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Cyclophilin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Cyclophilin-like [ 50890]
Superfamily:   Cyclophilin-like [ 50891] (4)
Families:   Cyclophilin (peptidylprolyl isomerase) [ 50892] (12)
  Outer surface protein, C-terminal domain [ 110278]
  TM1367-like [ 141519]
  PH0987 C-terminal domain-like [ 159249]


Superfamily statistics
Genomes (2,845) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 18,243 79,824 38
Proteins 17,617 75,533 38


Functional annotation
General category Processes_IC
Detailed category Protein modification

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)macromolecule metabolic process0.00073780.0000005019Least InformativeDirect
Biological Process (BP)biological regulation0.058031Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.48850.04904Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.45790.8504Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.45370.964Least InformativeInherited
Biological Process (BP)primary metabolic process0.24180.01177Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.63580.9669Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.6080.9918Least InformativeInherited
Biological Process (BP)cellular protein modification process0.000040190.00000000001548Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.35211Moderately InformativeInherited
Biological Process (BP)gene expression0.4570.4226Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.24170.3868Moderately InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.0000082780InformativeDirect
Biological Process (BP)mRNA processing0.00000046170.00001219Highly InformativeDirect
Biological Process (BP)protein folding00Highly InformativeDirect
Biological Process (BP)RNA splicing0.00000066390.000000129Highly InformativeDirect
Biological Process (BP)regulation of generation of precursor metabolites and energy0.000023030.00001946Highly InformativeDirect
Biological Process (BP)regulation of viral process0.000000000014220.00000000002198Highly InformativeDirect
Biological Process (BP)regulation of ATP metabolic process0.000010860.000003535Highly InformativeDirect
Molecular Function (MF)binding0.013710.03436Least InformativeInherited
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)amide binding0.0000000000000053890InformativeDirect
Molecular Function (MF)drug binding00Highly InformativeDirect
Molecular Function (MF)peptide binding00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0016380.000002894Least InformativeInherited
Cellular Component (CC)intracellular organelle part10.02183Least InformativeInherited
Cellular Component (CC)nuclear part0.17780.00007582Moderately InformativeInherited
Cellular Component (CC)spliceosomal complex0.000000000082550Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) macromolecule metabolic process 0.0000005019 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.04904 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8504 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.964 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.01177 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.9669 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9918 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.00000000001548 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.4226 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.3868 Moderately Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) mRNA processing 0.00001219 Highly Informative Direct
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) RNA splicing 0.000000129 Highly Informative Direct
Biological Process (BP) regulation of generation of precursor metabolites and energy 0.00001946 Highly Informative Direct
Biological Process (BP) regulation of viral process 0.00000000002198 Highly Informative Direct
Biological Process (BP) regulation of ATP metabolic process 0.000003535 Highly Informative Direct
Molecular Function (MF) binding 0.03436 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) macromolecular complex binding 0 Informative Direct
Molecular Function (MF) receptor binding 0.1535 Informative Inherited
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) peptide binding 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000002894 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.02183 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00007582 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.02078 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0.02049 Informative Inherited
Cellular Component (CC) nuclear pore 0.000004303 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0 Highly Informative Direct
Cellular Component (CC) thylakoid 0.0006254 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processUbl conjugation pathway0.000000006546Moderately InformativeDirect
Biological processApoptosis0.00004327Moderately InformativeDirect
Biological processmRNA processing0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndoplasmic reticulum0.0000000000003046Moderately InformativeDirect
Cellular componentSpliceosome0InformativeDirect
DomainTPR repeat0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationChaperone0.0000000009039InformativeDirect
Post-translational modificationRotamase0Highly InformativeDirect
Post-translational modificationAcetylation0.0000000000001389Least InformativeDirect
Post-translational modificationIsopeptide bond0.00000002042Moderately InformativeDirect
Post-translational modificationUbl conjugation0.00001003Moderately InformativeDirect
Post-translational modificationS-nitrosylation0.0000001303InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015891 SSF50891 Protein matches
Abstract

This entry represents the core beta-barrel (8,10) domain found in cyclophilin (peptidylprolyl isomerise). This domain is related to a beta-barrel domain found in several outer membrane proteins, usually at the C-terminus; in these proteins, the beta-barrel (7,10) lacks the N-terminal strand of the cyclophilin domain, but remains closed.

Cyclophilin is the major high-affinity binding protein in vertebrates for the immunosuppressive drug cyclosporin A (CSA), but is also found in other organisms. It exhibits a peptidyl-prolyl cis-trans isomerase activity (PPIase or rotamase). PPIase is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides [PubMed2186809]. It is probable that CSA mediates some of its effects via an forming a tight complex with cyclophilin that inhibits the phosphatase activity of calcineurin [PubMed7514602], [PubMed8117697]. Cyclophilin A is a cytosolic and highly abundant protein. The protein belongs to a family of isozymes, including cyclophilins B and C, and natural killer cell cyclophilin-related protein [PubMed1464374, PubMed8404888, PubMed7526121]. Major isoforms have been found throughout the cell, including the ER, and some are even secreted. The sequences of the different forms of cyclophilin-type PPIases are well conserved.

  • Note: FKBP's, a family of proteins that bind the immunosuppressive drug FK506, are also PPIases, but their sequence is not at all related to that of cyclophilin (see ).

  • 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 29 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 Cyclophilin-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 29 hidden Markov models representing the Cyclophilin-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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]