501
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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502
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Radical new paradigm for heme degradation in Escherichia coli O157:H7. Proc Natl Acad Sci U S A 2016; 113:12138-12143. [PMID: 27791000 DOI: 10.1073/pnas.1603209113] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All of the heme-degrading enzymes that have been characterized to date require molecular oxygen as a cosubstrate. Escherichia coli O157:H7 has been shown to express heme uptake and transport proteins, as well as use heme as an iron source. This enteric pathogen colonizes the anaerobic space of the lower intestine in mammals, yet no mechanism for anaerobic heme degradation has been reported. Herein we provide evidence for an oxygen-independent heme-degradation pathway. Specifically, we demonstrate that ChuW is a radical S-adenosylmethionine methyltransferase that catalyzes a radical-mediated mechanism facilitating iron liberation and the production of the tetrapyrrole product we termed "anaerobilin." We further demonstrate that anaerobilin can be used as a substrate by ChuY, an enzyme that is coexpressed with ChuW in vivo along with the heme uptake machinery. Our findings are discussed in terms of the competitive advantage this system provides for enteric bacteria, particularly those that inhabit an anaerobic niche in the intestines.
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503
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504
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Horning BD, Suciu RM, Ghadiri DA, Ulanovskaya OA, Matthews ML, Lum KM, Backus KM, Brown SJ, Rosen H, Cravatt BF. Chemical Proteomic Profiling of Human Methyltransferases. J Am Chem Soc 2016; 138:13335-13343. [PMID: 27689866 DOI: 10.1021/jacs.6b07830] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methylation is a fundamental mechanism used in Nature to modify the structure and function of biomolecules, including proteins, DNA, RNA, and metabolites. Methyl groups are predominantly installed into biomolecules by a large and diverse class of S-adenosyl methionine (SAM)-dependent methyltransferases (MTs), of which there are ∼200 known or putative members in the human proteome. Deregulated MT activity contributes to numerous diseases, including cancer, and several MT inhibitors are in clinical development. Nonetheless, a large fraction of the human MT family remains poorly characterized, underscoring the need for new technologies to characterize MTs and their inhibitors in native biological systems. Here, we describe a suite of S-adenosyl homocysteine (SAH) photoreactive probes and their application in chemical proteomic experiments to profile and enrich a large number of MTs (>50) from human cancer cell lysates with remarkable specificity over other classes of proteins. We further demonstrate that the SAH probes can enrich MT-associated proteins and be used to screen for and assess the selectivity of MT inhibitors, leading to the discovery of a covalent inhibitor of nicotinamide N-methyltransferase (NNMT), an enzyme implicated in cancer and metabolic disorders. The chemical proteomics probes and methods for their utilization reported herein should prove of value for the functional characterization of MTs, MT complexes, and MT inhibitors in mammalian biology and disease.
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Affiliation(s)
- Benjamin D Horning
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Radu M Suciu
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Darian A Ghadiri
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Olesya A Ulanovskaya
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Megan L Matthews
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Kenneth M Lum
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Keriann M Backus
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Steven J Brown
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Hugh Rosen
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Benjamin F Cravatt
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
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505
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Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes. Nat Chem Biol 2016; 12:905-907. [PMID: 27642865 PMCID: PMC5069167 DOI: 10.1038/nchembio.2187] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 08/16/2016] [Indexed: 01/04/2023]
Abstract
Nikkomycins and polyoxins are antifungal peptidylnucleoside antibiotics active against human and plant pathogens. Here we report that during peptidylnucleoside biosynthesis in Streptomyces cacaoi and S. tendae, the C5' extension of the nucleoside essential for downstream structural diversification is catalyzed by a conserved radical S-adenosyl-L-methionine (SAM) enzyme, PolH or NikJ. This is distinct from the nucleophilic mechanism reported for antibacterial nucleosides and represents a new mechanism of nucleoside natural product biosynthesis.
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506
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Adhikari S, Lin G, Li L. Reversible Hydrolysis Reaction with the Spore Photoproduct under Alkaline Conditions. J Org Chem 2016; 81:8570-6. [PMID: 27537985 DOI: 10.1021/acs.joc.6b01846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA lesions may reduce the electron density at the nucleobases, making them prone to further modifications upon the alkaline treatment. The dominant DNA photolesion found in UV-irradiated bacterial endospores is a thymine dimer, 5-thyminyl-5,6-dihydrothymine, i.e., the spore photoproduct (SP). Here we report a stepwise addition/elimination reaction in the SP hydrolysis product under strong basic conditions where a ureido group is added to the carboxyl moiety to form a cyclic amide, regenerating SP after eliminating a hydroxide ion. Direct amidation of carboxylic acids by reaction with amines in the presence of a catalyst is well documented; however, it is very rare for an amidation reaction to occur without activation. This uncatalyzed SP reverse reaction in aqueous solution is even more surprising because the carboxyl moiety is not a good electrophile due to the negative charge it carries. Examination of the base-catalyzed hydrolyses of two other saturated pyrimidine lesions, 5,6-dihydro-2'-deoxyuridine and pyrimidine (6-4) pyrimidone photoproduct, reveals that neither reaction is reversible even though all three hydrolysis reactions may share the same gem-diol intermediate. Therefore, the SP structure where the two thymine residues maintain a stacked conformation likely provides the needed framework enabling this highly unusual carboxyl addition/elimination reaction.
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Affiliation(s)
- Surya Adhikari
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
| | - Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana, 46202, United States.,Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
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507
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Mechanistic insights into class B radical-S-adenosylmethionine methylases: ubiquitous tailoring enzymes in natural product biosynthesis. Curr Opin Chem Biol 2016; 35:73-79. [PMID: 27632683 DOI: 10.1016/j.cbpa.2016.08.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 01/06/2023]
Abstract
Class B radical S-adenosylmethionine (SAM) methylases are notable for their ability to catalyse methylation reactions in the biosynthesis of a wide variety of natural products, including polyketides, ribosomally biosynthesised and post-translationally modified peptides (RiPPs), nonribosomal peptides (NRPs), aminoglycosides, β-lactams, phosphonates, enediynes, aminocoumarins and terpenes. Here, we discuss the diversity of substrates and catalytic mechanism utilised by such enzymes, highlighting the stereochemical course of methylation reactions at un-activated carbon centres and the ability of some members of the family to catalyse multiple methylations.
