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 (475) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 836 876 1
Proteins 821 875 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 0.00000004905 Least Informative Direct
Biological Process (BP) developmental process 0.01358 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.2806 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02174 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.02097 Least Informative Inherited
Biological Process (BP) response to stimulus 0.003292 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.07623 Least Informative Inherited
Biological Process (BP) macromolecule localization 0.00000001751 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0000006229 Moderately Informative Direct
Biological Process (BP) cellular localization 0.000001857 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.00001983 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0001152 Moderately Informative Direct
Biological Process (BP) signal transduction 0.000218 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0006193 Moderately Informative Direct
Biological Process (BP) protein localization to organelle 0 Informative Direct
Biological Process (BP) cytoplasmic transport 0 Informative Direct
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) single-organism cellular localization 0.00000000009427 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.00000003762 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.0000001157 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.0001678 Informative Direct
Biological Process (BP) nitrogen compound transport 0.03182 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.05539 Informative Inherited
Biological Process (BP) protein import 0 Highly Informative Direct
Biological Process (BP) single-organism nuclear import 0 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.00000000000263 Highly Informative Direct
Biological Process (BP) nucleus organization 0.0000000005075 Highly Informative Direct
Biological Process (BP) stem cell development 0.000000002953 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.00000001527 Highly Informative Direct
Biological Process (BP) phagocytosis 0.000001028 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.000003421 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.003282 Highly Informative Inherited
Molecular Function (MF) structural molecule activity 0.000004969 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.000294 Moderately Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000000002746 Least Informative Direct
Cellular Component (CC) protein complex 0.00000000005328 Least Informative Direct
Cellular Component (CC) membrane 0.000000002647 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000001884 Least Informative Direct
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000000006711 Moderately Informative Direct
Cellular Component (CC) integral component of 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 0.00005399 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 componentMembrane0.000002238Least InformativeDirect
DomainRepeat0.00000000516Least InformativeDirect
Post-translational modificationAutocatalytic cleavage0.0000000006966InformativeDirect

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 ]