cd09862: PIN_Rrp44 (this model, PSSM-Id:189032 is obsolete and has been replaced by 350211)
PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic homologs.
PIN (PilT N terminus) domain of the Saccharomyces cerevisiae exosome subunit Rrp44 (Ribosomal RNA-processing protein 44 or Protein Dis3 homolog) and other similar eukaryotic homologs are included in this family. The eukaryotic exosome is a conserved macromolecular complex responsible for many RNA-processing and RNA-degradation reactions. It is composed of nine core subunits that directly binds Rrp44. The Rrp44 nuclease is the catalytic subunit of the exosome and has endonuclease activity in the PIN domain and an exoribonuclease activity in its RNase II-like region. Rrp44 binding to the exosome is mediated mainly by the PIN domain and by subunits Rrp41-Rrp45, and binding predictions indicate that the PIN domain active site is positioned on the outer surface of the exosome. These PIN domains are structural homologs of flap endonuclease-1 (FEN1)-like PIN domains, but lack the extensive arch/clamp region and the H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region, seen in FEN1-like PIN domains. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Recombinant Rrp44 was shown to possess manganese-dependent endonuclease activity in vitro that was abolished by point mutations in the putative metal binding residues of its PIN domain.
Comment:Recombinant Rrp44 was shown to possess manganese-dependent endonuclease activity in vitro that was abolished by point mutations in the putative metal binding residues of its PIN domain.
Comment:Based on homology with known nucleases such as flap endonuclease-1 and T4 RNase H nuclease, as well as, experimental evidence for ribonuclease activity demonstrated for PIN domain-containing homologs: VapC-1, Nob1, Smg6, and PAE2754.
Jiyao W et al.(2023). "The conserved domain database in 2023.",