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508
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Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016; 55:11845-8. [DOI: 10.1002/anie.201605917] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
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509
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Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
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510
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Dong M, Horitani M, Dzikovski B, Pandelia ME, Krebs C, Freed JH, Hoffman BM, Lin H. Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme. J Am Chem Soc 2016; 138:9755-8. [PMID: 27465315 DOI: 10.1021/jacs.6b04155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pyrococcus horikoshii Dph2 (PhDph2) is an unusual radical S-adenosylmethionine (SAM) enzyme involved in the first step of diphthamide biosynthesis. It catalyzes the reaction by cleaving SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. To probe the reaction mechanism, we synthesized a SAM analogue (SAMCA), in which the ACP group of SAM is replaced with a 3-carboxyallyl group. SAMCA is cleaved by PhDph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, α-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Electron-nuclear double resonance (ENDOR) measurements with (13)C and (2)H isotopically labeled SAMCA support a π-complex between the C═C double bond of α-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster. This is the first example of a radical SAM-related [4Fe-4S](+) cluster forming an organometallic complex with an alkene, shedding additional light on the mechanism of PhDph2 and expanding our current notions for the reactivity of [4Fe-4S] clusters in radical SAM enzymes.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02453, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University , Ithaca, New York 14853, United States
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511
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Abstract
Prior to 1950, the consensus was that biological transformations occurred in two-electron steps, thereby avoiding the generation of free radicals. Dramatic advances in spectroscopy, biochemistry, and molecular biology have led to the realization that protein-based radicals participate in a vast array of vital biological mechanisms. Redox processes involving high-potential intermediates formed in reactions with O2 are particularly susceptible to radical formation. Clusters of tyrosine (Tyr) and tryptophan (Trp) residues have been found in many O2-reactive enzymes, raising the possibility that they play an antioxidant protective role. In blue copper proteins with plastocyanin-like domains, Tyr/Trp clusters are uncommon in the low-potential single-domain electron-transfer proteins and in the two-domain copper nitrite reductases. The two-domain muticopper oxidases, however, exhibit clusters of Tyr and Trp residues near the trinuclear copper active site where O2 is reduced. These clusters may play a protective role to ensure that reactive oxygen species are not liberated during O2 reduction.
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Affiliation(s)
- Harry B Gray
- Beckman Institute, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA 91125, USA
| | - Jay R Winkler
- Beckman Institute, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA 91125, USA
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512
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The physiology and habitat of the last universal common ancestor. Nat Microbiol 2016; 1:16116. [DOI: 10.1038/nmicrobiol.2016.116] [Citation(s) in RCA: 545] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/21/2016] [Indexed: 02/03/2023]
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513
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Birrell JA, Laurich C, Reijerse EJ, Ogata H, Lubitz W. Importance of Hydrogen Bonding in Fine Tuning the [2Fe-2S] Cluster Redox Potential of HydC from Thermotoga maritima. Biochemistry 2016; 55:4344-55. [PMID: 27396836 DOI: 10.1021/acs.biochem.6b00341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron-sulfur clusters form one of the largest and most diverse classes of enzyme cofactors in nature. They may serve as structural factors, form electron transfer chains between active sites and external redox partners, or form components of enzyme active sites. Their specific role is a consequence of the cluster type and the surrounding protein environment. The relative effects of these factors are not completely understood, and it is not yet possible to predict the properties of iron-sulfur clusters based on amino acid sequences or rationally tune their properties to generate proteins with new desirable functions. Here, we generate mutations in a [2Fe-2S] cluster protein, the TmHydC subunit of the trimeric [FeFe]-hydrogenase from Thermotoga maritima, to study the factors that affect its redox potential. Saturation mutagenesis of Val131 was used to tune the redox potential over a 135 mV range and revealed that cluster redox potential and electronic properties correlate with amino acid hydrophobicity and the ability to form hydrogen bonds to the cluster. Proline scanning mutagenesis between pairs of ligating cysteines was used to remove backbone amide hydrogen bonds to the cluster and decrease the redox potential by up to 132 mV, without large structural changes in most cases. However, substitution of Gly83 with proline caused a change of HydC to a [4Fe-4S] cluster protein with a redox potential of -526 mV. Together, these results confirm the importance of hydrogen bonding in tuning cluster redox potentials and demonstrate the versatility of iron-sulfur cluster protein folds at binding different types of clusters.
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Affiliation(s)
- James A Birrell
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Christoph Laurich
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward J Reijerse
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
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514
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Ding W, Ji X, Li Y, Zhang Q. Catalytic Promiscuity of the Radical S-adenosyl-L-methionine Enzyme NosL. Front Chem 2016; 4:27. [PMID: 27446906 PMCID: PMC4916742 DOI: 10.3389/fchem.2016.00027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
Catalytic promiscuity plays a key role in enzyme evolution and the acquisition of novel biological functions. Because of the high reactivity of radical species, in our view enzymes involving radical-mediated mechanisms could intrinsically be more prone to catalytic promiscuity. This mini-review summarizes the recent advances in the study of NosL, a radical S-adenosyl-L-methionine (SAM)-dependent L-tryptophan (L-Trp) lyase. We demonstrate here the interesting chemistry and remarkable catalytic promiscuity of NosL, and attempt to highlight the high evolvability of radical SAM enzymes and the potential to engineer these enzymes for novel and improved activities.
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Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University Shanghai, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University Shanghai, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University Shanghai, China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai, China
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515
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Wilcoxen J, Arragain S, Scandurra AA, Jimenez-Vicente E, Echavarri-Erasun C, Pollmann S, Britt RD, Rubio LM. Electron Paramagnetic Resonance Characterization of Three Iron-Sulfur Clusters Present in the Nitrogenase Cofactor Maturase NifB from Methanocaldococcus infernus. J Am Chem Soc 2016; 138:7468-71. [PMID: 27268267 DOI: 10.1021/jacs.6b03329] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NifB utilizes two equivalents of S-adenosyl methionine (SAM) to insert a carbide atom and fuse two substrate [Fe-S] clusters forming the NifB cofactor (NifB-co), which is then passed to NifEN for further modification to form the iron-molybdenum cofactor (FeMo-co) of nitrogenase. Here, we demonstrate that NifB from the methanogen Methanocaldococcus infernus is a radical SAM enzyme able to reductively cleave SAM to 5'-deoxyadenosine radical and is competent in FeMo-co maturation. Using electron paramagnetic resonance spectroscopy we have characterized three [4Fe-4S] clusters, one SAM binding cluster, and two auxiliary clusters probably acting as substrates for NifB-co formation. Nitrogen coordination to one or more of the auxiliary clusters in NifB was observed, and its mechanistic implications for NifB-co dissociation from the maturase are discussed.
