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 485 529 5
Proteins 485 529 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 2.688e-13 Least Informative Direct
Biological Process (BP) regulation of cellular process 9.229e-09 Least Informative Direct
Biological Process (BP) developmental process 1.707e-07 Least Informative Direct
Biological Process (BP) multicellular organismal process 1.02e-06 Least Informative Direct
Biological Process (BP) protein metabolic process 0.006704 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.0268 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5175 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.07366 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 9.796e-13 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 8.131e-07 Moderately Informative Direct
Biological Process (BP) reproduction 5.19e-06 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 2.656e-05 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 4.407e-05 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0002661 Moderately Informative Direct
Biological Process (BP) organ development 0.2162 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.3433 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2059 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.003977 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.005168 Moderately Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 4.046e-09 Informative Direct
Biological Process (BP) chromosome organization 1.51e-07 Informative Direct
Biological Process (BP) positive regulation of gene expression 2.267e-06 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 3.761e-06 Informative Direct
Biological Process (BP) reproductive system development 6.988e-06 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1.012e-05 Informative Direct
Biological Process (BP) embryonic organ development 1.199e-05 Informative Direct
Biological Process (BP) gland development 1.855e-05 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 2.988e-05 Informative Direct
Biological Process (BP) growth 4.766e-05 Informative Direct
Biological Process (BP) tube development 0.0002755 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.0004448 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.1955 Informative Inherited
Biological Process (BP) epithelium development 0.01686 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.001974 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.0104 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.001317 Informative Inherited
Biological Process (BP) internal protein amino acid acetylation 3.752e-15 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 1.177e-13 Highly Informative Direct
Biological Process (BP) histone modification 2.176e-10 Highly Informative Direct
Biological Process (BP) branching morphogenesis of an epithelial tube 1.243e-09 Highly Informative Direct
Biological Process (BP) placenta development 1.294e-08 Highly Informative Direct
Biological Process (BP) mammary gland epithelium development 9.461e-08 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 4.639e-05 Highly Informative Direct
Biological Process (BP) developmental growth 0.000424 Highly Informative Direct
Biological Process (BP) development of primary female sexual characteristics 0.06233 Highly Informative Inherited
Molecular Function (MF) binding 1.286e-11 Least Informative Direct
Molecular Function (MF) transferase activity 0.0006662 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.0001245 Moderately Informative Direct
Molecular Function (MF) chromatin binding 0 Informative Direct
Molecular Function (MF) receptor binding 1.47e-13 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 1.752e-11 Informative Direct
Molecular Function (MF) DNA binding 6.413e-06 Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 1.189e-14 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 6.446e-06 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.06658 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 3.614e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.01882 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 disease0.0003406Moderately InformativeDirect
Disease Ontology (DO)autosomal dominant disease1.4e-05InformativeDirect

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 homeostasis0.05345Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.1466Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1766Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)integument phenotype0.004348Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukopoiesis0.009812Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.0223Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hormone level0.03144Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.04174Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal circulating leptin level8.51e-05InformativeDirect
Mammalian Phenotype (MP)abnormal B cell differentiation0.0009919InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland morphology0.003631InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology0.0101InformativeInherited
Mammalian Phenotype (MP)increased hematopoietic cell number0.01262InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.01385InformativeInherited
Mammalian Phenotype (MP)increased circulating leptin level1.056e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development2.703e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal megakaryocyte morphology0.0002185Highly InformativeDirect
Mammalian Phenotype (MP)increased lymphocyte cell number0.002977Highly InformativeInherited

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 rhythms1.097e-12InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainBromodomain7.937e-13Highly InformativeDirect
Post-translational modificationTransferase6.44e-05Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationAcyltransferase0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation1.686e-12Least InformativeDirect
Post-translational modificationIsopeptide bond4.708e-10Moderately InformativeDirect
Post-translational modificationMethylation1.073e-07Moderately InformativeDirect
Post-translational modificationUbl conjugation2.053e-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 ]