Protein universe containing a PUA RNA-binding domain.

Here, we review current knowledge about pseudouridine synthase and archaeosine transglycosylase (PUA)-domain-containing proteins to illustrate progress in this field. A methodological analysis of the literature about the topic was carried out, together with a 'qualitative comparative analysis' to give a more comprehensive review. Bioinformatics methods for whole-protein or protein-domain identification are commonly based on pairwise protein sequence comparisons; we added comparison of structures to detect the whole universe of proteins containing the PUA domain. We present an update of proteins having this domain, focusing on the specific proteins present in Homo sapiens (dyskerin, MCT1, Nip7, eIF2D and Nsun6), and explore the existence of these in other species. We also analyze the phylogenetic distribution of the PUA domain in different species and proteins. Finally, we performed a structural comparison of the PUA domain through data mining of structural databases, determining a conserved structural motif, despite the differences in the sequence, even among eukaryotes, archaea and bacteria. All data discussed in this review, both bibliographic and analytical, corroborate the functional importance of the PUA domain in RNA-binding proteins.

Differential effect of spermine on nuclear and cytoplasmic transfer RNA methyl transferases from Xenopus laevis Oocytes.

X laevis ovarian tissue or isolated oocytes contain two major tRNA methyl transferase activities capable of methylating total E. coli tRNA using S-adenosyl methionine as a methyl donor. These enzymes can be resolved by chromatography on DEAE-cellulose or by gel filtration on Sephadex G-200 into fractions I and II. The tRNA methyl transferase I which is present mainly in the oocyte nuclei, has a molecular weight of 190,000 and an apparent Km for S-adenosyl methionine of 1.5 microM. The activity of peak II which exists predominantly in the oocyte cytoplasm, has a molecular weight of 125,000 and an apparent Km for S-adenosyl methionine of 17 microM. The most striking difference between these two enzymes, however, resides in their response to spermine or magnesium ions. The nuclear enzyme is activated more that 8 fold by spermine and 4 fold by Mg2+ while the cytoplsmic activity is slightly inhibited by the polyamine and unaffected by Mg2+. The effect of spermine on the nuclear tRNA methyl transferase is highly dependent on the salt concentration since the stimulatory effect of the polyamine decrease at KCI concentrations above 100 mM becoming inhibitory above 200 mM. Spermine increases 4 fold the Vmax of the reaction catalyzed by the nuclear enzyme but does not affect its apparent Km for tRNA which is approximately 2.9 microM. The apparent Km for tRNA of the cytoplasmic enzyme is 3.3 microM.