SUPERFAMILY 1.75 HMM library and genome assignments server


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 (55) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,035 11,445 1
Proteins 10,868 11,124 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)regulation of cellular process0.88681Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.90650.9936Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.10487.187e-05Moderately InformativeInherited
Biological Process (BP)regulation of biosynthetic process0.29040.0008223Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.30690.001616Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.31230.001319Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.57910.9625Moderately InformativeInherited
Biological Process (BP)negative regulation of gene expression0.008332.411e-09InformativeInherited
Biological Process (BP)negative regulation of nitrogen compound metabolic process0.0091937.618e-11InformativeInherited
Biological Process (BP)negative regulation of biosynthetic process0.013652.181e-09InformativeInherited
Biological Process (BP)regulation of transcription from RNA polymerase II promoter0.017281InformativeInherited
Biological Process (BP)negative regulation of transcription, DNA-dependent0.0038096.199e-09Highly 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) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.9936 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 7.187e-05 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.0008223 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.9625 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.001616 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.001319 Moderately Informative Inherited
Biological Process (BP) negative regulation of gene expression 2.411e-09 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 7.618e-11 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 2.181e-09 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of cell cycle process 1 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 6.199e-09 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 0.5428 Highly Informative Inherited
Biological Process (BP) positive regulation of cell cycle process 0.1843 Highly Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 0.3673 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) cation binding 0.01192 Moderately Informative Inherited
Molecular Function (MF) transition metal ion binding 1.015e-06 Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)X-linked inheritance0InformativeDirect

Document: HP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

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
Coding sequence diversityPolymorphism0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately 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) · Human Phenotype (HP) · 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 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) · Human Phenotype (HP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]