title: Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases.
abstract: Using a combination of several methods for protein sequence comparison and motif analysis, it is shown that the four recently described pseudouridine syntheses with different specificities belong to four distinct families. Three of these families share two conserved motifs that are likely to be directly involved in catalysis. One of these motifs is detected also in two other families of enzymes that specifically bind uridine, namely deoxycitidine triphosphate deaminases and deoxyuridine triphosphatases. It is proposed that this motif is an essential part of the uridine-binding site. Two of the pseudouridine syntheses, one of which modifies the anticodon arm of tRNAs and the other is predicted to modify a portion of the large ribosomal subunit RNA belonging to the peptidyltransferase center, are encoded in all extensively sequenced genomes, including the 'minimal' genome of Mycoplasma genitalium. These particular RNA modifications and the respective enzymes are likely to be essential for the functioning of any cell.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: E V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D005075:Biological Evolution; D017124:Conserved Sequence; D029968:Escherichia coli Proteins; D019751:Intramolecular Transferases; D007535:Isomerases / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D008969:Molecular Sequence Data; D009709:Nucleotide Deaminases / Q000378:metabolism*; D011560:Pseudouridine / Q000378:metabolism*; D011755:Pyrophosphatases / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D014529:Uridine / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D011560:Pseudouridine; D009709:Nucleotide Deaminases; C019988:dCTP deaminase; D011755:Pyrophosphatases; C023278:uridine triphosphatase; D007535:Isomerases; D019751:Intramolecular Transferases; C094732:16S RNA pseudouridine 516 synthase, E coli; C096995:pseudouridine synthases; C023199:tRNA-pseudouridine synthase I; D014529:Uridine