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Affiliation(s)
- Jarett Wilcoxen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Simon Arragain
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - Alessandro A Scandurra
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - Emilio Jimenez-Vicente
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
| | - R David Britt
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid , Pozuelo de Alarcón, Madrid 28223, Spain
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516
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Mono- and binuclear non-heme iron chemistry from a theoretical perspective. J Biol Inorg Chem 2016; 21:619-44. [DOI: 10.1007/s00775-016-1357-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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517
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Lv M, Ji X, Zhao J, Li Y, Zhang C, Su L, Ding W, Deng Z, Yu Y, Zhang Q. Characterization of a C3 Deoxygenation Pathway Reveals a Key Branch Point in Aminoglycoside Biosynthesis. J Am Chem Soc 2016; 138:6427-35. [PMID: 27120352 DOI: 10.1021/jacs.6b02221] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Apramycin is a clinically interesting aminoglycoside antibiotic (AGA) containing a highly unique bicyclic octose moiety, and this octose is deoxygenated at the C3 position. Although the biosynthetic pathways for most 2-deoxystreptamine-containing AGAs have been well characterized, the pathway for apramycin biosynthesis, including the C3 deoxygenation process, has long remained unknown. Here we report detailed investigation of apramycin biosynthesis by a series of genetic, biochemical and bioinformatical studies. We show that AprD4 is a novel radical S-adenosyl-l-methionine (SAM) enzyme, which uses a noncanonical CX3CX3C motif for binding of a [4Fe-4S] cluster and catalyzes the dehydration of paromamine, a pseudodisaccharide intermediate in apramycin biosynthesis. We also show that AprD3 is an NADPH-dependent reductase that catalyzes the reduction of the dehydrated product from AprD4-catalyzed reaction to generate lividamine, a C3' deoxygenated product of paromamine. AprD4 and AprD3 do not form a tight catalytic complex, as shown by protein complex immunoprecipitation and other assays. The AprD4/AprD3 enzyme system acts on different pseudodisaccharide substrates but does not catalyze the deoxygenation of oxyapramycin, an apramycin analogue containing a C3 hydroxyl group on the octose moiety, suggesting that oxyapramycin and apramycin are partitioned into two parallel pathways at an early biosynthetic stage. Functional dissection of the C6 dehydrogenase AprQ shows the crosstalk between different AGA biosynthetic gene clusters from the apramycin producer Streptomyces tenebrarius, and reveals the remarkable catalytic versatility of AprQ. Our study highlights the intriguing chemistry in apramycin biosynthesis and nature's ingenuity in combinatorial biosynthesis of natural products.
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Affiliation(s)
- Meinan Lv
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Junfeng Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China.,Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Chen Zhang
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Li Su
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Wei Ding
- Department of Chemistry, Fudan University , Shanghai, 200433, China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , Wuhan, 430071, China
| | - Qi Zhang
- Department of Chemistry, Fudan University , Shanghai, 200433, China
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518
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Bruender NA, Bandarian V. The Radical S-Adenosyl-l-methionine Enzyme MftC Catalyzes an Oxidative Decarboxylation of the C-Terminus of the MftA Peptide. Biochemistry 2016; 55:2813-6. [PMID: 27158836 DOI: 10.1021/acs.biochem.6b00355] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are encoded in the genomes of a wide variety of microorganisms, in the proximity of open reading frames that encode enzymes that conduct extensive modifications, many of which are novel. Recently, members of the radical S-adenosyl-l-methionine (SAM) superfamily have been identified in these biosynthetic clusters. Herein, we demonstrate the putative radical SAM enzyme, MftC, oxidatively decarboxylates the C-terminus of the MftA peptide in the presence of the accessory protein MftB. The reaction catalyzed by MftC expands the repertoire of peptide-based radical SAM chemistry beyond the intramolecular cross-links.
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Affiliation(s)
- Nathan A Bruender
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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519
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Horitani M, Shisler K, Broderick WE, Hutcheson RU, Duschene KS, Marts AR, Hoffman BM, Broderick JB. Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond. Science 2016; 352:822-5. [PMID: 27174986 DOI: 10.1126/science.aaf5327] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/29/2016] [Indexed: 11/02/2022]
Abstract
Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes.
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Affiliation(s)
- Masaki Horitani
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Krista Shisler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Rachel U Hutcheson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Kaitlin S Duschene
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Amy R Marts
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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520
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Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an astonishing array of complex and chemically challenging reactions across all domains of life. Of approximately 114,000 of these enzymes, 8 are known to be present in humans: MOCS1, molybdenum cofactor biosynthesis; LIAS, lipoic acid biosynthesis; CDK5RAP1, 2-methylthio-N(6)-isopentenyladenosine biosynthesis; CDKAL1, methylthio-N(6)-threonylcarbamoyladenosine biosynthesis; TYW1, wybutosine biosynthesis; ELP3, 5-methoxycarbonylmethyl uridine; and RSAD1 and viperin, both of unknown function. Aberrations in the genes encoding these proteins result in a variety of diseases. In this review, we summarize the biochemical characterization of these 8 radical S-adenosylmethionine enzymes and, in the context of human health, describe the deleterious effects that result from such genetic mutations.
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Affiliation(s)
- Bradley J Landgraf
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Erin L McCarthy
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802.,The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802;
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521
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Aussignargues C, Pandelia ME, Sutter M, Plegaria JS, Zarzycki J, Turmo A, Huang J, Ducat DC, Hegg EL, Gibney BR, Kerfeld CA. Structure and Function of a Bacterial Microcompartment Shell Protein Engineered to Bind a [4Fe-4S] Cluster. J Am Chem Soc 2016; 138:5262-70. [PMID: 26704697 DOI: 10.1021/jacs.5b11734] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles composed of a selectively permeable protein shell and encapsulated enzymes. They are considered promising templates for the engineering of designed bionanoreactors for biotechnology. In particular, encapsulation of oxidoreductive reactions requiring electron transfer between the lumen of the BMC and the cytosol relies on the ability to conduct electrons across the shell. We determined the crystal structure of a component protein of a synthetic BMC shell, which informed the rational design of a [4Fe-4S] cluster-binding site in its pore. We also solved the structure of the [4Fe-4S] cluster-bound, engineered protein to 1.8 Å resolution, providing the first structure of a BMC shell protein containing a metal center. The [4Fe-4S] cluster was characterized by optical and EPR spectroscopies; it has a reduction potential of -370 mV vs the standard hydrogen electrode (SHE) and is stable through redox cycling. This remarkable stability may be attributable to the hydrogen-bonding network provided by the main chain of the protein scaffold. The properties of the [4Fe-4S] cluster resemble those in low-potential bacterial ferredoxins, while its ligation to three cysteine residues is reminiscent of enzymes such as aconitase and radical S-adenosymethionine (SAM) enzymes. This engineered shell protein provides the foundation for conferring electron-transfer functionality to BMC shells.
