite. On the basis of kinetic data, the nature of the reactive oxidants was suggested, i.e., HS2O3(-) (for oxidation by thiosulfate), S2O5(2-), HSO3(-), and aquated SO2 (for oxidation by sulfite), and S2O4(2-) and SO2(-) (for oxidation by dithionite). No difference was observed in kinetics with cob(i)alamin or cob(i)inamide as reductants.
Collapse
Affiliation(s)
- Ilia A Dereven'kov
- State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000 Ivanovo, Russia.
| | | | | | | | | |
Collapse
|
31
|
Salnikov DS, Kucherenko PN, Dereven'kov IA, Makarov SV, van Eldik R. Kinetics and Mechanism of the Reaction of Hydrogen Sulfide with Cobalamin in Aqueous Solution. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201301340] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
32
|
Kim HJ, McCarty RM, Ogasawara Y, Liu YN, Mansoorabadi SO, LeVieux J, Liu HW. GenK-catalyzed C-6' methylation in the biosynthesis of gentamicin: isolation and characterization of a cobalamin-dependent radical SAM enzyme. J Am Chem Soc 2013; 135:8093-6. [PMID: 23679096 PMCID: PMC3796153 DOI: 10.1021/ja312641f] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The existence of cobalamin (Cbl)-dependent enzymes that are members of the radical S-adenosyl-l-methionine (SAM) superfamily was previously predicted on the basis of bioinformatic analysis. A number of these are Cbl-dependent methyltransferases, but the details surrounding their reaction mechanisms have remained unclear. In this report we demonstrate the in vitro activity of GenK, a Cbl-dependent radical SAM enzyme that methylates an unactivated sp(3) carbon during the biosynthesis of gentamicin, an aminoglycoside antibiotic. Experiments to investigate the stoichiometry of the GenK reaction revealed that 1 equiv each of 5'-deoxyadenosine and S-adenosyl-homocysteine are produced for each methylation reaction catalyzed by GenK. Furthermore, isotope-labeling experiments demonstrate that the S-methyl group from SAM is transferred to Cbl and the aminoglycoside product during the course of the reaction. On the basis of these results, one mechanistic possibility for the GenK reaction can be ruled out, and further questions regarding the mechanisms of Cbl-dependent radical SAM methyltransferases, in general, are discussed.
Collapse
Affiliation(s)
- Hak Joong Kim
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Reid M. McCarty
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yasushi Ogasawara
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yung-nan Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Steven O. Mansoorabadi
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jake LeVieux
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
33
|
Dereven'kov IA, Salnikov DS, Makarov SV, Surducan M, Silaghi-Dumitrescu R, Boss GR. Comparative study of reaction of cobalamin and cobinamide with thiocyanate. J Inorg Biochem 2013; 125:32-9. [PMID: 23685470 DOI: 10.1016/j.jinorgbio.2013.04.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 11/24/2022]
Abstract
The interaction of Co(III) and Co(II) cobalamin (Cbl) and cobinamide (Cbi) with thiocyanate was examined with UV-vis and EPR spectra. S/N-linkage isomerism was explored on Co(III) and Co(II) Cbl and Cbi models using density functional theory (DFT; BP86, B3LYP). Performed calculations suggest the prevalence of isothiocyanato isomers over thiocyanato complexes on both Co(III) and Co(II) centers. The formation of Cbl(II) complex with thiocyanate was observed at high ligand concentrations which was proposed to be hexacoordinated. DFT data maintain the possibility of hexacoordinated Co(II) complexes with thiocyanate in which one of extra-ligands is weakly coordinated. It is found that high thiocyanate concentrations could retard cyanide binding to cobalamin but not to cobinamide.
