Radical Sam Enzymes
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Radical Sam Enzymes
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Author :
language : en
Publisher: Academic Press
Release Date : 2018-08-08
Radical Sam Enzymes written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-08 with Science categories.
Radical SAM Enzymes, Volume 606, the latest release in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on the Characterization of the glycyl radical enzyme choline trimethylamine-lyase and its radical S-adenosylmethionine activating enzyme, Diphathimide biosynthesis, Radical SAM glycyl radical activating enzymes, Radical SAM enzyme BioB in the biosynthesis of biotin, Biogenesis of the PQQ cofactor, Role of MoaAC in the biogenesis of the molybdenum cofactor, Biosynthesis of the nitrogenase cofactor, Bioinformatics of the radical SAM superfamily, The involvement of SAM radical enzymes in the biosynthesis of methanogenic coenzymes, methanopterin and coenzyme F420, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Covers radical SAN enzymes in detail
Radical Sam Enzymes
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Author :
language : en
Publisher: Academic Press
Release Date : 2018-08-09
Radical Sam Enzymes written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-09 with Science categories.
Radical SAM Enzymes, Volume 606, the latest release in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on the Characterization of the glycyl radical enzyme choline trimethylamine-lyase and its radical S-adenosylmethionine activating enzyme, Diphathimide biosynthesis, Radical SAM glycyl radical activating enzymes, Radical SAM enzyme BioB in the biosynthesis of biotin, Biogenesis of the PQQ cofactor, Role of MoaAC in the biogenesis of the molybdenum cofactor, Biosynthesis of the nitrogenase cofactor, Bioinformatics of the radical SAM superfamily, The involvement of SAM radical enzymes in the biosynthesis of methanogenic coenzymes, methanopterin and coenzyme F420, and more.
Radical Sam Enzymes And Radical Enzymology
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Author : Squire J. Booker
language : en
Publisher:
Release Date : 2012
Radical Sam Enzymes And Radical Enzymology written by Squire J. Booker and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
Identification And Characterization Of Two Radical Sam Enzymes Involved In Biosynthesis Of The Fe Hydrogenase Cofactor
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Author : Francisco Javier Arriaza Gallardo
language : de
Publisher:
Release Date : 2022
Identification And Characterization Of Two Radical Sam Enzymes Involved In Biosynthesis Of The Fe Hydrogenase Cofactor written by Francisco Javier Arriaza Gallardo and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022 with categories.
Radical Sam Enzymes Involved In Tetrapyrrole Biosynthesis And Insertion
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Author : Gunhild Layer
language : en
Publisher:
Release Date : 2022
Radical Sam Enzymes Involved In Tetrapyrrole Biosynthesis And Insertion written by Gunhild Layer and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022 with categories.
Abstract: The anaerobic biosyntheses of heme, heme d1, and bacteriochlorophyll all require the action of radical SAM enzymes. During heme biosynthesis in some bacteria, coproporphyrinogen III dehydrogenase (CgdH) catalyzes the decarboxylation of two propionate side chains of coproporphyrinogen III to the corresponding vinyl groups of protoporphyrinogen IX. Its solved crystal structure was the first published structure for a radical SAM enzyme. In bacteria, heme is inserted into enzymes by the cytoplasmic heme chaperone HemW, a radical SAM enzyme structurally highly related to CgdH. In an alternative heme biosynthesis route found in archaea and sulfate-reducing bacteria, the two radical SAM enzymes AhbC and AhbD catalyze the removal of two acetate groups (AhbC) or the decarboxylation of two propionate side chains (AhbD). NirJ, a close homologue of AhbC, is required for propionate side chain removal during the formation of heme d1 in some denitrifying bacteria. Biosynthesis of the fifth ring (ring E) of all chlorophylls is based on an unusual six-electron oxidative cyclization step. The sophisticated conversion of Mg-protoporphyrin IX monomethylester to protochlorophyllide is facilitated by an oxygen-independent cyclase termed BchE, which is a cobalamin-dependent radical SAM enzyme. Most of the radical SAM enzymes involved in tetrapyrrole biosynthesis were recognized as such by Sofia et al. in 2001 ( Nucleic Acids Res. 2001, 29, 1097−1106) and were biochemically characterized thereafter. Although much has been achieved, the challenging tetrapyrrole substrates represent a limiting factor for enzyme/substrate cocrystallization and the ultimate elucidation of the corresponding enzyme mechanisms
Biochemical And Structural Characterization Of Radical Sam Enzymes Elp3 And Viperin
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Author : Kiruthika Selvadurai
language : en
Publisher:
Release Date : 2016
Biochemical And Structural Characterization Of Radical Sam Enzymes Elp3 And Viperin written by Kiruthika Selvadurai and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Investigating The Structural And Mechanistic Paramters Of Two Radical Sam Enzymes Spore Photoproduct Lyase And Hyde
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Author : Shourjo Ghose
language : en
Publisher:
Release Date : 2013
Investigating The Structural And Mechanistic Paramters Of Two Radical Sam Enzymes Spore Photoproduct Lyase And Hyde written by Shourjo Ghose and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with Adenosylmethionine categories.