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Affiliation(s)
| | - Maria-Eirini Pandelia
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Markus Sutter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | | | | | | | | | | | | | - Brian R Gibney
- Department of Chemistry, Brooklyn College , Brooklyn, New York 11210, United States
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York , New York, New York 10016, United States
| | - Cheryl A Kerfeld
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
- Berkeley Synthetic Biology Institute , Berkeley, California 94720, United States
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522
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Ding W, Li Q, Jia Y, Ji X, Qianzhu H, Zhang Q. Emerging Diversity of the Cobalamin-Dependent Methyltransferases Involving Radical-Based Mechanisms. Chembiochem 2016; 17:1191-7. [PMID: 27028019 DOI: 10.1002/cbic.201600107] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Indexed: 11/10/2022]
Abstract
Cobalamins comprise a group of cobalt-containing organometallic cofactors that play important roles in cellular metabolism. Although many cobalamin-dependent methyltransferases (e.g., methionine synthase MetH) have been extensively studied, a new group of methyltransferases that are cobalamin-dependent and utilize radical chemistry in catalysis is just beginning to be appreciated. In this Concept article, we summarize recent advances in the understanding of the radical-based and cobalamin-dependent methyltransferases and discuss the functional and mechanistic diversity of this emerging class of enzymes.
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Affiliation(s)
- Wei Ding
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qien Li
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Youli Jia
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Haocheng Qianzhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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523
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Rohac R, Amara P, Benjdia A, Martin L, Ruffié P, Favier A, Berteau O, Mouesca JM, Fontecilla-Camps JC, Nicolet Y. Carbon–sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE. Nat Chem 2016; 8:491-500. [DOI: 10.1038/nchem.2490] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 02/25/2016] [Indexed: 11/09/2022]
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524
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Polytheonamide biosynthesis showcasing the metabolic potential of sponge-associated uncultivated ‘Entotheonella’ bacteria. Curr Opin Chem Biol 2016; 31:8-14. [DOI: 10.1016/j.cbpa.2015.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/12/2015] [Accepted: 11/01/2015] [Indexed: 01/14/2023]
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525
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Bruender NA, Wilcoxen J, Britt RD, Bandarian V. Biochemical and Spectroscopic Characterization of a Radical S-Adenosyl-L-methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link. Biochemistry 2016; 55:2122-34. [PMID: 27007615 DOI: 10.1021/acs.biochem.6b00145] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide-derived natural products are a class of metabolites that afford the producing organism a selective advantage over other organisms in their biological niche. While the polypeptide antibiotics produced by the nonribosomal polypeptide synthetases (NRPS) are the most widely recognized, the ribosomally synthesized and post-translationally modified peptides (RiPPs) are an emerging group of natural products with diverse structures and biological functions. Both the NRPS derived peptides and the RiPPs undergo extensive post-translational modifications to produce structural diversity. Here we report the first characterization of the six cysteines in forty-five (SCIFF) [Haft, D. H. and Basu M. K. (2011) J. Bacteriol. 193, 2745-2755] peptide maturase Tte1186, which is a member of the radical S-adenosyl-l-methionine (SAM) superfamily. Tte1186 catalyzes the formation of a thioether cross-link in the peptide Tte1186a encoded by an orf located upstream of the maturase, under reducing conditions in the presence of SAM. Tte1186 contains three [4Fe-4S] clusters that are indispensable for thioether cross-link formation; however, only one cluster catalyzes the reductive cleavage of SAM. Mechanistic imperatives for the reaction catalyzed by the thioether forming radical SAM maturases will be discussed.
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Affiliation(s)
- Nathan A Bruender
- Chemistry Department, University of Utah , Salt Lake City, Utah 84112, United States
| | - Jarett Wilcoxen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Vahe Bandarian
- Chemistry Department, University of Utah , Salt Lake City, Utah 84112, United States
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526
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Sicoli G, Mouesca JM, Zeppieri L, Amara P, Martin L, Barra AL, Fontecilla-Camps JC, Gambarelli S, Nicolet Y. Fine-tuning of a radical-based reaction by radical S-adenosyl-L-methionine tryptophan lyase. Science 2016; 351:1320-3. [DOI: 10.1126/science.aad8995] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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527
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Barr I, Latham JA, Iavarone AT, Chantarojsiri T, Hwang JD, Klinman JP. Demonstration That the Radical S-Adenosylmethionine (SAM) Enzyme PqqE Catalyzes de Novo Carbon-Carbon Cross-linking within a Peptide Substrate PqqA in the Presence of the Peptide Chaperone PqqD. J Biol Chem 2016; 291:8877-84. [PMID: 26961875 DOI: 10.1074/jbc.c115.699918] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 02/05/2023] Open
Abstract
The radical S-adenosylmethionine (SAM) protein PqqE is predicted to function in the pyrroloquinoline quinone (PQQ) biosynthetic pathway via catalysis of carbon-carbon bond formation between a glutamate and tyrosine side chain within the small peptide substrate PqqA. We report here that PqqE activity is dependent on the accessory protein PqqD, which was recently shown to bind PqqA tightly. In addition, PqqE activity in vitro requires the presence of a flavodoxin- and flavodoxin reductase-based reduction system, with other reductants leading to an uncoupled cleavage of the co-substrate SAM. These results indicate that PqqE, in conjunction with PqqD, carries out the first step in PQQ biosynthesis: a radical-mediated formation of a new carbon-carbon bond between two amino acid side chains on PqqA.