Collapse
Affiliation(s)
- Ilia A Dereven'kov
- State University of Chemistry and Technology, Engels str. 7, 153000 Ivanovo, Russia
| | | | | | | | | | | |
Collapse
|
34
|
Kornobis K, Ruud K, Kozlowski PM. Cob(I)alamin: insight into the nature of electronically excited states elucidated via quantum chemical computations and analysis of absorption, CD and MCD data. J Phys Chem A 2013; 117:863-76. [PMID: 23281629 DOI: 10.1021/jp310446c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The nature of electronically excited states of the super-reduced form of vitamin B(12) (i.e., cob(I)alamin or B(12s)), a ubiquitous B(12) intermediate, was investigated by performing quantum-chemical calculations within the time-dependent density functional theory (TD-DFT) framework and by establishing their correspondence to experimental data. Using response theory, the electronic absorption (Abs), circular dichroism (CD) and magnetic CD (MCD) spectra of cob(I)alamin were simulated and directly compared with experiment. Several issues have been taken into considerations while performing the TD-DFT calculations, such as strong dependence on the applied exchange-correlation (XC) functional or structural simplification imposed on the cob(I)alamin. In addition, the low-lying transitions were also validated by performing CASSCF/MC-XQDPT2 calculations. By comparing computational results with existing experimental data a new level of understanding of electronic excitations has been established at the molecular level. The present study extends and confirms conclusions reached for other cobalamins. In particular, the better performance of the BP86 functional, rather than hybrid-type, was observed in terms of the excitations associated with both Co d and corrin π localized transitions. In addition, the lowest energy band was associated with multiple metal-to-ligand charge transfer excitations as opposed to the commonly assumed view of a single π → π* transition followed by vibrational progression. Finally, the use of the full cob(I)alamin structure, instead of simplified molecular models, shed new light on the spectral analyses of cobalamin systems and revealed new challenges of this approach related to long-range charge transfer excitations involving side chains.
Collapse
Affiliation(s)
- Karina Kornobis
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | | | | |
Collapse
|
35
|
|
36
|
Electromerism and linkage isomerism in biologically-relevant FeSO complexes. J Inorg Biochem 2013; 118:13-20. [DOI: 10.1016/j.jinorgbio.2012.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 09/11/2012] [Accepted: 09/12/2012] [Indexed: 11/17/2022]
|
37
|
Salnikov DS, Dereven’kov IA, Artyushina EN, Makarov SV. Interaction of cyanocobalamin with sulfur-containing reducing agents in aqueous solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024413010226] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
38
|
Affiliation(s)
- Sergei V. Makarov
- a Department of Food Chemistry and Biotechnology , State University of Chemistry and Technology , Engels Street 7, Ivanovo , 153000 , Russia
| | - Radu Silaghi-Dumitrescu
- b Faculty of Chemistry and Chemical Engineering , “Babes-Bolyai” University , 11 Arany Janos Street, Cluj-Napoca , RO-400028 , Romania
| |
Collapse
|
39
|
Amir A, Lee W. Enhanced reductive dechlorination of tetrachloroethene during reduction of cobalamin (III) by nano-mackinawite. JOURNAL OF HAZARDOUS MATERIALS 2012; 235-236:359-366. [PMID: 22939091 DOI: 10.1016/j.jhazmat.2012.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 08/03/2012] [Accepted: 08/06/2012] [Indexed: 06/01/2023]
Abstract
We demonstrated adsorption and reduction of cobalamin(III) (Co(III)) on nano-mackinawite (nFeS) surface and their impact on reductive dechlorination of tetrachloroethene (PCE). The adsorption of Co(III) on the nFeS surface followed Langmuir isotherm and the reduction of Co(III) provided different reactive surface chemical species on nFeS surface. Content of Fe(2+)S on nFeS surface decreased (45.9-14.5%) as Fe(2+)S was oxidized to Fe(3+)S and Fe(3+)O coupled with the surface reduction of Co(III) to cobalamin(II) (Co(II)). S(2-) and S(n)(2-) contents on the nFeS surface also decreased by 48.5% and 82.3%, respectively during the formation of sulfidecobalamin(II) (≡S(2-)Co(II)) by the reactive surface sulfur. PCE was fully degraded in nFeSCo(III) suspension at pH 8.3 in 120 h. The dechlorination kinetic rate constant of PCE in the nFeSCo(III) suspension (k(FeSCo(III))=0.188±0.003 h(-1)) was 145 times greater than that in nFeS suspension, showing a potential role of ≡S(2-)Co(II) as an electron transfer mediator to shuttle electrons for the enhanced reductive dechlorination. PCE was transformed to acetylene and 1,3-butadiene as major products via reductive β-elimination and isomerization reactions, respectively. The experimental findings can provide basic knowledge to identify a reaction mechanism for the enhanced reductive dechlorination of chlorinated organic by biogeochemical reactions possibly observed in natural reducing environments.
Collapse
Affiliation(s)
- Amnorzahira Amir
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-Gu, Daejeon 305-701, South Korea
| | | |
Collapse
|