The resistance of Bacterial spores to UV radiation makes them a causative agent in many diseases and poses a threat to humans and animals alike. This unique resistance stems from the repair of a thymine dimer, 5-thyminyl-5,6-dihydrothymine (spore photoproduct, or SP)on exposure to UV irradiation. During the early stages of germination, this SP is repaired by an enzyme, spore photoproduct lyase (SPL) into two thymines. SPL is a member of the radical SAM superfamily of enzymes and requires S-adenosylmethionine (SAM) and a [4Fe-4S]1+/2+ cluster to perform its catalysis. The first part of this dissertation is dedicated towards understanding the solution phase dynamics of this protein on binding with its substrate and co-factor via hydrogen deuterium exchange. Analyses of the effects of SAM binding to SPL indicate that the protein does go through a conformational change localized around its active site. We have also demonstrated that the concomitant binding of SAM and dinucleotide SP contributes more significantly to the active site stabilization than what is observed with just SAM binding. Moreover we have provided initial evidence that the SPL might be utilizing the deformation of the phosphodiester back bone of SP to recognize, bind and initiate catalysis. We have unequivocally demonstrated that the catalytic [4Fe-4S] cluster plays a significant role in substrate/cofactor binding most likely due to the stabilization of the 8 residue loop region it resides on. The second part of this dissertation is focused towards understanding the role of maturase proteins in the assembly of the active site of [FeFe]- hydrogenase. The assembly and biosynthesis of the H-cluster requires three accessory enzymes HydE, HydG and HydF. Herein show that HydE utilizes cysteine as a substrate. We have also shown through LCMS and specifically deuterium labeled substrate, that catalysis is initiated via a H atom abstraction from the beta carbon of cysteine. Our investigations into the mechanism of HydG mediated turnover of tyrosine reveal that catalysis is initiated via a single H atom abstraction from the phenolic position of the substrate. Taken together we believe that our investigations have provided some critical insights into specific roles of these enzymes.