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Affiliation(s)
- Ian Barr
- From the Department of Chemistry, Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - John A Latham
- From the Department of Chemistry, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Anthony T Iavarone
- From the Department of Chemistry, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | | | | | - Judith P Klinman
- From the Department of Chemistry, Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
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528
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Kim HJ, LeVieux J, Yeh YC, Liu HW. C3'-Deoxygenation of Paromamine Catalyzed by a Radical S-Adenosylmethionine Enzyme: Characterization of the Enzyme AprD4 and Its Reductase Partner AprD3. Angew Chem Int Ed Engl 2016; 55:3724-8. [PMID: 26879038 PMCID: PMC4943880 DOI: 10.1002/anie.201510635] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 11/06/2022]
Abstract
C3'-deoxygenation of aminoglycosides results in their decreased susceptibility to phosphorylation thereby increasing their efficacy as antibiotics. However, the biosynthetic mechanism of C3'-deoxygenation is unknown. To address this issue, aprD4 and aprD3 genes from the apramycin gene cluster in Streptomyces tenebrarius were expressed in E. coli and the resulting gene products were characterized in vitro. AprD4 is shown to be a radical S-adenosylmethionine (SAM) enzyme, catalyzing homolysis of SAM to 5'-deoxyadenosine (5'-dAdo) in the presence of paromamine. [4'-(2) H]-Paromamine was prepared and used to show that its C4'-H is transferred to 5'-dAdo by AprD4, during which the substrate is dehydrated to a product consistent with 4'-oxolividamine. In contrast, paromamine is reduced to a deoxy product when incubated with AprD4/AprD3/NADPH. These results show that AprD4 is the first radical SAM diol-dehydratase and, along with AprD3, is responsible for 3'-deoxygenation in aminoglycoside biosynthesis.
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Affiliation(s)
- Hak Joong Kim
- Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jake LeVieux
- Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yu-Cheng Yeh
- Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hung-Wen Liu
- Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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529
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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.
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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
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530
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C3′-Deoxygenation of Paromamine Catalyzed by a RadicalS-Adenosylmethionine Enzyme: Characterization of the Enzyme AprD4 and Its Reductase Partner AprD3. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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531
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Ji X, Li Y, Jia Y, Ding W, Zhang Q. Mechanistic Insights into the RadicalS-adenosyl-l-methionine Enzyme NosL From a Substrate Analogue and the Shunt Products. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509900] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xinjian Ji
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Youli Jia
- Department of Chemistry; Fudan University; Shanghai 200433 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering; Gansu Province Lanzhou 730000 China
| | - Wei Ding
- Department of Chemistry; Fudan University; Shanghai 200433 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering; Gansu Province Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
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532
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Ji X, Li Y, Jia Y, Ding W, Zhang Q. Mechanistic Insights into the RadicalS-adenosyl-l-methionine Enzyme NosL From a Substrate Analogue and the Shunt Products. Angew Chem Int Ed Engl 2016; 55:3334-7. [DOI: 10.1002/anie.201509900] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Xinjian Ji
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Youli Jia
- Department of Chemistry; Fudan University; Shanghai 200433 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering; Gansu Province Lanzhou 730000 China
| | - Wei Ding
- Department of Chemistry; Fudan University; Shanghai 200433 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering; Gansu Province Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
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533
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Suess DLM, Pham CC, Bürstel I, Swartz JR, Cramer SP, Britt RD. The Radical SAM Enzyme HydG Requires Cysteine and a Dangler Iron for Generating an Organometallic Precursor to the [FeFe]-Hydrogenase H-Cluster. J Am Chem Soc 2016; 138:1146-9. [PMID: 26764535 DOI: 10.1021/jacs.5b12512] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Three maturase enzymes-HydE, HydF, and HydG-synthesize and insert the organometallic component of the [FeFe]-hydrogenase active site (the H-cluster). HydG generates the first organometallic intermediates in this process, ultimately producing an [Fe(CO)2(CN)] complex. A limitation in understanding the mechanism by which this complex forms has been uncertainty regarding the precise metallocluster composition of HydG that comprises active enzyme. We herein show that the HydG auxiliary cluster must bind both l-cysteine and a dangler Fe in order to generate the [Fe(CO)2(CN)] product. These findings support a mechanistic framework in which a [(Cys)Fe(CO)2(CN)](-) species is a key intermediate in H-cluster maturation.
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Affiliation(s)
- Daniel L M Suess
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Cindy C Pham
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | | | | | - Stephen P Cramer
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
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534
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Darensbourg MY, Llobet A. Preface for Small Molecule Activation: From Biological Principles to Energy Applications. Part 3: Small Molecules Related to (Artificial) Photosynthesis. Inorg Chem 2016; 55:371-7. [PMID: 26782691 DOI: 10.1021/acs.inorgchem.5b02925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marcetta Y Darensbourg
- Department of Chemistry, Texas A&M University , College Station, Texas 77845, United States
| | - Antoni Llobet
- Departament de Quı́mica, Universitat Autònoma de Barcelona , Cerdanyola del Vallès, 08193 Barcelona, Spain
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535
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Suess DLM, Kuchenreuther JM, De La Paz L, Swartz JR, Britt RD. Biosynthesis of the [FeFe] Hydrogenase H Cluster: A Central Role for the Radical SAM Enzyme HydG. Inorg Chem 2016; 55:478-87. [PMID: 26703931 PMCID: PMC4780679 DOI: 10.1021/acs.inorgchem.5b02274] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hydrogenase enzymes catalyze the rapid and reversible interconversion of H2 with protons and electrons. The active site of the [FeFe] hydrogenase is the H cluster, which consists of a [4Fe-4S]H subcluster linked to an organometallic [2Fe]H subcluster. Understanding the biosynthesis and catalytic mechanism of this structurally unusual active site will aid in the development of synthetic and biological hydrogenase catalysts for applications in solar fuel generation. The [2Fe]H subcluster is synthesized and inserted by three maturase enzymes-HydE, HydF, and HydG-in a complex process that involves inorganic, organometallic, and organic radical chemistry. HydG is a member of the radical S-adenosyl-l-methionine (SAM) family of enzymes and is thought to play a prominent role in [2Fe]H subcluster biosynthesis by converting inorganic Fe(2+), l-cysteine (Cys), and l-tyrosine (Tyr) into an organometallic [(Cys)Fe(CO)2(CN)](-) intermediate that is eventually incorporated into the [2Fe]H subcluster. In this Forum Article, the mechanism of [2Fe]H subcluster biosynthesis is discussed with a focus on how this key [(Cys)Fe(CO)2(CN)](-) species is formed. Particular attention is given to the initial metallocluster composition of HydG, the modes of substrate binding (Fe(2+), Cys, Tyr, and SAM), the mechanism of SAM-mediated Tyr cleavage to CO and CN(-), and the identification of the final organometallic products of the reaction.
