SUPERFAMILY 1.75 HMM library and genome assignments server


C-terminal autoproteolytic domain of nucleoporin nup98 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   C-terminal autoproteolytic domain of nucleoporin nup98 [ 82214]
Superfamily:   C-terminal autoproteolytic domain of nucleoporin nup98 [ 82215]
Families:   C-terminal autoproteolytic domain of nucleoporin nup98 [ 82216]


Superfamily statistics
Genomes (462) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 804 876 1
Proteins 791 875 1


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) localization 8.114e-07 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.005653 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.0719 Least Informative Inherited
Biological Process (BP) developmental process 0.04583 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.08697 Least Informative Inherited
Biological Process (BP) response to stimulus 0.01656 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1412 Least Informative Inherited
Biological Process (BP) cellular localization 6.215e-11 Moderately Informative Direct
Biological Process (BP) macromolecule localization 2.843e-08 Moderately Informative Direct
Biological Process (BP) organic substance transport 1.003e-06 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 2.447e-05 Moderately Informative Direct
Biological Process (BP) signal transduction 0.0002334 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0004489 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0005288 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0.06527 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.06391 Moderately Informative Inherited
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) protein localization to organelle 0 Informative Direct
Biological Process (BP) negative regulation of developmental process 2.195e-08 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.0001484 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0001586 Informative Direct
Biological Process (BP) nitrogen compound transport 0.03652 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.06419 Informative Inherited
Biological Process (BP) nuclear import 0 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 0 Highly Informative Direct
Biological Process (BP) protein import 0 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0 Highly Informative Direct
Biological Process (BP) stem cell development 3.38e-09 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 8.069e-09 Highly Informative Direct
Biological Process (BP) nucleus organization 6.231e-08 Highly Informative Direct
Biological Process (BP) phagocytosis 1.081e-06 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 4.363e-06 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.003409 Highly Informative Inherited
Molecular Function (MF) structural molecule activity 1.724e-05 Moderately Informative Direct
Cellular Component (CC) protein complex 2.569e-09 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 4.947e-08 Least Informative Direct
Cellular Component (CC) membrane 1.91e-07 Least Informative Direct
Cellular Component (CC) intracellular organelle part 2.659e-06 Least Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 1.608e-15 Moderately Informative Direct
Cellular Component (CC) nuclear part 4.036e-08 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.04837 Moderately Informative Inherited
Cellular Component (CC) integral to membrane 0 Informative Direct
Cellular Component (CC) nuclear envelope 0 Informative Direct
Cellular Component (CC) pore complex 0 Highly Informative Direct
Cellular Component (CC) nuclear membrane 3.918e-05 Highly Informative Direct

Document: GO annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Biological processTranslocation0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane2.18e-06Least InformativeDirect
DomainRepeat5.105e-09Least InformativeDirect
Post-translational modificationAutocatalytic cleavage7.097e-10InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR007230 SSF82215 Protein matches
Abstract

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 [PubMed10542288].

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 [PubMed12191480].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 1 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a C-terminal autoproteolytic domain of nucleoporin nup98 domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 1 hidden Markov models representing the C-terminal autoproteolytic domain of nucleoporin nup98 superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]