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Reyes JS, Fuentes-Lemus E, Aspée A, Davies MJ, Monasterio O, López-Alarcón C. M. jannaschii FtsZ, a key protein in bacterial cell division, is inactivated by peroxyl radical-mediated methionine oxidation. Free Radic Biol Med 2021; 166:53-66. [PMID: 33588048 DOI: 10.1016/j.freeradbiomed.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022]
Abstract
Oxidation and inactivation of FtsZ is of interest due to the key role of this protein in bacterial cell division. In the present work, we studied peroxyl radical (from AAPH, 2,2'-azobis(2-methylpropionamidine)dihydrochloride) mediated oxidation of the highly stable FtsZ protein (MjFtsZ) from M. jannaschii, a thermophilic microorganism. MjFtsZ contains eleven Met, and single Tyr and Trp residues which would be expected to be susceptible to oxidation. We hypothesized that exposure of MjFtsZ to AAPH-derived radicals would induce Met oxidation, and cross-linking (via di-Tyr and di-Trp formation), with concomitant loss of its functional polymerization and depolymerization (GTPase) activities. Solutions containing MjFtsZ and AAPH (10 or 100 mM) were incubated at 37 °C for 3 h. Polymerization/depolymerization were assessed by light scattering, while changes in mass were analyzed by SDS-PAGE. Amino acid consumption was quantified by HPLC with fluorescence detection, or direct fluorescence (Trp). Oxidation products and modifications at individual Met residues were quantified by UPLC with mass detection. Oxidation inhibited polymerization-depolymerization activity, and yielded low levels of irreversible protein dimers. With 10 mM AAPH only Trp and Met were consumed giving di-alcohols, kynurenine and di-Trp (from Trp) and the sulfoxide (from Met). With 100 mM AAPH low levels of Tyr oxidation (but not di-Tyr formation) were also observed. Correlation with the functional analyses indicates that Met oxidation, and particularly Met164 is the key driver of MjFtsZ inactivation, probably as a result of the position of this residue at the protein-protein interface of longitudinal interactions and in close proximity to the GTP binding site.
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Affiliation(s)
- Juan Sebastián Reyes
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile; Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
| | - Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Alexis Aspée
- Departamento de Ciencias Del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile.
| | - Camilo López-Alarcón
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile.
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2
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Cornell KA, Knippel RJ, Cortright GR, Fonken M, Guerrero C, Hall AR, Mitchell KA, Thurston JH, Erstad P, Tao A, Xu D, Parveen N. Characterization of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases from Borrelia burgdorferi: Antibiotic targets for Lyme disease. Biochim Biophys Acta Gen Subj 2019; 1864:129455. [PMID: 31669585 DOI: 10.1016/j.bbagen.2019.129455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/23/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Borrelia burgdorferi causes Lyme disease, the most common tick-borne illness in the United States. The Center for Disease Control and Prevention estimates that the occurrence of Lyme disease in the U.S. has now reached approximately 300,000 cases annually. Early stage Borrelia burgdorferi infections are generally treatable with oral antibiotics, but late stage disease is more difficult to treat and more likely to lead to post-treatment Lyme disease syndrome. METHODS Here we examine three unique 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidases (MTNs or MTANs, EC 3.2.2.9) responsible for salvage of adenine and methionine in B. burgdorferi and explore their potential as antibiotic targets to treat Lyme disease. Recombinant Borrelia MTNs were expressed and purified from E. coli. The enzymes were extensively characterized for activity, specificity, and inhibition using a UV spectrophotometric assay. In vitro antibiotic activities of MTN inhibitors were assessed using a bioluminescent BacTiter-Glo™ assay. RESULTS The three Borrelia MTNs showed unique activities against the native substrates MTA, SAH, and 5'-deoxyadenosine. Analysis of substrate analogs revealed that specific activity rapidly dropped as the length of the 5'-alkylthio substitution increased. Non-hydrolysable nucleoside transition state analogs demonstrated sub-nanomolar enzyme inhibition constants. Lastly, two late stage transition state analogs exerted in vitro IC50 values of 0.3-0.4 μg/mL against cultured B. burgdorferi cells. CONCLUSION B. burgdorferi is unusual in that it expresses three distinct MTNs (cytoplasmic, membrane bound, and secreted) that are effectively inactivated by nucleoside analogs. GENERAL SIGNIFICANCE The Borrelia MTNs appear to be promising targets for developing new antibiotics to treat Lyme disease.
