The pseudouridine synthase and archaeosine transglycosylase (PUA) domain is a compact and highly conserved RNA-binding motif that is widespread among diverse types of proteins from the three kingdoms of life. Its three-dimensional architecture is well established, and the structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA. The PUA domain is often part of RNA modification enzymes and ribonucleoproteins, but it has also been unexpectedly found fused to enzymes involved in proline biosynthesis, where it plays an unknown role. The functional impact of the domain varies with the protein studied, ranging from minor to essential effects. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases.
"The Smu776 structure was resolved at 2.20 Å, and consists of an N-terminal PUA domain, a central EEHEE domain, and a C-terminal methyltransferase domain that contains a single SAH molecule (Figure 2B). The PUA domain is a small RNA-binding region found in many other RNA modification enzymes (45) as well as two functionally uncharacterized Smu776 orthologs in the PDB database (3K0B and 3LDU). The only other characterized structure with similar PUA and EEHEE domains is that of YccW/RlmI (15), which is also a member of the COG1092 methyltransferase family and is responsible for the E. coli 23S RNA nucleotide m5C1962 methylation (11). "
[Show abstract][Hide abstract] ABSTRACT: The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.
Nucleic Acids Research 02/2012; 40(11):5138-48. DOI:10.1093/nar/gks160 · 9.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: T his chapter provides a short review of the structural biology of RNA modification enzymes, focused on comparative aspects. All modifications are introduced by protein enzymes, from relatively simple standalone catalytic domains to subunits of protein complexes or ribonucleoprotein particles. These enzymes typically comprise domains that are often specialized in the catalysis of the modification reaction or in recognition and binding of the macromolecular RNA substrate, underscoring structural and functional modularization of proteins and the interplay of these modules in complex macromolecular systems. We provide a catalog of three‑dimensional folds and molecular functions of domains implicated in RNA modifications and discuss evolution‑ ary pathways that connect different modes used by enzymes to interact with their substrates. We highlight cases of convergent evolution for unrelated enzymatic domains catalyzing very similar reactions and 'promiscuous' domains used for substrate recognition.
[Show abstract][Hide abstract] ABSTRACT: The conserved protein Nip7 is involved in ribosome biogenesis, being required for proper 27S pre-rRNA processing and 60S ribosome subunit assembly in Saccharomyces cerevisiae. Yeast Nip7p interacts with nucleolar proteins and with the exosome subunit Rrp43p, but its molecular function remains to be determined. Solution of the Pyrococcus abyssi Nip7 (PaNip7) crystal structure revealed a monomeric protein composed by two alpha-beta domains. The N-terminal domain is formed by a five-stranded antiparallel beta-sheet surrounded by three alpha-helices and a 310 helix while the C-terminal, a mixed beta-sheet domain composed by strands beta8 to beta12, one alpha-helix, and a 310 helix, corresponds to the conserved PUA domain (after Pseudo-Uridine synthases and Archaeosine-specific transglycosylases). By combining structural analyses and RNA interaction assays, we assessed the ability of both yeast and archaeal Nip7 orthologues to interact with RNA. Structural alignment of the PaNip7 PUA domain with the RNA-interacting surface of the ArcTGT (archaeosine tRNA-guanine transglycosylase) PUA domain indicated that in the archaeal PUA domain positively charged residues (R151, R152, K155, and K158) are involved in RNA interaction. However, equivalent positions are occupied by mostly hydrophobic residues (A/G160, I161, F164, and A167) in eukaryotic Nip7 orthologues. Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain as determined by site-directed mutagenesis. This work provides experimental verification that the PUA domain mediates Nip7 interaction with RNA and reveals that the preference for interaction with polyuridine sequences is conserved in Archaea and eukaryotic Nip7 proteins.
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