1
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Levin BJ, Huang YY, Peck SC, Wei Y, Martínez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science 2017; 355:355/6325/eaai8386. [PMID: 28183913 DOI: 10.1126/science.aai8386] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/04/2017] [Indexed: 12/14/2022]
Abstract
The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate trans-4-hydroxy-l-proline, the product of the most abundant human posttranslational modification. This "chemically guided functional profiling" workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities.
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Affiliation(s)
- B J Levin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Y Y Huang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - S C Peck
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Y Wei
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Martínez-Del Campo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - J A Marks
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - E A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute, Cambridge, MA 02139, USA
| | - C Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute, Cambridge, MA 02139, USA
| | - E P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. .,Broad Institute, Cambridge, MA 02139, USA
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2
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Selvaraj B, Buckel W, Golding BT, Ullmann GM, Martins BM. Structure and Function of 4-Hydroxyphenylacetate Decarboxylase and Its Cognate Activating Enzyme. J Mol Microbiol Biotechnol 2016; 26:76-91. [DOI: 10.1159/000440882] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
4-Hydroxyphenylacetate decarboxylase (4Hpad) is the prototype of a new class of Fe-S cluster-dependent glycyl radical enzymes (Fe-S GREs) acting on aromatic compounds. The two-enzyme component system comprises a decarboxylase responsible for substrate conversion and a dedicated activating enzyme (4Hpad-AE). The decarboxylase uses a glycyl/thiyl radical dyad to convert 4-hydroxyphenylacetate into <i>p</i>-cresol (4-methylphenol) by a biologically unprecedented Kolbe-type decarboxylation. In addition to the radical dyad prosthetic group, the decarboxylase unit contains two [4Fe-4S] clusters coordinated by an extra small subunit of unknown function. 4Hpad-AE reductively cleaves S-adenosylmethionine (SAM or AdoMet) at a site-differentiated [4Fe-4S]<sup>2+/+</sup> cluster (RS cluster) generating a transient 5′-deoxyadenosyl radical that produces a stable glycyl radical in the decarboxylase by the abstraction of a hydrogen atom. 4Hpad-AE binds up to two auxiliary [4Fe-4S] clusters coordinated by a ferredoxin-like insert that is C-terminal to the RS cluster-binding motif. The ferredoxin-like domain with its two auxiliary clusters is not vital for SAM-dependent glycyl radical formation in the decarboxylase, but facilitates a longer lifetime for the radical. This review describes the 4Hpad and cognate AE families and focuses on the recent advances and open questions concerning the structure, function and mechanism of this novel Fe-S-dependent class of GREs.
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3
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Shibata N, Toraya T. Molecular architectures and functions of radical enzymes and their (re)activating proteins. J Biochem 2015; 158:271-92. [PMID: 26261050 DOI: 10.1093/jb/mvv078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023] Open
Abstract
Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named 'radical enzymes'. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undesired side reactions of highly reactive radicals and how they are (re)activated when inactivated by extinction of radicals. This review highlights molecular architectures of radical B12 enzymes, radical SAM enzymes, tyrosyl radical enzymes, glycyl radical enzymes and their (re)activating proteins that support their functions. For generalization, comparisons of the recently reported structures of radical enzymes with those of canonical radical enzymes are summarized here.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan and
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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4
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Lundin D, Berggren G, Logan DT, Sjöberg BM. The origin and evolution of ribonucleotide reduction. Life (Basel) 2015; 5:604-36. [PMID: 25734234 PMCID: PMC4390871 DOI: 10.3390/life5010604] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs.
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Affiliation(s)
- Daniel Lundin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Gustav Berggren
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
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5
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Khelifi N, Amin Ali O, Roche P, Grossi V, Brochier-Armanet C, Valette O, Ollivier B, Dolla A, Hirschler-Réa A. Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus. THE ISME JOURNAL 2014; 8:2153-66. [PMID: 24763368 PMCID: PMC4992073 DOI: 10.1038/ismej.2014.58] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/11/2014] [Accepted: 03/16/2014] [Indexed: 11/08/2022]
Abstract
The thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain VC-16 (DSM 4304), which is known to oxidize fatty acids and n-alkenes, was shown to oxidize saturated hydrocarbons (n-alkanes in the range C10-C21) with thiosulfate or sulfate as a terminal electron acceptor. The amount of n-hexadecane degradation observed was in stoichiometric agreement with the theoretically expected amount of thiosulfate reduction. One of the pathways used by anaerobic microorganisms to activate alkanes is addition to fumarate that involves alkylsuccinate synthase as a key enzyme. A search for genes encoding homologous enzymes in A. fulgidus identified the pflD gene (locus-tag AF1449) that was previously annotated as a pyruvate formate lyase. A phylogenetic analysis revealed that this gene is of bacterial origin and was likely acquired by A. fulgidus from a bacterial donor through a horizontal gene transfer. Based on three-dimensional modeling of the corresponding protein and molecular dynamic simulations, we hypothesize an alkylsuccinate synthase activity for this gene product. The pflD gene expression was upregulated during the growth of A. fulgidus on an n-alkane (C16) compared with growth on a fatty acid. Our results suggest that anaerobic alkane degradation in A. fulgidus may involve the gene pflD in alkane activation through addition to fumarate. These findings highlight the possible importance of hydrocarbon oxidation at high temperatures by A. fulgidus in hydrothermal vents and the deep biosphere.