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Affiliation(s)
- Kenneth A Cornell
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA; Biomolecular Research Center, Boise State University, Boise, ID, USA.
| | - Reece J Knippel
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Gerald R Cortright
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Meghan Fonken
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Christian Guerrero
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Amy R Hall
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID, USA
| | - Kristen A Mitchell
- Biomolecular Research Center, Boise State University, Boise, ID, USA; Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - John H Thurston
- Department of Chemistry, The College of Idaho, Caldwell, ID, USA
| | - Patrick Erstad
- Department of Chemistry, The College of Idaho, Caldwell, ID, USA; Department of Biomedical & Pharmaceutical Sciences, Idaho State University, Meridian, ID, USA
| | - Aoxiang Tao
- Department of Biomedical & Pharmaceutical Sciences, Idaho State University, Meridian, ID, USA
| | - Dong Xu
- Department of Biomedical & Pharmaceutical Sciences, Idaho State University, Meridian, ID, USA
| | - Nikhat Parveen
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
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Vagstad AL, Kuranaga T, Püntener S, Pattabiraman VR, Bode JW, Piel J. Introduction of
d
‐Amino Acids in Minimalistic Peptide Substrates by an
S
‐Adenosyl‐
l
‐Methionine Radical Epimerase. Angew Chem Int Ed Engl 2019; 58:2246-2250. [DOI: 10.1002/anie.201809508] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/08/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Anna L. Vagstad
- Institute of MicrobiologyEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical SciencesKyoto University Kyoto 606-8501 Japan
| | - Salome Püntener
- Institute of MicrobiologyEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Vijaya R. Pattabiraman
- Laboratory of Organic ChemistryEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jeffrey W. Bode
- Laboratory of Organic ChemistryEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jörn Piel
- Institute of MicrobiologyEidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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4
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Vagstad AL, Kuranaga T, Püntener S, Pattabiraman VR, Bode JW, Piel J. Introduction of d
-Amino Acids in Minimalistic Peptide Substrates by an S
-Adenosyl-l
-Methionine Radical Epimerase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809508] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Anna L. Vagstad
- Institute of Microbiology; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences; Kyoto University; Kyoto 606-8501 Japan
| | - Salome Püntener
- Institute of Microbiology; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Vijaya R. Pattabiraman
- Laboratory of Organic Chemistry; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jeffrey W. Bode
- Laboratory of Organic Chemistry; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jörn Piel
- Institute of Microbiology; Eidgenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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5
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Miller DV, Rauch BJ, Harich K, Xu H, Perona JJ, White RH. Promiscuity of methionine salvage pathway enzymes in Methanocaldococcus jannaschii. MICROBIOLOGY-SGM 2018; 164:969-981. [PMID: 29877790 DOI: 10.1099/mic.0.000670] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The methionine salvage pathway (MSP) is critical for regeneration of S-adenosyl-l-methionine (SAM), a widely used cofactor involved in many essential metabolic reactions. The MSP has been completely elucidated in aerobic organisms, and found to rely on molecular oxygen. Since anaerobic organisms do not use O2, an alternative pathway(s) must be operating. We sought to evaluate whether the functions of two annotated MSP enzymes from Methanocaldococcus jannaschii, a methylthioinosine phosphorylase (MTIP) and a methylthioribose 1-phosphate isomerase (MTRI), are consistent with functioning in a modified anaerobic MSP (AnMSP). We show here that recombinant MTIP is active with six different purine nucleosides, consistent with its function as a general purine nucleoside phosphorylase for both AnMSP and purine salvage. Recombinant MTRI is active with both 5-methylthioribose 1-phosphate and 5-deoxyribose 1-phosphate as substrates, which are generated from phosphororolysis of 5'-methylthioinosine and 5'-deoxyinosine by MTIP, respectively. Together, these data suggest that MTIP and MTRI may function in a novel pathway for recycling the 5'-deoxyadenosine moiety of SAM in M. jannaschii. These enzymes may also enable biosynthesis of 6-deoxy-5-ketofructose 1-phosphate (DKFP), an essential intermediate in aromatic amino acid biosynthesis. Finally, we utilized a homocysteine auxotrophic strain of Methanosarcina acetivorans Δma1821-22Δoahs (HcyAux) to identify potential AnMSP intermediates in vivo. Growth recovery experiments of the M. acetivorans HcyAux were performed with known and proposed intermediates for the AnMSP. Only one metabolite, 2-keto-(4-methylthio)butyric acid, rescued growth of M. acetivorans HcyAux in the absence of homocysteine. This observation may indicate that AnMSP pathways substantially differ among methanogens from phylogenetically divergent genera.
