| Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. | |
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MedLine Citation:
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PMID: 20423905 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Unlike classical 2-oxoglutarate and iron-dependent dioxygenases, which include several nucleic acid modifiers, the structurally similar jumonji-related dioxygenase superfamily was only known to catalyze peptide modifications. Using comparative genomics methods, we predict that a family of jumonji-related enzymes catalyzes wybutosine hydroxylation/peroxidation at position 37 of eukaryotic tRNAPhe. Identification of this enzyme raised questions regarding the emergence of protein- and nucleic acid-modifying activities among jumonji-related domains. We addressed these with a natural classification of DSBH domains and reconstructed the precursor of the dioxygenases as a sugar-binding domain. This precursor gave rise to sugar epimerases and metal-binding sugar isomerases. The sugar isomerase active site was exapted for catalysis of oxygenation, with a radiation of these enzymes in bacteria, probably due to impetus from the primary oxygenation event in Earth's history. 2-Oxoglutarate-dependent versions appear to have further expanded with rise of the tricarboxylic acid cycle. We identify previously under-appreciated aspects of their active site and multiple independent innovations of 2-oxoacid-binding basic residues among these superfamilies. We show that double-stranded β-helix dioxygenases diversified extensively in biosynthesis and modification of halogenated siderophores, antibiotics, peptide secondary metabolites and glycine-rich collagen-like proteins in bacteria. Jumonji-related domains diversified into three distinct lineages in bacterial secondary metabolism systems and these were precursors of the three major clades of eukaryotic enzymes. The specificity of wybutosine hydroxylase/peroxidase probably relates to the structural similarity of the modified moiety to the ancestral amino acid substrate of this superfamily. |
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Authors:
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Lakshminarayan M Iyer; Saraswathi Abhiman; Robson F de Souza; L Aravind |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural Date: 2010-04-27 |
Journal Detail:
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Title: Nucleic acids research Volume: 38 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2010 Sep |
Date Detail:
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Created Date: 2010-09-13 Completed Date: 2010-10-13 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0411011 Medline TA: Nucleic Acids Res Country: England |
Other Details:
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Languages: eng Pagination: 5261-79 Citation Subset: IM |
Affiliation:
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National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Amino Acid Sequence Bacteria / enzymology Catalytic Domain Dioxygenases / chemistry*, genetics, metabolism Eukaryota / enzymology Evolution, Molecular* Genes, Bacterial Mixed Function Oxygenases / chemistry*, metabolism Molecular Sequence Data Nucleosides / metabolism* Peptides / metabolism Peroxidases / chemistry*, metabolism Protein Folding Protein Structure, Secondary Protein Structure, Tertiary RNA, Transfer, Phe / metabolism Sequence Homology, Amino Acid |
| Chemical | |
Reg. No./Substance:
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0/Nucleosides; 0/Peptides; 0/RNA, Transfer, Phe; 0/wybutosine; EC 1.-/Mixed Function Oxygenases; EC 1.11.1.-/Peroxidases; EC 1.13.11.-/Dioxygenases |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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