InterPro domain: IPR033411

PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation [ 1 ]. PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay [ 2 ] and in processing of 18S ribosomal RNA [ 3 ]. In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin [ 4 ].

This is a PIN domain found in eukaryotic ribonuclease Nob1 and archaeal ribonuclease VapC1 [ 4 ].

RNA-binding protein NOB1 has a nuclear location [ 5 ] and contains a PIN domain and binds a single zinc ion. Budding yeast Nob1 is involved in proteasomal and 40S ribosomal subunit biogenesis [ 6 ]. It is also required for maturation of the small subunit ribosomal RNA by catalyzing cleavage at site D after export of the preribosomal subunit into the cytoplasm. Nob1 is also found in archaea, where it is manganese-dependent and also processes RNA-substrates [ 7 ]. This domain can also be found in VapC1, which is a toxic component and a ribonuclease of a toxin-antitoxin (TA) module [ 7 ].

1. The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array. Protein Eng. Des. Sel. 24, 33-40
2. Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. EMBO J. 25, 5117-25
3. Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain. Proc. Natl. Acad. Sci. U.S.A. 106, 14259-64
4. Structural and functional analysis of the archaeal endonuclease Nob1. Nucleic Acids Res. 40, 3259-74
5. Cloning, expression and characterization of the human NOB1 gene. Mol. Biol. Rep. 32, 185-9
6. Nob1p, a new essential protein, associates with the 26S proteasome of growing saccharomyces cerevisiae cells. Gene 243, 37-45
7. Analysis of non-typeable Haemophilous influenzae VapC1 mutations reveals structural features required for toxicity and flexibility in the active site. PLoS ONE 9, e112921