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Affiliation(s)
- Danielle V Miller
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.,Present address: Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Benjamin J Rauch
- Department of Chemistry, Portland State University, Portland, OR, USA.,Present address: Zymergen, Inc., 1650 65th Street, Emeryville, CA 94608, USA
| | - Kim Harich
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Huimin Xu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - John J Perona
- Department of Chemistry, Portland State University, Portland, OR, USA.,Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR, USA
| | - Robert H White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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6
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Dinis P, Wieckowski BM, Roach PL. Metallocofactor assembly for [FeFe]-hydrogenases. Curr Opin Struct Biol 2016; 41:90-97. [PMID: 27344601 DOI: 10.1016/j.sbi.2016.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/05/2016] [Accepted: 06/06/2016] [Indexed: 11/27/2022]
Abstract
Hydrogenases are a potential source of environmentally benign bioenergy, using complex cofactors to catalyze the reversible reduction of protons to form hydrogen. The most active subclass, the [FeFe]-hydrogenases, is dependent on a metallocofactor, the H cluster, that consists of a two iron subcluster ([2Fe]H) bridging to a classical cubane cluster ([4Fe-4S]H). The ligands coordinating to the diiron subcluster include an azadithiolate, three carbon monoxides, and two cyanides. To assemble this complex cofactor, three maturase enzymes, HydG, HydE and HydF are required. The biosynthesis of the diatomic ligands proceeds by an unusual fragmentation mechanism, and structural studies in combination with spectroscopic analysis have started to provide insights into the HydG mediated assembly of a [2Fe]H subcluster precursor.
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Affiliation(s)
- Pedro Dinis
- Chemistry and the Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Beata M Wieckowski
- Chemistry and the Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Peter L Roach
- Chemistry and the Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
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7
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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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8
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Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions. Biochem J 2015; 464:123-33. [PMID: 25100160 DOI: 10.1042/bj20140895] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Lipoyl cofactors are essential for living organisms and are produced by the insertion of two sulfur atoms into the relatively unreactive C-H bonds of an octanoyl substrate. This reaction requires lipoyl synthase, a member of the radical S-adenosylmethionine (SAM) enzyme superfamily. In the present study, we solved crystal structures of lipoyl synthase with two [4Fe-4S] clusters bound at opposite ends of the TIM barrel, the usual fold of the radical SAM superfamily. The cluster required for reductive SAM cleavage conserves the features of the radical SAM superfamily, but the auxiliary cluster is bound by a CX4CX5C motif unique to lipoyl synthase. The fourth ligand to the auxiliary cluster is an extremely unusual serine residue. Site-directed mutants show this conserved serine ligand is essential for the sulfur insertion steps. One crystallized lipoyl synthase (LipA) complex contains 5'-methylthioadenosine (MTA), a breakdown product of SAM, bound in the likely SAM-binding site. Modelling has identified an 18 Å (1 Å=0.1 nm) deep channel, well-proportioned to accommodate an octanoyl substrate. These results suggest that the auxiliary cluster is the likely sulfur donor, but access to a sulfide ion for the second sulfur insertion reaction requires the loss of an iron atom from the auxiliary cluster, which the serine ligand may enable.
