InterPro : IPR007230

Name  Peptidase S59, nucleoporin Short Name  Peptidase_S59
Type  Domain Description  Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [].Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].This group of autocatalytic serine endopeptidases belong to MEROPS peptidase family S59 (clan SP).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 [].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 [].The following nucleoporins share an ~150-residue C-terminal domain responsible for NPC targeting [, ]: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 S59autoproteolytic activity. The autoproteolytic sites of Nup98 and Nup145each occur immediately C-terminal to the NUP C-terminal domain. Thus, althoughthis domain occurs in the middle of each precursor polypeptide, it winds up atthe C-terminal end of the N-terminal cleavage product. Cleavage of the peptidechains are necessary for the proper targeting to the nuclear pore [, ].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 [, ].
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5 Publications

First Author Title Year Journal Volume Pages
Rawlings ND Evolutionary families of peptidases. 1993 Biochem J 290 ( Pt 1) 205-18
Rawlings ND Families of serine peptidases. 1994 Methods Enzymol 244 19-61
Teixeira MT Self-catalyzed cleavage of the yeast nucleoporin Nup145p precursor. 1999 J Biol Chem 274 32439-44
Hodel AE The three-dimensional structure of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98. 2002 Mol Cell 10 347-58
Robinson MA Multiple conformations in the ligand-binding site of the yeast nuclear pore-targeting domain of Nup116p. 2005 J Biol Chem 280 35723-32



To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)