SUPERFAMILY 1.75 HMM library and genome assignments server


A DNA-binding domain in eukaryotic transcription factors superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   A DNA-binding domain in eukaryotic transcription factors [ 47453]
Superfamily:   A DNA-binding domain in eukaryotic transcription factors [ 47454]
Families:   A DNA-binding domain in eukaryotic transcription factors [ 47455] (2)


Superfamily statistics
Genomes (306) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,479 2,463 3
Proteins 1,479 2,462 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) regulation of metabolic process 1.649e-10 Least Informative Direct
Biological Process (BP) multicellular organismal process 1.994e-10 Least Informative Direct
Biological Process (BP) developmental process 2.201e-11 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.03614 Least Informative Inherited
Biological Process (BP) response to stimulus 0.007863 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.002675 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.05667 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.03621 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01275 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01077 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.006256 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.02492 Least Informative Inherited
Biological Process (BP) immune system process 2.123e-09 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 1.817e-08 Moderately Informative Direct
Biological Process (BP) gene expression 2.355e-06 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0003589 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1.521e-06 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 7.609e-07 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 3.346e-08 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 7.305e-06 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 3.489e-08 Moderately Informative Direct
Biological Process (BP) cell differentiation 6.412e-13 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 1.593e-06 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 7.478e-07 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 2.979e-08 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 2.194e-06 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 5.708e-06 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.0001508 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 2.855e-07 Moderately Informative Direct
Biological Process (BP) organ development 0.04645 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.07698 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-dependent 2.89e-13 Informative Direct
Biological Process (BP) response to wounding 0.0003891 Informative Direct
Biological Process (BP) response to inorganic substance 2.432e-05 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 2.545e-05 Informative Direct
Biological Process (BP) positive regulation of gene expression 4.014e-06 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.0001349 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 2.481e-09 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 5.539e-06 Informative Direct
Biological Process (BP) embryonic organ development 0.02286 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.1951 Informative Inherited
Biological Process (BP) cardiovascular system development 0.07248 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.05671 Informative Inherited
Biological Process (BP) placenta development 0.0006975 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 4.276e-05 Highly Informative Direct
Biological Process (BP) response to calcium ion 7.36e-07 Highly Informative Direct
Biological Process (BP) cellular response to metal ion 6.194e-05 Highly Informative Direct
Biological Process (BP) ossification 0.001251 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 4.784e-06 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 6.458e-05 Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 3.221e-08 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.01497 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1505 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.008332 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1.282e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.04989 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0002993 Informative Direct
Cellular Component (CC) nucleoplasm part 0.01221 Informative Inherited
Cellular Component (CC) transcription factor complex 8.634e-15 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.02884Least InformativeInherited
Disease Ontology (DO)hematologic cancer0.0001734Moderately InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the globe0Moderately InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.1281Least InformativeInherited
Mammalian Phenotype (MP)oxidative stress0.0007714Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DiseaseProto-oncogene2.199e-15Moderately InformativeDirect
DiseaseTumor suppressor2.024e-06Moderately InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainSignal-anchor4.064e-05InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationKinase0.2459Moderately InformativeInherited
Post-translational modificationSerine/threonine-protein kinase0.0003003InformativeDirect
Post-translational modificationPhosphoprotein5.593e-08Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond3.934e-12Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008917 SSF47454 Protein matches
Abstract

The DNA-binding domain of certain eukaryotic transcription factors displays a distinctive helix-turn-helix (HTH) motif. The MafG basic region-leucine zipper (bZIP) protein and the C. elegans Skn-1 transcription factor share this HTH motif.

MafG is a member of the Maf family of proteins, which are a subgroup of bZIP proteins that function as transcriptional regulators of cellular differentiation. Mafs can form either homodimers, or heterodimers with other bZIP proteins through their leucine zipper domains. MafG proteins are small Mafs that lack a putative transactivation domain. The DNA-binding domain of MafG contains the conserved Maf extended homology region (EHR), which is not present in other bZIP proteins. The EHR together with the basic region are responsible for the DNA-binding specificity of Mafs.

Skn-1 is a transcription factor that specifies mesodermal development in C. elegans. Skn-1 and MafG share a conserved DNA-binding motif, however Skn-1 lacks the leucine zipper dimerisation domain that is found in all bZIP proteins. Skn-1 acts as a monomer.

The DNA-binding domains in MafG [PubMed11875518] and Skn-1 [PubMed9628487] share structural similarity, despite a sequence identity of only 25%. The domain fold consists of three (MafG) to four (Skn-1) helices, where the long C-terminal helix protrudes from the domain and binds to DNA. MafG lacks the N-terminal helix of Skn-1. A basic cluster of residues is present on the surface of the domain, which together with the amino acid sequence motif, NXXYAXXCR, forms a DNA-binding surface. MafG and Skn-1 may use a common DNA-binding mode. However, the involvement of helix 2 (H2) in DNA recognition differs between MafG and Skn-1, with two residues at the beginning of H2 in MafG contributing to the unique DNA-binding specificity of Mafs.


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) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 A DNA-binding domain in eukaryotic transcription factors 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 A DNA-binding domain in eukaryotic transcription factors 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) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]