SUPERFAMILY 1.75 HMM library and genome assignments server

Prion-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Prion-like [ 54097]
Superfamily:   Prion-like [ 54098]
Families:   Prion-like [ 54099] (2)


Superfamily statistics
Genomes (61) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 121 941 35
Proteins 121 940 35


Functional annotation
General category Other
Detailed category Unknown function

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) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.5419 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1531 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.05386 Moderately Informative Inherited
Biological Process (BP) cellular chemical homeostasis 0.0000009332 Informative Direct
Biological Process (BP) cation homeostasis 0.000001365 Informative Direct
Biological Process (BP) regulation of ion transport 0.00001455 Informative Direct
Biological Process (BP) response to oxidative stress 0.0001879 Informative Direct
Biological Process (BP) negative regulation of cell death 0.0009561 Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.00000000008637 Highly Informative Direct
Biological Process (BP) regulation of ion transmembrane transport 0.00000003276 Highly Informative Direct
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) cation binding 0 Moderately Informative Direct
Molecular Function (MF) protein complex binding 0 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0 Informative Direct
Molecular Function (MF) tubulin binding 0 Highly Informative Direct
Molecular Function (MF) copper ion binding 0 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) membrane region 0 Moderately Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentGPI-anchor0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCopper0InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000817 SSF54098 Protein matches
Abstract

Prion protein (PrP-c) [PubMed2572197, PubMed1916104, PubMed2908696] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) [PubMed12354606].

The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process.

In humans, PrP is a 253 amino acid protein, which has a molecular weight of 3536 kDa. It has two hexapeptides and repeated octapeptides at the N-terminus, a disulphide bond and is associated at the C-terminus with a GPI, which enables it to anchor to the external part of the cell membrane. The secondary structure of PrP-c is mainly composed of alpha-helices, whereas PrP-sc is mainly beta-sheets: transconformation of alpha-helices into beta-sheets has been proposed as the structural basis by which PrP acquires pathogenicity in TSEs. The three-dimensional structures shows the protein to be made of a globular domain which includes three alpha-helices and two small antiparallel beta-sheet structures, and a long flexible tail whose conformation depends on the biophysical parameters of the environment. Crystals of the globular domain of PrP have recently been obtained; their analysis suggests a possible dimerisation of the protein through the three-dimensional swapping of the C-terminal helix 3 and rearrangement of the disulphide bond.


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) · 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 12 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 Prion-like 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 12 hidden Markov models representing the Prion-like 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) · UniProtKB KeyWords (KW) · Internal database links ]