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Affiliation(s)
- Daniel L. M. Suess
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Jon M. Kuchenreuther
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Liliana De La Paz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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536
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Saichana N, Tanizawa K, Pechoušek J, Novák P, Yakushi T, Toyama H, Frébortová J. PqqE from Methylobacterium extorquens AM1: a radical S-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen. J Biochem 2016; 159:87-99. [PMID: 26188050 PMCID: PMC4882640 DOI: 10.1093/jb/mvv073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/01/2015] [Indexed: 11/12/2022] Open
Abstract
Methylobacterium extorquens AM1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (PQQ), a cofactor of a number of bacterial dehydrogenases, into the culture medium. To elucidate the molecular mechanism of PQQ biosynthesis, we are focusing on PqqE which is believed to be the enzyme catalysing the first reaction of the pathway. PqqE belongs to the radical S-adenosyl-l-methionine (SAM) superfamily, in which most, if not all, enzymes are very sensitive to dissolved oxygen and rapidly inactivated under aerobic conditions. We here report that PqqE from M. extorquens AM1 is markedly oxygen-tolerant; it was efficiently expressed in Escherichia coli cells grown aerobically and affinity-purified to near homogeneity. The purified and reconstituted PqqE contained multiple (likely three) iron-sulphur clusters and showed the reductive SAM cleavage activity that was ascribed to the consensus [4Fe-4S](2+) cluster bound at the N-terminus region. Mössbauer spectrometric analyses of the as-purified and reconstituted enzymes revealed the presence of [4Fe-4S](2+) and [2Fe-2S](2+) clusters as the major forms with the former being predominant in the reconstituted enzyme. PqqE from M.extorquens AM1 may serve as a convenient tool for studying the molecular mechanism of PQQ biosynthesis, avoiding the necessity of establishing strictly anaerobic conditions.
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Affiliation(s)
- Natsaran Saichana
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research
| | - Katsuyuki Tanizawa
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research
| | - Jiří Pechoušek
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Petr Novák
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, 783 71 Olomouc, Czech Republic
| | - Toshiharu Yakushi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515; and
| | - Hirohide Toyama
- Department of Bioscience and Biotechnology, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Jitka Frébortová
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research;
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537
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Ji X, Liu WQ, Yuan S, Yin Y, Ding W, Zhang Q. Mechanistic study of the radical SAM-dependent amine dehydrogenation reactions. Chem Commun (Camb) 2016; 52:10555-8. [DOI: 10.1039/c6cc05661j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Radical SAM-dependent amine dehydrogenation of tryptophan andl–tyrosine has resulted from the 5′-deoxyadenosyl radical-mediated hydrogen abstraction from the Cα of the substrates.
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Affiliation(s)
- Xinjian Ji
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Wan-Qiu Liu
- Department of Chemistry
- Fudan University
- Shanghai
- China
- School of Life Sciences
| | - Shuguang Yuan
- Institute of Chemical Sciences and Engineering
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Lausanne
- Switzerland
| | - Yue Yin
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Wei Ding
- Department of Chemistry
- Fudan University
- Shanghai
- China
- School of Life Sciences
| | - Qi Zhang
- Department of Chemistry
- Fudan University
- Shanghai
- China
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538
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CO and CN- syntheses by [FeFe]-hydrogenase maturase HydG are catalytically differentiated events. Proc Natl Acad Sci U S A 2015; 113:104-9. [PMID: 26699472 DOI: 10.1073/pnas.1515842113] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The synthesis and assembly of the active site [FeFe] unit of [FeFe]-hydrogenases require at least three maturases. The radical S-adenosyl-l-methionine HydG, the best characterized of these proteins, is responsible for the synthesis of the hydrogenase CO and CN(-) ligands from tyrosine-derived dehydroglycine (DHG). We speculated that CN(-) and the CO precursor (-):CO2H may be generated through an elimination reaction. We tested this hypothesis with both wild type and HydG variants defective in second iron-sulfur cluster coordination by measuring the in vitro production of CO, CN(-), and (-):CO2H-derived formate. We indeed observed formate production under these conditions. We conclude that HydG is a multifunctional enzyme that produces DHG, CN(-), and CO at three well-differentiated catalytic sites. We also speculate that homocysteine, cysteine, or a related ligand could be involved in Fe(CO)x(CN)y transfer to the HydF carrier/scaffold.
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539
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Salamone M, Bietti M. Tuning reactivity and selectivity in hydrogen atom transfer from aliphatic C-H bonds to alkoxyl radicals: role of structural and medium effects. Acc Chem Res 2015; 48:2895-903. [PMID: 26545103 DOI: 10.1021/acs.accounts.5b00348] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hydrogen atom transfer (HAT) is a fundamental reaction that takes part in a wide variety of chemical and biological processes, with relevant examples that include the action of antioxidants, damage to biomolecules and polymers, and enzymatic and biomimetic reactions. Moreover, great attention is currently devoted to the selective functionalization of unactivated aliphatic C-H bonds, where HAT based procedures have been shown to play an important role. In this Account, we describe the results of our recent studies on the role of structural and medium effects on HAT from aliphatic C-H bonds to the cumyloxyl radical (CumO(•)). Quantitative information on the reactivity and selectivity patterns observed in these reactions has been obtained by time-resolved kinetic studies, providing a deeper understanding of the factors that govern HAT from carbon and leading to the definition of useful guidelines for the activation or deactivation of aliphatic C-H bonds toward HAT. In keeping with the electrophilic character of alkoxyl radicals, polar effects can play an important role in the reactions of CumO(•). Electron-rich C-H bonds are activated whereas those that are α to electron withdrawing groups are deactivated toward HAT, with these effects being able to override the thermodynamic preference for HAT from the weakest C-H bond. Stereoelectronic effects can also influence the reactivity of the C-H bonds of ethers, amines, and amides. HAT is most rapid when these bonds can be eclipsed with a lone pair on an adjacent heteroatom or with the π-system of an amide functionality, thus allowing for optimal orbital overlap. In HAT from cyclohexane derivatives, tertiary axial C-H bond deactivation and tertiary equatorial C-H bond activation have been observed. These effects have been explained on the basis of an increase in torsional strain or a release in 1,3-diaxial strain in the HAT transition states, with kH(eq)/kH(ax) ratios that have been shown to exceed one order of magnitude. Medium effects on HAT from aliphatic C-H bonds to CumO(•) have been also investigated. With basic substrates, from large to very large decreases in kH have been measured with increasing solvent hydrogen bond donor (HBD) ability or after addition of protic acids or alkali and alkaline earth metal ions, with kinetic effects that exceed 2 orders of magnitude in the reactions of tertiary alkylamines and alkanamides. Solvent hydrogen bonding, protonation, and metal ion binding increase the electron deficiency and the strength of the C-H bonds of these substrates deactivating these bonds toward HAT, with the extent of this deactivation being modulated by varying the nature of the substrate, solvent, protic acid, and metal ion. These results indicate that through these interactions careful control over the HAT reactivity of basic substrates toward CumO(•) and other electrophilic radicals can be achieved, suggesting moreover that these effects can be exploited in an orthogonal fashion for selective C-H bond functionalization of substrates bearing different basic functionalities.
