SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,837) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 18,052 76,611 38
Proteins 17,436 73,875 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)protein metabolic process0.000055960.0000001024Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.000000000031680Least InformativeDirect
Biological Process (BP)regulation of cellular process0.13891Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.99981Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.98461Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.97931Least InformativeInherited
Biological Process (BP)cellular protein modification process0.87151Moderately InformativeInherited
Biological Process (BP)regulation of localization0.55140.9169Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.53870.6945Moderately InformativeInherited
Biological Process (BP)gene expression0.71080.9522Moderately InformativeInherited
Biological Process (BP)RNA processing0.000025650.00000001201InformativeDirect
Biological Process (BP)peptidyl-amino acid modification0.0000000099410InformativeDirect
Biological Process (BP)regulation of ion transport0.0056010.0314InformativeInherited
Biological Process (BP)mRNA processing0.00049910.000104Highly InformativeDirect
Biological Process (BP)protein folding0.0000000009860Highly InformativeDirect
Biological Process (BP)regulation of proton transport0.0000025080.00000007641Highly InformativeDirect
Biological Process (BP)peptidyl-proline modification00Highly InformativeDirect
Biological Process (BP)regulation of multi-organism process0.00000000041370.000001794Highly InformativeDirect
Biological Process (BP)RNA splicing0.0025090.000004721Highly InformativeInherited
Molecular Function (MF)binding0.086370.07157Least InformativeInherited
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)amide binding0.000000000000025510InformativeDirect
Molecular Function (MF)drug binding0.0000000000000026380Highly InformativeDirect
Molecular Function (MF)peptide binding0.0000000000000052090Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.066040.1616Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.033980.0005368Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.79180.02386Least InformativeInherited
Cellular Component (CC)cytosol0.000037450.0002058Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex0.017220.00008192Moderately InformativeInherited
Cellular Component (CC)nuclear part0.35620.003758Moderately InformativeInherited
Cellular Component (CC)spliceosomal complex0.0000000020530.000000000000006018Highly 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) protein metabolic process 0.0000001024 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.9169 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.3766 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.6945 Moderately Informative Inherited
Biological Process (BP) gene expression 0.9522 Moderately Informative Inherited
Biological Process (BP) RNA processing 0.00000001201 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) regulation of ion transport 0.0314 Informative Inherited
Biological Process (BP) mRNA processing 0.000104 Highly Informative Direct
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) RNA splicing 0.000004721 Highly Informative Direct
Biological Process (BP) regulation of proton transport 0.00000007641 Highly Informative Direct
Biological Process (BP) peptidyl-proline modification 0 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 0.000001794 Highly Informative Direct
Molecular Function (MF) binding 0.07157 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) protein complex binding 0.0000000000001295 Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
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 0.0005368 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.1616 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.02386 Least Informative Inherited
Cellular Component (CC) cytosol 0.0002058 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0.00008192 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.003758 Moderately Informative Inherited
Cellular Component (CC) plastid 0.01501 Informative Inherited
Cellular Component (CC) spliceosomal complex 0.000000000000006018 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.0000661Least InformativeDirect
Worm Phenotype (WP)protein aggregation variant0.000000003439Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0000000669Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)freeze-thaw resistance0.00003845Highly InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.0005331InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases0.8692InformativeInherited
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase0.00000000004329Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0.00003539Moderately InformativeDirect
Biological processmRNA splicing0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndoplasmic reticulum0.00000000000003529Moderately InformativeDirect
Cellular componentSpliceosome0InformativeDirect
DomainTPR repeat0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationChaperone0.000000002871InformativeDirect
Post-translational modificationRotamase0Highly InformativeDirect
Post-translational modificationAcetylation0.000000000001582Least InformativeDirect
Post-translational modificationIsopeptide bond0.00000003336Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0001637Moderately InformativeDirect
Post-translational modificationS-nitrosylation0.0000086InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0.0001799Least InformativeDirect
UniPathway (UP)protein sumoylation0.000000000000005322Highly InformativeDirect

Document: UP 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

    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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]