SUPERFAMILY 1.75 HMM library and genome assignments server

PAH2 domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   PAH2 domain [ 47761]
Superfamily:   PAH2 domain [ 47762]
Families:   PAH2 domain [ 47763] (2)


Superfamily statistics
Genomes (452) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,461 3,199 3
Proteins 1,537 1,401 3


Functional annotation
General category Regulation
Detailed category DNA-binding

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) developmental process 0.00000001388 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0000001053 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.000004196 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00005154 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.002294 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.04001 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01295 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.005031 Least Informative Inherited
Biological Process (BP) localization 0.009994 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00000000109 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000000001233 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00000000289 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000006747 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000000007693 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0000003133 Moderately Informative Direct
Biological Process (BP) immune system process 0.00008041 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.00008081 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0009354 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.00444 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.561 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.8237 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.07267 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.07168 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2972 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1608 Moderately Informative Inherited
Biological Process (BP) organ development 0.003982 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.8274 Moderately Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.000000003434 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00000001736 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00000002695 Informative Direct
Biological Process (BP) chromosome organization 0.000007245 Informative Direct
Biological Process (BP) locomotion 0.000009391 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.00005023 Informative Direct
Biological Process (BP) regulation of locomotion 0.00005299 Informative Direct
Biological Process (BP) localization of cell 0.0005362 Informative Direct
Biological Process (BP) generation of neurons 0.9145 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.1615 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.006059 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.001813 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.01504 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.02409 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.03214 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.003962 Informative Inherited
Biological Process (BP) cell projection organization 0.009891 Informative Inherited
Biological Process (BP) muscle structure development 0.001326 Informative Inherited
Biological Process (BP) cellular component movement 0.02896 Informative Inherited
Biological Process (BP) protein deacylation 0.000000000007917 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.00000004306 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0000002392 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.000003334 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 0.000003685 Highly Informative Direct
Biological Process (BP) aging 0.00001518 Highly Informative Direct
Biological Process (BP) neuron projection development 0.00002935 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 0.00003917 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00005047 Highly Informative Direct
Biological Process (BP) histone modification 0.000311 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0006254 Highly Informative Direct
Molecular Function (MF) binding 0.002002 Least Informative Inherited
Molecular Function (MF) chromatin binding 0.00003273 Informative Direct
Molecular Function (MF) protein dimerization activity 0.006191 Informative Inherited
Molecular Function (MF) transcription factor binding transcription factor activity 0.000000000005256 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.00000002676 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.000003084 Least Informative Direct
Cellular Component (CC) protein complex 0.00000333 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0005383 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8074 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000419 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00002917 Moderately Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00000001701 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0000001593 Highly Informative Direct
Cellular Component (CC) chromatin 0.008312 Highly Informative Inherited

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)E expanded cotyledon 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.04 four leaves visible stage0Least InformativeDirect

Document: AP 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
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.00004341Least InformativeDirect
Post-translational modificationUbl conjugation0.0000009516Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR003822 SSF47762 Protein matches
Abstract

This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 [PubMed11101889]. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin [PubMed14705930]. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [PubMed15235594].


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) · Arabidopsis Plant Ontology (AP) · 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 2 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 PAH2 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 2 hidden Markov models representing the PAH2 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]