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KRAB domain (Kruppel-associated box) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   KRAB domain (Kruppel-associated box) [ 109639]
Superfamily:   KRAB domain (Kruppel-associated box) [ 109640]
Families:   KRAB domain (Kruppel-associated box) [ 109641]


Superfamily statistics
Genomes (54) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 11,034 14,299 1
Proteins 10,867 13,901 1


Functional annotation
General category Regulation
Detailed category RNA binding, metabolism and transport

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)biological regulation0.93121Least InformativeInherited
Biological Process (BP)response to stimulus11Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)multicellular organismal process11Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.011020.00007831Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.022840.001519Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.14910.7432Moderately InformativeInherited
Biological Process (BP)tissue development0.068361Moderately InformativeInherited
Biological Process (BP)single organism signaling0.33631Moderately InformativeInherited
Biological Process (BP)cell communication0.45911Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.012610.0001769Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.053160.009158Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.0120.0002398Moderately InformativeInherited
Biological Process (BP)anatomical structure morphogenesis0.15671Moderately InformativeInherited
Biological Process (BP)cell differentiation0.22941Moderately InformativeInherited
Biological Process (BP)negative regulation of macromolecule biosynthetic process0.000013540.00000000000002436InformativeDirect
Biological Process (BP)negative regulation of cellular biosynthetic process0.000029920.0000000000002226InformativeDirect
Biological Process (BP)negative regulation of gene expression0.00019180.0000000001773InformativeDirect
Biological Process (BP)cell surface receptor signaling pathway0.0065221InformativeInherited
Biological Process (BP)growth0.014061InformativeInherited
Biological Process (BP)localization of cell0.011381InformativeInherited
Biological Process (BP)movement of cell or subcellular component0.025071InformativeInherited
Biological Process (BP)locomotion0.030681InformativeInherited
Biological Process (BP)circulatory system development0.0010191InformativeInherited
Biological Process (BP)vasculogenesis0.00000000060940.0001214Highly InformativeDirect
Biological Process (BP)negative regulation of RNA metabolic process0.000003250Highly InformativeDirect
Biological Process (BP)muscle tissue development0.0000005870.2105Highly InformativeInherited
Biological Process (BP)enzyme linked receptor protein signaling pathway0.0000026250.6555Highly InformativeInherited

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) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00007831 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0002398 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0001769 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.001519 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.7432 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.009158 Moderately Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.00000000000002436 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.0000000000002226 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0000000001773 Informative Direct
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) growth 1 Informative Inherited
Biological Process (BP) localization of cell 1 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 1 Informative Inherited
Biological Process (BP) locomotion 1 Informative Inherited
Biological Process (BP) circulatory system development 1 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) vasculogenesis 0.0001214 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0 Highly Informative Direct
Biological Process (BP) muscle tissue development 0.2105 Highly Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.6555 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) metal ion binding 0.276 Moderately Informative Inherited
Molecular Function (MF) zinc ion binding 0.00000005456 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.005044 Informative Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Coding sequence diversityPolymorphism0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001909 SSF109640 Protein matches
Abstract

The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) [PubMed14519192]. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box [PubMed2023909].

The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [PubMed8183939, PubMed8183940]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [PubMed10653693, PubMed10748030].

KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome [PubMed10360839]. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.


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) · 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 1 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 KRAB domain (Kruppel-associated box) 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 1 hidden Markov models representing the KRAB domain (Kruppel-associated box) 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) · UniProtKB KeyWords (KW) · Internal database links ]