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9
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Cammack R, Balk J. Iron-sulfur Clusters. BINDING, TRANSPORT AND STORAGE OF METAL IONS IN BIOLOGICAL CELLS 2014. [DOI: 10.1039/9781849739979-00333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Iron-sulfur clusters are universally distributed groups occurring in iron-sulfur proteins. They have a wide range of cellular functions which reflect the chemistry of the clusters. Some clusters are involved in electron transport and energy transduction in photosynthesis and respiration. Others can bind substrates and participate in enzyme catalysis. Regulatory functions have also been documented for clusters that respond to oxygen partial pressure and iron availability. Finally, there are some for which no function has been defined; they may act as stabilizing structures, for example, in enzymes involved in nucleic acid metabolism. The clusters are constructed intracellularly and inserted into proteins, which can then be transported to intracellular targets, in some cases, across membranes. Three different types of iron-sulfur cluster assembly machinery have evolved in prokaryotes: NIF, ISC and SUF. Each system involves a scaffold protein on which the cluster is constructed (encoded by genes nifU, iscU, sufU or sufB) and a cysteine desulfurase (encoded by nifS, iscS or sufS) which provides the sulfide sulfur. In eukaryotic cells, clusters are formed in the mitochondria for the many iron-sulfur proteins in this organelle. The mitochondrial biosynthesis pathway is linked to the cytoplasmic iron-sulfur assembly system (CIA) for the maturation of cytoplasmic and nuclear iron-sulfur proteins. In plant cells, a SUF-type system is used for cluster assembly in the plastids. Many accessory proteins are involved in cluster transfer before insertion into the appropriate sites in Fe-S proteins.
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Affiliation(s)
- Richard Cammack
- King's College London, Department of Biochemistry, 150 Stamford Street London SE1 9NH UK
| | - Janneke Balk
- John Innes Centre and University of East Anglia Norwich Research Park, Colney Lane Norwich NR4 7UH UK
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10
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X-ray analysis of butirosin biosynthetic enzyme BtrN redefines structural motifs for AdoMet radical chemistry. Proc Natl Acad Sci U S A 2013; 110:15949-54. [PMID: 24048029 DOI: 10.1073/pnas.1312228110] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 2-deoxy-scyllo-inosamine (DOIA) dehydrogenases are key enzymes in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics. In contrast to most DOIA dehydrogenases, which are NAD-dependent, the DOIA dehydrogenase from Bacillus circulans (BtrN) is an S-adenosyl-l-methionine (AdoMet) radical enzyme. To examine how BtrN employs AdoMet radical chemistry, we have determined its structure with AdoMet and substrate to 1.56 Å resolution. We find a previously undescribed modification to the core AdoMet radical fold: instead of the canonical (β/α)6 architecture, BtrN displays a (β5/α4) motif. We further find that an auxiliary [4Fe-4S] cluster in BtrN, thought to bind substrate, is instead implicated in substrate-radical oxidation. High structural homology in the auxiliary cluster binding region between BtrN, fellow AdoMet radical dehydrogenase anSME, and molybdenum cofactor biosynthetic enzyme MoaA provides support for the establishment of an AdoMet radical structural motif that is likely common to ~6,400 uncharacterized AdoMet radical enzymes.
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11
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Palmer LD, Downs DM. The thiamine biosynthetic enzyme ThiC catalyzes multiple turnovers and is inhibited by S-adenosylmethionine (AdoMet) metabolites. J Biol Chem 2013; 288:30693-30699. [PMID: 24014032 DOI: 10.1074/jbc.m113.500280] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ThiC (4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase; EC 4.1.99.17) is a radical S-adenosylmethionine (AdoMet) enzyme that uses a [4Fe-4S](+) cluster to reductively cleave AdoMet to methionine and a 5'-deoxyadenosyl radical that initiates catalysis. In plants and bacteria, ThiC converts the purine intermediate 5-aminoimidazole ribotide to 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate, an intermediate of thiamine pyrophosphate (coenzyme B1) biosynthesis. In this study, assay conditions were implemented that consistently generated 5-fold molar excess of HMP, demonstrating that ThiC undergoes multiple turnovers. ThiC activity was improved by in situ removal of product 5'-deoxyadenosine. The activity was inhibited by AdoMet metabolites S-adenosylhomocysteine, adenosine, 5'-deoxyadenosine, S-methyl-5'-thioadenosine, methionine, and homocysteine. Neither adenosine nor S-methyl-5'-thioadenosine had been shown to inhibit radical AdoMet enzymes, suggesting that ThiC is distinct from other family members. The parameters for improved ThiC activity and turnover described here will facilitate kinetic and mechanistic analyses of ThiC.
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Affiliation(s)
- Lauren D Palmer
- From the Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Diana M Downs
- From the Department of Microbiology, University of Georgia, Athens, Georgia 30602.