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Affiliation(s)
- Nadia Khelifi
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, Marseille, France
| | - Oulfat Amin Ali
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, Marseille, France
| | - Philippe Roche
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Vincent Grossi
- Université de Lyon, Université Lyon 1, CNRS, UMR 5276, Laboratoire de Géologie de Lyon, Villeurbanne, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB UMR 7283, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, CNRS, LCB UMR 7283, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, Marseille, France
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6
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Bharadwaj VS, Dean AM, Maupin CM. Insights into the Glycyl Radical Enzyme Active Site of Benzylsuccinate Synthase: A Computational Study. J Am Chem Soc 2013; 135:12279-88. [DOI: 10.1021/ja404842r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vivek S. Bharadwaj
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - Anthony M. Dean
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
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7
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Diversity of benzylsuccinate synthase-like (bssA) genes in hydrocarbon-polluted marine sediments suggests substrate-dependent clustering. Appl Environ Microbiol 2013; 79:3667-76. [PMID: 23563947 DOI: 10.1128/aem.03934-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The potential of hydrocarbon biodegradation in marine sediments was determined through the detection of a functional biomarker, the bssA gene, coding for benzylsuccinate synthase, the key enzyme of anaerobic toluene degradation. Eight bssA clone libraries (409 sequences) were constructed from polluted sediments affected by the Prestige oil spill in the Atlantic Islands National Park and from hydrocarbon-amended sediment microcosms in Mallorca. The amplified products and database-derived bssA-like sequences grouped into four major clusters, as determined by phylogenetic reconstruction, principal coordinate analysis (PCoA), and a subfamily prediction tool. In addition to the classical bssA sequences that were targeted, we were able to detect sequences homologous to the naphthylmethylsuccinate synthase gene (nmsA) and the alkylsuccinate synthase gene (assA), the bssA homologues for anaerobic 2-methylnaphthalene and alkane degradation, respectively. The detection of bssA-like variants was determined by the persistence and level of pollution in the marine samples. The observed level of gene diversity was lower in the Mallorca sediments, which were dominated by assA-like sequences. In contrast, the Atlantic Islands samples, which were highly contaminated with methylnaphthalene-rich crude oil, showed a high proportion of nmsA-like sequences. Some of the detected genes were phylogenetically related to Deltaproteobacteria communities, previously described as the predominant hydrocarbon degraders at these sites. Differences between all detected bssA-like genes described to date indicate separation between marine and terrestrial sequences and further subgrouping according to taxonomic affiliation. Global analysis suggested that bssA homologues appeared to cluster according to substrate specificity. We observed undetected divergent gene lineages of bssA homologues, which evidence the existence of new degrader groups in these environments.
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8
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Dowling DP, Croft AK, Drennan CL. Radical use of Rossmann and TIM barrel architectures for controlling coenzyme B12 chemistry. Annu Rev Biophys 2013; 41:403-27. [PMID: 22577824 DOI: 10.1146/annurev-biophys-050511-102225] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability of enzymes to harness free-radical chemistry allows for some of the most amazing transformations in nature, including reduction of ribonucleotides and carbon skeleton rearrangements. Enzyme cofactors involved in this chemistry can be large and complex, such as adenosylcobalamin (coenzyme B(12)), simpler, such as S-adenosylmethionine and an iron-sulfur cluster (i.e., poor man's B(12)), or very small, such as one nonheme iron atom coordinated by protein ligands. Although the chemistry catalyzed by these enzyme-bound cofactors is unparalleled, it does come at a price. The enzyme must be able to control these radical reactions, preventing unwanted chemistry and protecting the enzyme active site from damage. Here, we consider a set of radical folds: the (β/α)(8) or TIM barrel, combined with a Rossmann domain for coenzyme B(12)-dependent chemistry. Using specific enzyme examples, we consider how nature employs the common TIM barrel fold and its Rossmann domain partner for radical-based chemistry.
