SUPERFAMILY 1.75 HMM library and genome assignments server

Nuclear receptor coactivator interlocking domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Nuclear receptor coactivator interlocking domain [ 69124]
Superfamily:   Nuclear receptor coactivator interlocking domain [ 69125]
Families:   Nuclear receptor coactivator interlocking domain [ 69126] (3)


Superfamily statistics
Genomes (103) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 486 529 5
Proteins 486 529 5


Functional annotation
General category Regulation
Detailed category Signal transduction

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) regulation of metabolic process 0.0000000000001178 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.000000004181 Least Informative Direct
Biological Process (BP) developmental process 0.0000001682 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.000001015 Least Informative Direct
Biological Process (BP) protein metabolic process 0.005647 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.02235 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5198 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.07565 Least Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.0000000000005979 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0000009393 Moderately Informative Direct
Biological Process (BP) reproduction 0.000005251 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.00003084 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0002166 Moderately Informative Direct
Biological Process (BP) organ development 0.2165 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.3443 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2065 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.003697 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.005171 Moderately Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.000000003179 Informative Direct
Biological Process (BP) chromosome organization 0.0000001195 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.000002013 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.000004268 Informative Direct
Biological Process (BP) reproductive system development 0.000007114 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.00001 Informative Direct
Biological Process (BP) embryonic organ development 0.00001191 Informative Direct
Biological Process (BP) gland development 0.00001876 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.00002894 Informative Direct
Biological Process (BP) growth 0.000051 Informative Direct
Biological Process (BP) tube development 0.0002694 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.0004252 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.1915 Informative Inherited
Biological Process (BP) epithelium development 0.01711 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.002032 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.01115 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.00136 Informative Inherited
Biological Process (BP) internal protein amino acid acetylation 0.000000000000003755 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.00000000000008954 Highly Informative Direct
Biological Process (BP) histone modification 0.000000000168 Highly Informative Direct
Biological Process (BP) branching morphogenesis of an epithelial tube 0.0000000009469 Highly Informative Direct
Biological Process (BP) placenta development 0.000000012 Highly Informative Direct
Biological Process (BP) mammary gland epithelium development 0.00000009167 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.0000452 Highly Informative Direct
Biological Process (BP) developmental growth 0.0003947 Highly Informative Direct
Biological Process (BP) development of primary female sexual characteristics 0.0617 Highly Informative Inherited
Molecular Function (MF) binding 0.00000000001437 Least Informative Direct
Molecular Function (MF) transferase activity 0.0005295 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.0001003 Moderately Informative Direct
Molecular Function (MF) chromatin binding 0 Informative Direct
Molecular Function (MF) receptor binding 0.0000000000001432 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0000000000133 Informative Direct
Molecular Function (MF) DNA binding 0.000005177 Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.000000000000008977 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000006013 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.09498 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000007045 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.02887 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0Least InformativeDirect
Disease Ontology (DO)cell type cancer0Moderately InformativeDirect
Disease Ontology (DO)genetic disease0.0003398Moderately InformativeDirect
Disease Ontology (DO)autosomal dominant disease0.00001398InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal homeostasis0.05431Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.1484Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1783Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)integument phenotype0.004419Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukopoiesis0.009759Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.03237Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.03745Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal circulating leptin level0.00008488InformativeDirect
Mammalian Phenotype (MP)abnormal B cell differentiation0.0009486InformativeDirect
Mammalian Phenotype (MP)abnormal bone marrow cell morphology/development0.002744InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.003966InformativeInherited
Mammalian Phenotype (MP)increased circulating leptin level0.00001018Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.00002962Highly InformativeDirect
Mammalian Phenotype (MP)abnormal megakaryocyte morphology0.0002229Highly InformativeDirect

Document: MP 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processBiological rhythms0.000000000002387InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainBromodomain0.0000000000007832Highly InformativeDirect
Post-translational modificationTransferase0.00006442Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationAcyltransferase0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.000000000001695Least InformativeDirect
Post-translational modificationIsopeptide bond0.0000000005007Moderately InformativeDirect
Post-translational modificationMethylation0.0000001057Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000002152Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009110 SSF69125 Protein matches
Abstract

This entry represents the interlocking domain of various eukaryotic nuclear receptor coactivators, including CREBP, P300, Ncoa1, Ncoa2 and Ncoa3. The interlocking domain forms a 3-helical non-globular array that forms interlocked heterodimers with its target.

Nuclear receptors are ligand-activated transcription factors involved in the regulation of many processes, including development, reproduction and homeostasis. Nuclear receptor coactivators act to modulate the function of nuclear receptors. Coactivators associate with promoters and enhancers primarily through protein-protein contacts to facilitate the interaction between DNA-bound transcription factors and the transcription machinery. Many of these coactivators are structurally related, including CBP (CREB-binding protein), P300 and ACTR (activator for thyroid and retinoid receptors) [PubMed11823864]. CBP and P300 both have histone acetyltransferase activity . CBP/P300 proteins function synergistically to activate transcription, acting to remodel chromatin and to recruit RNA polymerase II and the basal transcription machinery. CBP is required for proper cell cycle control, differentiation and apoptosis. The interaction of CBP/P300 with transcription factors involves several small domains. The IBiD domain in the C-terminal of CBP is responsible for CBP interaction with IRF-3, as well as with the adenoviral oncoprotein E1A, TIF-2 coactivator, and the IRF homologue KSHV IRF-1 [PubMed11583620].

Ncoa1, Ncoa2 and Ncoa3 are all coactivators of various nuclear receptors. In addition, Ncoa1 and Ncoa3 both have histone acetyltransferase activity, but Ncoa2 does not [PubMed14757047, PubMed15145939].


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) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · 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 3 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 Nuclear receptor coactivator interlocking domain 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 3 hidden Markov models representing the Nuclear receptor coactivator interlocking domain 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) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]