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12
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X-ray structure of an AdoMet radical activase reveals an anaerobic solution for formylglycine posttranslational modification. Proc Natl Acad Sci U S A 2013; 110:8519-24. [PMID: 23650368 DOI: 10.1073/pnas.1302417110] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arylsulfatases require a maturating enzyme to perform a co- or posttranslational modification to form a catalytically essential formylglycine (FGly) residue. In organisms that live aerobically, molecular oxygen is used enzymatically to oxidize cysteine to FGly. Under anaerobic conditions, S-adenosylmethionine (AdoMet) radical chemistry is used. Here we present the structures of an anaerobic sulfatase maturating enzyme (anSME), both with and without peptidyl-substrates, at 1.6-1.8 Å resolution. We find that anSMEs differ from their aerobic counterparts in using backbone-based hydrogen-bonding patterns to interact with their peptidyl-substrates, leading to decreased sequence specificity. These anSME structures from Clostridium perfringens are also the first of an AdoMet radical enzyme that performs dehydrogenase chemistry. Together with accompanying mutagenesis data, a mechanistic proposal is put forth for how AdoMet radical chemistry is coopted to perform a dehydrogenation reaction. In the oxidation of cysteine or serine to FGly by anSME, we identify D277 and an auxiliary [4Fe-4S] cluster as the likely acceptor of the final proton and electron, respectively. D277 and both auxiliary clusters are housed in a cysteine-rich C-terminal domain, termed SPASM domain, that contains homology to ~1,400 other unique AdoMet radical enzymes proposed to use [4Fe-4S] clusters to ligate peptidyl-substrates for subsequent modification. In contrast to this proposal, we find that neither auxiliary cluster in anSME bind substrate, and both are fully ligated by cysteine residues. Instead, our structural data suggest that the placement of these auxiliary clusters creates a conduit for electrons to travel from the buried substrate to the protein surface.
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13
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Grove TL, Ahlum JH, Qin RM, Lanz ND, Radle MI, Krebs C, Booker SJ. Further characterization of Cys-type and Ser-type anaerobic sulfatase maturating enzymes suggests a commonality in the mechanism of catalysis. Biochemistry 2013; 52:2874-87. [PMID: 23477283 DOI: 10.1021/bi400136u] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The anaerobic sulfatase-maturating enzyme from Clostridium perfringens (anSMEcpe) catalyzes the two-electron oxidation of a cysteinyl residue on a cognate protein to a formylglycyl residue (FGly) using a mechanism that involves organic radicals. The FGly residue plays a unique role as a cofactor in a class of enzymes termed arylsulfatases, which catalyze the hydrolysis of various organosulfate monoesters. anSMEcpe has been shown to be a member of the radical S-adenosylmethionine (SAM) family of enzymes, [4Fe-4S] cluster-requiring proteins that use a 5'-deoxyadenosyl 5'-radical (5'-dA(•)) generated from a reductive cleavage of SAM to initiate radical-based catalysis. Herein, we show that anSMEcpe contains in addition to the [4Fe-4S] cluster harbored by all radical SAM (RS) enzymes, two additional [4Fe-4S] clusters, similar to the radical SAM protein AtsB, which catalyzes the two-electron oxidation of a seryl residue to a FGly residue. We show by size-exclusion chromatography that both AtsB and anSMEcpe are monomeric proteins, and site-directed mutagenesis studies of AtsB reveal that individual Cys → Ala substitutions at seven conserved positions result in an insoluble protein, consistent with those residues acting as ligands to the two additional [4Fe-4S] clusters. Ala substitutions at an additional conserved Cys residue (C291 in AtsB and C276 in anSMEcpe) afford proteins that display intermediate behavior. These proteins exhibit reduced solubility and drastically reduced activity, behavior that is conspicuously similar to that of a critical Cys residue in BtrN, another radical SAM dehydrogenase [Grove, T. L., et al. (2010) Biochemistry 49, 3783-3785]. We also show that wild-type anSMEcpe acts on peptides containing other oxidizable amino acids at the target position. Moreover, we show that the enzyme will convert threonyl peptides to the corresponding ketone product, and also allo-threonyl peptides, but with a significantly reduced efficiency, suggesting that the pro-S hydrogen atom of the normal cysteinyl substrate is stereoselectively removed during turnover. Lastly, we show that the electron generated during catalysis by AtsB and anSMEcpe can be utilized for multiple turnovers, albeit through a reduced flavodoxin-mediated pathway.
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Affiliation(s)
- Tyler L Grove
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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