The Evolution of Function within the Nudix Superfamily

Описание

The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 "select" Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based…

Описание из Zenodo, сокращённое.

Файлы (28)

• PY3DCOMB_alignment.py8,1 МБ
• Rgenerate_score_biochem_genetic.R892 Б
• CSVscore_biochem_genetic_soverall.csv40 кБ
• FA78-PDB_alignment.fa32 кБ
• Rgenerate_score_final.R1,3 кБ
• CSVscore_final.csv99 кБ
• NEWICKNudix-clan_tree.newick1,4 МБ
• CSVscore_genetic.csv1,5 кБ
• DOCTable S1 updated.doc72 кБ
• CSVscore_biochem_genetic.csv40 кБ
• PDFThe_layout_of_the_Nudix_MySQL_database.pdf282 кБ
• DENDRO347-select_tree_reconciled.dendro101 кБ
• FANudix-clan_alignment.fa108 МБ
• FA46-PDB_alignment.fa40 кБ
• XLSXNudix_data_collection.xlsx204 кБ
• SQLmysql_dump_char_nudix_04062014.sql880 кБ
• PDFFigure_7_347-select_tree_high_resolution.pdf978 кБ
• PDFFigure_8_Nudix-clan_tree_high_resolution.pdf1,8 МБ
• PDFPipelines_to_build_sequence_alignments_of_the_Nudix_superfamily.pdf1,6 МБ
• XLSXFinal_score_assignment.xlsx167 кБ
• XLSXGOA_analysis_results.xlsx5,5 МБ
• NEWICK347-select_tree.newick14 кБ
• CSVscore_biochem.csv68 кБ
• FA347-select_alignment.fa183 кБ
• XLSX340_select_nudix_proteins.xlsx50 кБ
• FA324-core_alignment.fa158 кБ
• XLSXInitial_score_assignment.xlsx173 кБ
• DENDRONudix-clan_tree_reconciled.dendro10 МБ

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