Progress Towards Reprogramming The Nucleotide Transforming Radical Sam Enzyme Thic
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Author : Callie D. Smith
language : en
Publisher:
Release Date : 2021
Progress Towards Reprogramming The Nucleotide Transforming Radical Sam Enzyme Thic written by Callie D. Smith and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
The radical S-adenosyl-L-methionine (SAM) enzyme, ThiC, catalyzes the conversion of aminoimidazole ribotide (AIR) to a precursor molecule of thiamine (vitamin B1), 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P). ThiC has a noncanonical active site architecture in which a CX2CX4C motif binds a [4Fe-4S]2+ cluster in contrast to the more typical CX3CX2C motif. Further, X-ray crystallographic results show that the carboxylate and amino groups of SAM bind to a divalent metal ion rather than the unique iron of the [4Fe-4S]2+ cluster. Electron transfer from the cluster to the bound SAM molecule causes its cleavage to form methionine and a 5′-deoxyadenosyl radical that then abstracts an H-atom from AIR to begin its conversion to HMP-P. These same unique active site features are thought to be shared by another radical SAM enzyme, BzaF, which also operates on AIR. BzaF, however, catalyzes a dramatically different carbon skeleton rearrangement of AIR to form 5-hydroxybenzimidazole (HBI) that is ultimately used as the lower, cobalt-binding ligand of cobalamin (vitamin B12). The protein sequences of the two enzymes have a 44% identity and 66% similarity but only 4 of the 21 amino acid residues within 4 Å of AIR are different. We hypothesize that the three of these different residues which interact directly with the substrate are responsible for their respective enzyme's distinct AIR chemistry. In this work, site-directed mutagenesis was used to exchange one, two, and all three of the differing ThiC residues for the corresponding residues in BzaF. Each ThiC variant was reacted with AIR and assessed for SAM cleavage (5′-dAdoH production) using HPLC. In each variant, 5′-dAdoH production was enhanced by addition of AIR indicating that binding of AIR and reductive cleavage of SAM both still occur. While we do not yet know the fate of AIR, these results support the viability of our approach to use these variants to precisely define mechanistic roles of the active site residues in ThiC and BzaF.
Mechanistic And Spectroscopic Investigations Of Pyruvate Formate Lyase Activating Enzyme
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Author : Rachel Ann Udelhoven Hutcheson
language : en
Publisher:
Release Date : 2012
Mechanistic And Spectroscopic Investigations Of Pyruvate Formate Lyase Activating Enzyme written by Rachel Ann Udelhoven Hutcheson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with Adenosylmethionine categories.
Radical S-adenosylmethionine (SAM) enzymes are a large and rapidly growing superfamily composed of thousands of members catalyzing a wide diversity of reactions by utilizing a reduced [4Fe-4S] 1 + cluster and SAM to create a 5'-deoxyadenosyl radical capable of initiating controlled radical chemistry in important and difficult biochemical reactions. The prevalence of radical SAM enzymes in all kingdoms of life underscores the central role played by these enzymes. For the vast majority of putative radical SAM enzymes little is known regarding the reaction catalyzed or the mechanism of catalysis. Nevertheless, it is possible to gain insight into these enzymes from the radical SAM enzyme pyruvate formate-lyase activating enzyme (PFL-AE), which catalyzes the formation of a catalytically essential glycyl (G734) radical of pyruvate formate-lyase (PFL). The studies presented herein provide further understanding and characterization of PFL-AE as well as other radical SAM enzymes. The relevance and effect of the monovalent cation found in the active site of PFL-AE upon further analysis of the crystal structure was probed using coupled enzyme activity assays. Five different monovalent cations, Na +, K +, NH 4 +, Rb +, and Cs +, were investigated by calculating the specific activity of PFL-AE in the presence of each. PFL-AE was active in the presence of all tested cations, with specific activities correlating with cation size. Nuclear resonance vibrational spectroscopy performed on PFL-AE with an 57 Fe labeled cluster showed a enzyme stiffening around the cluster and elongation of Fe-S bonds upon substrate and substrate analog binding. Rapid freeze-quench was used to mix PFL-AE with PFL and SAM on a millisecond time scale. The resulting samples were analyzed by electron paramagnetic resonance, which revealed a newly observed radical intermediate. To attempt characterization of this radical intermediate, electron nuclear double resonance spectroscopy (ENDOR) was used with site-specifically labeled SAM. The ENDOR signal detected was too weak to be analyzed; however, other labeled SAM molecules will be used in the future. To help further expand knowledge of radical SAM enzymes, an initial characterization of a putative methylthiotransferase (a subclass of the radical SAM superfamily) was undertaken. Results indicated that the enzyme methylthiolated a ribosomal small protein and not tRNA.
Non Canonical Active Site Architecture Of The Radical Sam Thiamin Pyrimidine Synthase
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Author :
language : en
Publisher:
Release Date : 2015
Non Canonical Active Site Architecture Of The Radical Sam Thiamin Pyrimidine Synthase written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a [beta]-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the [beta]-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.