Homologous Superfamily

Peptidase S59, nucleoporin superfamily (IPR036903)

Short name: Peptidase_S59_sf

Overlapping entries


The nuclear pore complex protein plays a role in bidirectional transport across the nucleoporin complex in nucleocytoplasmic transport. The mammalian nuclear pore complex (NPC) is comprised of approximately 50 unique proteins, collectively known as nucleoporins. A number of the peptides are synthesised as precursors and undergo self-catalyzed cleavage.

The proteolytic cleavage site of yeast Nup145p has been mapped upstream of an evolutionary conserved serine residue. Cleavage occurs at the same site when a precursor is artificially expressed in Escherichia coli. A hydroxyl-containing residue is critical for the reaction, although a thiol-containing residue offers an acceptable replacement. In vitro kinetics experiments using a purified precursor molecule demonstrate that the cleavage is self-catalyzed and that the catalytic domain lies within the N-terminal moiety. Taken altogether, the data are consistent with a proteolytic mechanism involving an N>O acyl rearrangement and a subsequent ester intermediate uncovered in other self-processing proteins [PMID: 10542288].

Nup98 is a component of the nuclear pore that plays its primary role in the export of RNAs. Nup98 is expressed in two forms, derived from alternate mRNA splicing. Both forms are processed into two peptides through autoproteolysis mediated by the C-terminal domain of hNup98. The three-dimensional structure of the C-terminal domain reveals a novel protein fold, and thus a new class of autocatalytic proteases. The structure further reveals that the suggested nucleoporin RNA binding motif is unlikely to bind to RNA [PMID: 12191480].

The following nucleoporins share an ~150-residue C-terminal domain responsible for NPC targeting [PMID: 12191480, PMID: 16105837]:

  • Vertebrate Nup98, a component of the nuclear pore that plays its primary role in the export of RNAs.
  • Yeast Nup100, plays an important role in several nuclear export and import pathways including poly(A)+ RNA and protein transport.
  • Yeast Nup116, involved in mRNA export and protein transport.
  • Yeast Nup145, involved in nuclear poly(A)+ RNA and tRNA export.

The NUP C-terminal domains of Nup98 and Nup145 possess peptidase S59 autoproteolytic activity. The autoproteolytic sites of Nup98 and Nup145 each occur immediately C-terminal to the NUP C-terminal domain. Thus, although this domain occurs in the middle of each precursor polypeptide, it winds up at the C-terminal end of the N-terminal cleavage product. Cleavage of the peptide chains are necessary for the proper targeting to the nuclear pore [PMID: 12191480, PMID: 16105837].

The NUP C-terminal domain adopts a predominantly beta-strand structure. The molecule consists of a six-stranded beta-sheet sandwiched against a two-stranded beta-sheet and flanked by alpha-helical regions. The N-terminal helical region consists of two short helices, whereas the stretch on the opposite side of molecule consists of a single, longer helix [PMID: 12191480, PMID: 16105837].

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.