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Affiliation(s)
- Daniel P Dowling
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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9
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Moon YJ, Kwon J, Yun SH, Lim HL, Kim MS, Kang SG, Lee JH, Choi JS, Kim SI, Chung YH. Proteome analyses of hydrogen-producing hyperthermophilic archaeon Thermococcus onnurineus NA1 in different one-carbon substrate culture conditions. Mol Cell Proteomics 2012; 11:M111.015420. [PMID: 22232491 DOI: 10.1074/mcp.m111.015420] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Thermococcus onnurineus NA1, a sulfur-reducing hyperthermophilic archaeon, is capable of H(2)-producing growth, considered to be hydrogenogenic carboxydotrophy. Utilization of formate as a sole energy source has been well studied in T. onnurineus NA1. However, whether formate can be used as its carbon source remains unknown. To obtain a global view of the metabolic characteristics of H(2)-producing growth, a quantitative proteome analysis of T. onnurineus NA1 grown on formate, CO, and starch was performed by combining one-dimensional SDS-PAGE with nano UPLC-MS(E). A total of 587 proteins corresponding to 29.7% of the encoding genes were identified, and the major metabolic pathways (especially energy metabolism) were characterized at the protein level. Expression of glycolytic enzymes was common but more highly induced in starch-grown cells. In contrast, enzymes involved in key steps of the gluconeogenesis and pentose phosphate pathways were strongly up-regulated in formate-grown cells, suggesting that formate could be utilized as a carbon source by T. onnurineus NA1. In accordance with the genomic analysis, comprehensive proteomic analysis also revealed a number of hydrogenase clusters apparently associated with formate metabolism. On the other hand, CODH and CO-induced hydrogenases belonging to the Hyg4-II cluster, as well as sulfhydrogenase-I and Mbx, were prominently expressed during CO culture. Our data suggest that CO can be utilized as a sole energy source for H(2) production via an electron transport mechanism and that CO(2) produced from catabolism or CO oxidation by CODH and CO-induced hydrogenases may subsequently be assimilated into the organic carbon. Overall, proteomic comparison of formate- and CO-grown cells with starch-grown cells revealed that a single carbon compound, such as formate and CO, can be utilized as an efficient substrate to provide cellular carbon and/or energy by T. onnurineus NA1.
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Affiliation(s)
- Yoon-Jung Moon
- Division of Life Science, Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
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10
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Martins BM, Blaser M, Feliks M, Ullmann GM, Buckel W, Selmer T. Structural Basis for a Kolbe-Type Decarboxylation Catalyzed by a Glycyl Radical Enzyme. J Am Chem Soc 2011; 133:14666-74. [DOI: 10.1021/ja203344x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Berta M. Martins
- Institute für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Martin Blaser
- Laboratorium für Mikrobiologie, FB Biologie, Philipps-Universität, D-35032 Marburg, Germany
- Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Mikolaj Feliks
- Structural Biology/Bioinformatics, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - G. Matthias Ullmann
- Structural Biology/Bioinformatics, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Wolfgang Buckel
- Laboratorium für Mikrobiologie, FB Biologie, Philipps-Universität, D-35032 Marburg, Germany
- Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Thorsten Selmer
- Laboratorium für Mikrobiologie, FB Biologie, Philipps-Universität, D-35032 Marburg, Germany
- AG Biotechnologie/Enzymtechnologie, Fachhochschule Aachen-Jülich, D-52428 Jülich, Germany
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11
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Pollack JD, Pan X, Pearl DK. Concentration of specific amino acids at the catalytic/active centers of highly-conserved "housekeeping" enzymes of central metabolism in archaea, bacteria and Eukaryota: is there a widely conserved chemical signal of prebiotic assembly? ORIGINS LIFE EVOL B 2010; 40:273-302. [PMID: 20069373 DOI: 10.1007/s11084-009-9188-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 11/04/2009] [Indexed: 10/20/2022]
Abstract
In alignments of 1969 protein sequences the amino acid glycine and others were found concentrated at most-conserved sites within approximately 15 A of catalytic/active centers (C/AC) of highly conserved kinases, dehydrogenases or lyases of Archaea, Bacteria and Eukaryota. Lysine and glutamic acid were concentrated at least-conserved sites furthest from their C/ACs. Logistic-regression analyses corroborated the "movement" of glycine towards and lysine away from their C/ACs: the odds of a glycine occupying a site were decreased by 19%, while the odds for a lysine were increased by 53%, for every 10 A moving away from the C/AC. Average conservation of MSA consensus sites was highest surrounding the C/AC and directly decreased in transition toward model's peripheries. Findings held with statistical confidence using sequences restricted to individual Domains or enzyme classes or to both. Our data describe variability in the rate of mutation and likelihoods for phylogenetic trees based on protein sequence data and endorse the extension of substitution models by incorporating data on conservation and distance to C/ACs rather than only using cumulative levels. The data support the view that in the most-conserved environment immediately surrounding the C/AC of taxonomically distant and highly conserved essential enzymes of central metabolism there are amino acids whose identity and degree of occupancy is similar to a proposed amino acid set and frequency associated with prebiotic evolution.
