title: The evolution of function within the Nudix homology clan.
abstract: The Nudix homology clan encompasses over 80,000 protein domains from all three domains of life, defined by homology to each other. Proteins with a domain from this clan fall into four general functional classes: pyrophosphohydrolases, isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), and nonenzymatic 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 a structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 "select" Nudix homology domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix homology clan revealed general monophyly with regard to function and a few instances of probable homoplasy. Proteins 2017; 85:775-811. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Plant and Microbial Biology Department, University of California, Berkeley, California, 94720.|Molecular and Cell Biology Department, University of California, Berkeley, California, 94720.
authors.forename: John R
authors.initials: JR
authors.lastname: Srouji
authors.affiliation: Graduate Study in Comparative Biochemistry, University of California, Berkeley, California, 94720.
authors.forename: Anting
authors.initials: A
authors.lastname: Xu
authors.affiliation: Molecular and Cell Biology Department, University of California, Berkeley, California, 94720.
authors.forename: Annsea
authors.initials: A
authors.lastname: Park
authors.affiliation: Molecular and Cell Biology Department, University of California, Berkeley, California, 94720.|Graduate Study in Comparative Biochemistry, University of California, Berkeley, California, 94720.
authors.forename: Jack F
authors.initials: JF
authors.lastname: Kirsch
authors.affiliation: Plant and Microbial Biology Department, University of California, Berkeley, California, 94720.|Molecular and Cell Biology Department, University of California, Berkeley, California, 94720.|Graduate Study in Comparative Biochemistry, University of California, Berkeley, California, 94720.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001419:Bacteria / Q000737:chemistry* / Q000201:enzymology; D001665:Binding Sites; D019295:Computational Biology; D030562:Databases, Protein; D005658:Fungi / Q000737:chemistry* / Q000201:enzymology; D063990:Gene Ontology; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D011755:Pyrophosphatases / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D013379:Substrate Specificity; D000096964:Nudix Hydrolases
chemical_list: D011755:Pyrophosphatases; D000096964:Nudix Hydrolases
keywords: Nudix; Nudix homology clan; homoplasy; hydrolase; sequence alignment; structural alignment