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 (92) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 438 446 5
Proteins 438 446 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 1.84e-13 Least Informative Direct
Biological Process (BP) regulation of cellular process 1.328e-08 Least Informative Direct
Biological Process (BP) developmental process 1.225e-07 Least Informative Direct
Biological Process (BP) multicellular organismal process 8.495e-07 Least Informative Direct
Biological Process (BP) protein metabolic process 0.01577 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.05683 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.4638 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1221 Least Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 7.835e-15 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 4.344e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 7.784e-06 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 4.523e-05 Moderately Informative Direct
Biological Process (BP) reproduction 7.964e-05 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0008825 Moderately Informative Direct
Biological Process (BP) organ development 0.156 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.2812 Moderately Informative Inherited
Biological Process (BP) tissue development 0.1225 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.09135 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.007954 Moderately Informative Inherited
Biological Process (BP) chordate embryonic development 1.243e-09 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 6.24e-09 Informative Direct
Biological Process (BP) chromosome organization 3.861e-07 Informative Direct
Biological Process (BP) positive regulation of gene expression 8.21e-07 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 2.305e-06 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 4.998e-06 Informative Direct
Biological Process (BP) embryonic organ development 7.903e-06 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 1.572e-05 Informative Direct
Biological Process (BP) reproductive system development 1.597e-05 Informative Direct
Biological Process (BP) gland development 4.484e-05 Informative Direct
Biological Process (BP) growth 8.637e-05 Informative Direct
Biological Process (BP) tube development 0.000129 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.0009748 Informative Direct
Biological Process (BP) epithelium development 0.06815 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.003586 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.002958 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.00166 Informative Inherited
Biological Process (BP) internal protein amino acid acetylation 7.835e-15 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 2.034e-13 Highly Informative Direct
Biological Process (BP) histone modification 4.964e-10 Highly Informative Direct
Biological Process (BP) mammary gland epithelium development 2.227e-07 Highly Informative Direct
Biological Process (BP) embryonic placenta development 5.029e-07 Highly Informative Direct
Biological Process (BP) developmental growth 0.0005476 Highly Informative Direct
Biological Process (BP) morphogenesis of a branching epithelium 0.002196 Highly Informative Inherited
Biological Process (BP) epithelial tube morphogenesis 0.05745 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.08408 Highly Informative Inherited
Molecular Function (MF) binding 1.248e-12 Least Informative Direct
Molecular Function (MF) transferase activity 0.001146 Least Informative Inherited
Molecular Function (MF) protein binding 0.1801 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.4109 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.4374 Moderately Informative Inherited
Molecular Function (MF) receptor binding 1.471e-12 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 6.195e-11 Informative Direct
Molecular Function (MF) DNA binding 2.12e-06 Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 2.744e-14 Highly Informative Direct
Molecular Function (MF) transcription factor binding 1.312e-13 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.03784 Least Informative Inherited
Cellular Component (CC) protein complex 0.02872 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1.947e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.01003 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.159 Informative Inherited
Cellular Component (CC) transcription factor complex 7.984e-05 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)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 disease0.00174Moderately InformativeInherited
Disease Ontology (DO)carcinoma0InformativeDirect
Disease Ontology (DO)autosomal dominant disease0.0001227InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.0476Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.1012Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.172Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)embryogenesis phenotype0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.003456Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.004083Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood homeostasis0.01137Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.02098Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.0335Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.03564Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.001942InformativeInherited
Mammalian Phenotype (MP)increased leukocyte cell number0.007562InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.01291InformativeInherited
Mammalian Phenotype (MP)abnormal circulating hormone level0.06662InformativeInherited
Mammalian Phenotype (MP)increased circulating leptin level9.703e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development3.5e-05Highly InformativeDirect
Mammalian Phenotype (MP)increased T cell number0.0007725Highly InformativeDirect

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least 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 acetyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainBromodomain1.059e-12Highly InformativeDirect
Molecular functionMetal-binding0.2742Least InformativeInherited
Molecular functionZinc-finger1.482e-05Moderately InformativeDirect
Post-translational modificationTransferase7.57e-05Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationAcyltransferase7.07e-07InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond3.659e-10Moderately InformativeDirect
Post-translational modificationAcetylation1.674e-09Moderately InformativeDirect
Post-translational modificationMethylation9.577e-08Moderately InformativeDirect
Post-translational modificationUbl conjugation1.485e-07Moderately 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 ]