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Affiliation(s)
- J Dennis Pollack
- Department of Molecular Virology, Immunology and Medical Genetics, The College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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12
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Marsh ENG, Patterson DP, Li L. Adenosyl radical: reagent and catalyst in enzyme reactions. Chembiochem 2010; 11:604-21. [PMID: 20191656 PMCID: PMC3011887 DOI: 10.1002/cbic.200900777] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 12/17/2022]
Abstract
Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.
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Affiliation(s)
- E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Dustin P. Patterson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University – Purdue University Indianapolis, Indianapolis, IN 46202, USA
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13
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Luttringer F, Mulliez E, Dublet B, Lemaire D, Fontecave M. The Zn center of the anaerobic ribonucleotide reductase from E. coli. J Biol Inorg Chem 2009; 14:923-33. [DOI: 10.1007/s00775-009-0505-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 04/07/2009] [Indexed: 11/24/2022]
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14
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Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme. Proc Natl Acad Sci U S A 2008; 105:16137-41. [PMID: 18852451 DOI: 10.1073/pnas.0806640105] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.
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15
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Identification of Quaternary Structure and Functional Domains of the CI Repressor from Bacteriophage TP901-1. J Mol Biol 2008; 376:983-96. [DOI: 10.1016/j.jmb.2007.12.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 12/10/2007] [Accepted: 12/11/2007] [Indexed: 11/21/2022]
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16
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Bahti P, Chen S, Li Y, Shaw N, Zhang X, Zhang M, Cheng C, Song G, Yin J, Zhang H, Che D, Abbas A, Xu H, Wang BC, Liu ZJ. Purification, crystallization and preliminary crystallographic analysis of the non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:91-3. [PMID: 18259057 PMCID: PMC2374175 DOI: 10.1107/s1744309107068649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 12/28/2007] [Indexed: 11/11/2022]
Abstract
A 10.5 kDa non-Pfam hypothetical protein, AF1514, from the hyperthermophilic archaeon Archeoglobus fulgidus has been overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted X-rays to 2.09 A resolution and a data set was collected at 100 K using Cu K alpha radiation from a rotating-anode X-ray source. The crystals belong to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 49.27, c = 106.61 A. The calculated Matthews coefficient was 3.16 A(3) Da(-1), suggesting the presence of one molecule in the asymmetric unit.
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Affiliation(s)
- Pazilat Bahti
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, People’s Republic of China
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Shunmei Chen
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yang Li
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Neil Shaw
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xuejun Zhang
- Department of Immunology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| | - Min Zhang
- Life Sciences College, Anhui University, Hefei 230039, People’s Republic of China
| | - Chongyun Cheng
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Gaojie Song
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Jie Yin
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hua Zhang
- SECSG, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30605, USA
| | - Dongsheng Che
- SECSG, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30605, USA
| | - Abdulla Abbas
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, People’s Republic of China
| | - Hao Xu
- SECSG, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30605, USA
| | - Bi-Cheng Wang
- SECSG, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30605, USA
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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17
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Kacprzak S, Reviakine R, Kaupp M. Understanding the electon paramagnetic resonance parameters of protein-bound glycyl radicals. J Phys Chem B 2007; 111:820-31. [PMID: 17249826 DOI: 10.1021/jp0674571] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The number of enzymes that require a glycyl-based radical for their function is growing. Here, we provide systematic quantum-chemical studies of spin-density distributions, electronic g-tensors, and hyperfine couplings of various models of protein-bound glycyl radicals. Similarly to what is found in a companion paper on N-acetylglycyl, the small g-anisotropy for this delocalized, unsymmetrical system presents appreciable challenges to state-of-the-art computational methodology. This pertains to the quality of structure optimization, as well as to the choice of the spin-orbit Hamiltonian and the gauge origin of the magnetic vector potential. Environmental effects due to hydrogen bonding are complicated and depend in a subtle fashion on the different intramolecular hydrogen bonding for different conformations of the radical. Indeed, the conformation has the largest overall effect on the computed g-tensors (less so on the hyperfine tensors). This is discussed in the context of different g-tensors obtained by recent high-field electron paramagnetic resonance (EPR) measurements for three different enzymes. On the basis of results of a parallel calibration study for N-acetylglycyl, it is suggested that the glycyl radical observed for E. coli anaerobic RNR may have a fully extended conformation, which differs from those of the corresponding radicals in pyruvate formate-lyase or benzylsuccinate synthase.