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Affiliation(s)
- Michela Salamone
- Dipartimento
di Scienze e
Tecnologie Chimiche, Università “Tor Vergata”, Via
della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Massimo Bietti
- Dipartimento
di Scienze e
Tecnologie Chimiche, Università “Tor Vergata”, Via
della Ricerca Scientifica, 1, I-00133 Rome, Italy
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540
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Identification and characterization of functional homologs of nitrogenase cofactor biosynthesis protein NifB from methanogens. Proc Natl Acad Sci U S A 2015; 112:14829-33. [PMID: 26627238 DOI: 10.1073/pnas.1510409112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogenase biosynthesis protein NifB catalyzes the radical S-adenosyl-L-methionine (SAM)-dependent insertion of carbide into the M cluster, the cofactor of the molybdenum nitrogenase from Azotobacter vinelandii. Here, we report the identification and characterization of two naturally "truncated" homologs of NifB from Methanosarcina acetivorans (NifB(Ma)) and Methanobacterium thermoautotrophicum (NifB(Mt)), which contain a SAM-binding domain at the N terminus but lack a domain toward the C terminus that shares homology with NifX, an accessory protein in M cluster biosynthesis. NifB(Ma) and NifB(Mt) are monomeric proteins containing a SAM-binding [Fe4S4] cluster (designated the SAM cluster) and a [Fe4S4]-like cluster pair (designated the K cluster) that can be processed into an [Fe8S9] precursor to the M cluster (designated the L cluster). Further, the K clusters in NifB(Ma) and NifB(Mt) can be converted to L clusters upon addition of SAM, which corresponds to their ability to heterologously donate L clusters to the biosynthetic machinery of A. vinelandii for further maturation into the M clusters. Perhaps even more excitingly, NifB(Ma) and NifB(Mt) can catalyze the removal of methyl group from SAM and the abstraction of hydrogen from this methyl group by 5'-deoxyadenosyl radical that initiates the radical-based incorporation of methyl-derived carbide into the M cluster. The successful identification of NifB(Ma) and NifB(Mt) as functional homologs of NifB not only enabled classification of a new subset of radical SAM methyltransferases that specialize in complex metallocluster assembly, but also provided a new tool for further characterization of the distinctive, NifB-catalyzed methyl transfer and conversion to an iron-bound carbide.
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541
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Prier CK, Arnold FH. Chemomimetic biocatalysis: exploiting the synthetic potential of cofactor-dependent enzymes to create new catalysts. J Am Chem Soc 2015; 137:13992-4006. [PMID: 26502343 DOI: 10.1021/jacs.5b09348] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Despite the astonishing breadth of enzymes in nature, no enzymes are known for many of the valuable catalytic transformations discovered by chemists. Recent work in enzyme design and evolution, however, gives us good reason to think that this will change. We describe a chemomimetic biocatalysis approach that draws from small-molecule catalysis and synthetic chemistry, enzymology, and molecular evolution to discover or create enzymes with non-natural reactivities. We illustrate how cofactor-dependent enzymes can be exploited to promote reactions first established with related chemical catalysts. The cofactors can be biological, or they can be non-biological to further expand catalytic possibilities. The ability of enzymes to amplify and precisely control the reactivity of their cofactors together with the ability to optimize non-natural reactivity by directed evolution promises to yield exceptional catalysts for challenging transformations that have no biological counterparts.
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Affiliation(s)
- Christopher K Prier
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
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542
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Kudo F, Eguchi T. Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs. CHEM REC 2015; 16:4-18. [PMID: 26455715 DOI: 10.1002/tcr.201500210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 11/07/2022]
Abstract
2-Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo-oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS-containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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543
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Lanz ND, Rectenwald JM, Wang B, Kakar ES, Laremore TN, Booker SJ, Silakov A. Characterization of a Radical Intermediate in Lipoyl Cofactor Biosynthesis. J Am Chem Soc 2015; 137:13216-9. [PMID: 26390103 DOI: 10.1021/jacs.5b04387] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipoyl synthase (LipA) catalyzes the final step in the biosynthesis of the lipoyl cofactor, the insertion of two sulfur atoms at C6 and C8 of an n-octanoyl chain. LipA is a member of the radical S-adenosylmethionine (SAM) superfamily of enzymes and uses two [4Fe-4S] clusters to catalyze its transformation. One cluster binds in contact with SAM and donates the requisite electron for the reductive cleavage of SAM to generate two 5'-deoxyadenosyl 5'-radicals, which abstract hydrogen atoms from C6 and C8 of the substrate. By contrast, the second, auxiliary [4Fe-4S] cluster, has been hypothesized to serve as the sulfur donor in the reaction. Such a sacrificial role for an iron-sulfur cluster during catalysis has not been universally accepted. Use of a conjugated 2,4-hexadienoyl-containing substrate analogue has allowed the substrate radical to be trapped and characterized by continuous-wave and pulsed electron paramagnetic resonance methods. Here we report the observation of a (57)Fe hyperfine coupling interaction with the paramagnetic signal, which indicates that the iron-sulfur cluster of LipA and its substrate are within bonding distance.
