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 (317) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,602 4,310 3
Proteins 1,601 4,309 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 1.391e-11 Least Informative Direct
Biological Process (BP) multicellular organismal process 7.198e-11 Least Informative Direct
Biological Process (BP) developmental process 6.877e-12 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.002559 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.06023 Least Informative Inherited
Biological Process (BP) response to stimulus 0.009577 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.03914 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.03868 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01341 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01139 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.007301 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.02625 Least Informative Inherited
Biological Process (BP) immune system process 2.301e-08 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 5.491e-08 Moderately Informative Direct
Biological Process (BP) gene expression 2.904e-06 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0002924 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 6.223e-07 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 7.511e-07 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 5.1e-08 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 4.392e-06 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 5.128e-08 Moderately Informative Direct
Biological Process (BP) cell differentiation 1.78e-12 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 7.55e-07 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 8.917e-07 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 4.915e-08 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 1.077e-05 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.0001711 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 3.933e-07 Moderately Informative Direct
Biological Process (BP) organ development 0.02064 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.035 Moderately Informative Inherited
Biological Process (BP) reproduction 0.06935 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6973 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-dependent 2.493e-13 Informative Direct
Biological Process (BP) response to wounding 0.0005804 Informative Direct
Biological Process (BP) response to inorganic substance 2.465e-05 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 6.128e-05 Informative Direct
Biological Process (BP) positive regulation of gene expression 9.196e-06 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.0002933 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 1.671e-05 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 9.583e-08 Informative Direct
Biological Process (BP) embryonic organ development 0.008946 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.3484 Informative Inherited
Biological Process (BP) cardiovascular system development 0.08942 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.03581 Informative Inherited
Biological Process (BP) sexual reproduction 0.2343 Informative Inherited
Biological Process (BP) single organism reproductive process 0.04082 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.006226 Informative Inherited
Biological Process (BP) placenta development 0.0007143 Highly Informative Direct
Biological Process (BP) female gamete generation 0.0002373 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.0001131 Highly Informative Direct
Biological Process (BP) response to calcium ion 8.543e-07 Highly Informative Direct
Biological Process (BP) cellular response to metal ion 6.455e-05 Highly Informative Direct
Biological Process (BP) ossification 0.001623 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 4.745e-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 1.644e-05 Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 8.999e-14 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 2.611e-14 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0006662 Least Informative Direct
Cellular Component (CC) protein complex 0.01642 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.09853 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 2.596e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.06733 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.006676 Informative Inherited

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.02926Least InformativeInherited
Disease Ontology (DO)hematologic cancer0.0001754Moderately 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)hematopoietic system phenotype0.0846Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.1626Least InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.1153Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.8594Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal bone marrow cell morphology/development0.1193InformativeInherited
Mammalian Phenotype (MP)abnormal erythrocyte morphology0.0002347Highly InformativeDirect
Mammalian Phenotype (MP)oxidative stress0.0008441Highly InformativeDirect
Mammalian Phenotype (MP)abnormal megakaryocyte morphology0.001603Highly InformativeInherited
Mammalian Phenotype (MP)abnormal liver size0.007508Highly InformativeInherited

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-oncogene1.525e-15Moderately InformativeDirect
DiseaseTumor suppressor1.822e-06Moderately InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainSignal-anchor4.075e-05InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationKinase0.2468Moderately InformativeInherited
Post-translational modificationSerine/threonine-protein kinase0.0002996InformativeDirect
Post-translational modificationPhosphoprotein5.639e-08Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond5.614e-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 ]