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Affiliation(s)
- Sylwia Kacprzak
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D 97074 Würzburg, Germany
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18
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Winderl C, Schaefer S, Lueders T. Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker. Environ Microbiol 2007; 9:1035-46. [PMID: 17359274 DOI: 10.1111/j.1462-2920.2006.01230.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzylsuccinate synthase (Bss) is the key enzyme of anaerobic toluene degradation and has been found in all anaerobic toluene degrading bacterial isolates tested. However, only a few pure cultures capable of anaerobic toluene oxidation are available to date, and it is important to understand the relevance of these model organisms for in situ bioremediation of hydrocarbon-contaminated aquifers. Due to their phylogenetic dispersal, it is not possible to specifically target anaerobic toluene degraders using marker rRNA genes. We therefore established an assay targeting a approximately 794 bp fragment within the Bss alpha-subunit (bssA) gene, which allows for the specific detection and affiliation of both known and unknown anaerobic degraders. Three distinct tar-oil-contaminated aquifer sites were screened for intrinsic bssA gene pools in order to identify and compare the diversity of hydrocarbon degraders present at these selected sites. We were able to show that local diversity patterns of degraders were entirely distinct, apparently highly specialized and well-adapted to local biogeochemical settings. Discovered at one of the sites were bssA genes closely related to that of Geobacter spp., which provides evidence for an importance of iron reduction for toluene degradation in these sediments. Retrieved from the other two sites, dominated by sulfate reduction, were previously unidentified bssA genes and also deeply branching putative bssA homologues. We provide evidence for a previously unrecognized diversity of anaerobic toluene degraders and also of other hydrocarbon degraders using fumarate-adding key reactions in contaminated aquifers. These findings enhance our current understanding of intrinsic hydrocarbon-degrading microbial communities in perturbed aquifers and may have potential for the future assessment and prediction of natural attenuation based on degradation genes.
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Affiliation(s)
- Christian Winderl
- Institute of Groundwater Ecology, GSF - National Research Center for Environment and Health, Neuherberg, Germany
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19
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Kacprzak S, Reviakine R, Kaupp M. Understanding the EPR Parameters of Glycine-Derived Radicals: The Case of N-Acetylglycyl in the N-Acetylglycine Single-Crystal Environment. J Phys Chem B 2006; 111:811-9. [PMID: 17249825 DOI: 10.1021/jp0660379] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a step toward an in-depth understanding of the electron paramagnetic resonance parameters of glycyl radicals in proteins, the hyperfine tensors and, particularly, the g-tensor of N-acetylglcyl in the environment of a single crystal of N-acetylglycine have been studied by systematic state-of-the-art quantum chemical calculations on various suitable model systems. The quantitative computation of the g-tensors for such glycyl-derived radicals is a veritable challenge, mainly because of the very small g-anisotropy combined with a nonsymmetrical, delocalized spin-density distribution and several atoms with comparable spin-orbit contributions to the g-tensors. The choice of gauge origin of the magnetic vector potential, and of approximate spin-orbit operators, both turn out to be more critical than found in previous studies of g-tensors for organic radicals. Environmental effects, included by supermolecular hydrogen-bonded models, were found to be moderate, because of a partial compensation between the influences from intramolecular and intermolecular hydrogen bonds. The largest effects on the g-tensor are caused by the conformation of the radical. The density functional theory methods employed systematically overestimate both the Delta gx and Delta gy components of the g-tensor. This is important for parallel investigations on the protein-glycyl radicals. The 1H alpha and 13C alpha hyperfine couplings depend only slightly on the supermolecular model chosen and appear less sensitive probes of detailed structure and environment.
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Affiliation(s)
- Sylwia Kacprzak
- Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D 97074 Würzburg, Germany
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