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Affiliation(s)
- Nicholas D Lanz
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology and §The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Justin M Rectenwald
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology and §The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Bo Wang
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology and §The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Elizabeth S Kakar
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology and §The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Tatiana N Laremore
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology and §The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Squire J Booker
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology and §The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Departments of †Chemistry and ‡Biochemistry and Molecular Biology and §The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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544
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Abstract
Carbon–sulfur biological chemistry encompasses a fascinating area of biochemistry and medicinal chemistry and includes the roles that methionine and S-adenosyl-l-methionine play in cells as well as the chemistry of intracellular thiols such as glutathione. This article, based on the 2014 Bernard Belleau Award lecture, provides an overview of some of the key investigations that were undertaken in this area from a bioorganic perspective. The research has ameliorated our fundamental knowledge of several of the enzymes utilizing these sulfur-containing molecules, has led to the development of several novel 19F biophysical probes, and has explored some of the medicinal chemistry associated with these processes.
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Affiliation(s)
- John F. Honek
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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545
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Density functional theory calculations on the active site of biotin synthase: mechanism of S transfer from the Fe2S2 cluster and the role of 1st and 2nd sphere residues. J Biol Inorg Chem 2015; 20:1147-62. [DOI: 10.1007/s00775-015-1296-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/02/2015] [Indexed: 10/23/2022]
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546
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Abstract
Proton reduction and H2 oxidation are key elementary reactions for solar fuel production. Hydrogenases interconvert H+ and H2 with remarkable efficiency and have therefore received much attention in this context. For [FeFe]-hydrogenases, catalysis occurs at a unique cofactor called the H-cluster. In this article, we discuss ways in which EPR spectroscopy has elucidated aspects of the bioassembly of the H-cluster, with a focus on four case studies: EPR spectroscopic identification of a radical en route to the CO and CN- ligands of the H-cluster, tracing 57Fe from the maturase HydG into the H-cluster, characterization of the auxiliary Fe-S cluster in HydG, and isotopic labeling of the CN- ligands of HydA for electronic structure studies of its Hox state. Advances in cell-free maturation protocols have enabled several of these mechanistic studies, and understanding H-cluster maturation may in turn provide insights leading to improvements in hydrogenase production for biotechnological applications.
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Affiliation(s)
- Daniel L. M. Suess
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - R. David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
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547
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Cysteine as a ligand platform in the biosynthesis of the FeFe hydrogenase H cluster. Proc Natl Acad Sci U S A 2015; 112:11455-60. [PMID: 26324916 DOI: 10.1073/pnas.1508440112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Hydrogenases catalyze the redox interconversion of protons and H2, an important reaction for a number of metabolic processes and for solar fuel production. In FeFe hydrogenases, catalysis occurs at the H cluster, a metallocofactor comprising a [4Fe-4S]H subcluster coupled to a [2Fe]H subcluster bound by CO, CN(-), and azadithiolate ligands. The [2Fe]H subcluster is assembled by the maturases HydE, HydF, and HydG. HydG is a member of the radical S-adenosyl-L-methionine family of enzymes that transforms Fe and L-tyrosine into an [Fe(CO)2(CN)] synthon that is incorporated into the H cluster. Although it is thought that the site of synthon formation in HydG is the "dangler" Fe of a [5Fe] cluster, many mechanistic aspects of this chemistry remain unresolved including the full ligand set of the synthon, how the dangler Fe initially binds to HydG, and how the synthon is released at the end of the reaction. To address these questions, we herein show that L-cysteine (Cys) binds the auxiliary [4Fe-4S] cluster of HydG and further chelates the dangler Fe. We also demonstrate that a [4Fe-4S]aux[CN] species is generated during HydG catalysis, a process that entails the loss of Cys and the [Fe(CO)2(CN)] fragment; on this basis, we suggest that Cys likely completes the coordination sphere of the synthon. Thus, through spectroscopic analysis of HydG before and after the synthon is formed, we conclude that Cys serves as the ligand platform on which the synthon is built and plays a role in both Fe(2+) binding and synthon release.
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548
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Chatgilialoglu C, Ferreri C, Matyjaszewski K. Radicals and Dormant Species in Biology and Polymer Chemistry. Chempluschem 2015; 81:11-29. [DOI: 10.1002/cplu.201500271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Indexed: 12/20/2022]
Affiliation(s)
| | - Carla Ferreri
- I.S.O.F.-BioFreeRadicals; Consiglio Nazionale delle Ricerche; Via P. Gobetti 101 Bologna 40129 Italy
| | - Krzysztof Matyjaszewski
- Department of Chemistry; Carnegie Mellon University; 4400 Fifth Avenue Pittsburgh PA 15213 USA
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549
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Consecutive radical S-adenosylmethionine methylations form the ethyl side chain in thienamycin biosynthesis. Proc Natl Acad Sci U S A 2015; 112:10354-8. [PMID: 26240322 DOI: 10.1073/pnas.1508615112] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite their broad anti-infective utility, the biosynthesis of the paradigm carbapenem antibiotic, thienamycin, remains largely unknown. Apart from the first two steps shared with a simple carbapenem, the pathway sharply diverges to the more structurally complex members of this class of β-lactam antibiotics, such as thienamycin. Existing evidence points to three putative cobalamin-dependent radical S-adenosylmethionine (RS) enzymes, ThnK, ThnL, and ThnP, as potentially being responsible for assembly of the ethyl side chain at C6, bridgehead epimerization at C5, installation of the C2-thioether side chain, and C2/3 desaturation. The C2 substituent has been demonstrated to be derived by stepwise truncation of CoA, but the timing of these events with respect to C2-S bond formation is not known. We show that ThnK of the three apparent cobalamin-dependent RS enzymes performs sequential methylations to build out the C6-ethyl side chain in a stereocontrolled manner. This enzymatic reaction was found to produce expected RS methylase coproducts S-adenosylhomocysteine and 5'-deoxyadenosine, and to require cobalamin. For double methylation to occur, the carbapenam substrate must bear a CoA-derived C2-thioether side chain, implying the activity of a previous sulfur insertion by an as-yet unidentified enzyme. These insights allow refinement of the central steps in complex carbapenem biosynthesis.
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550
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Albertini M, Galazzo L, Maso L, Vallese F, Berto P, De Rosa E, Di Valentin M, Costantini P, Carbonera D. Characterization of the [FeFe]-Hydrogenase Maturation Protein HydF by EPR Techniques: Insights into the Catalytic Mechanism. Top Catal 2015. [DOI: 10.1007/s11244-015-0413-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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