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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 (323) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 1,622 4,307 3
Proteins 1,621 4,301 3


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.03186Least InformativeInherited
Disease Ontology (DO)hematologic cancer0.0001649Moderately 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

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.1023Least InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.009341Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.1688Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.1903Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.6228Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal liver size0.01051Highly InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell number0.0189Highly InformativeInherited
Mammalian Phenotype (MP)abnormal bone marrow cell morphology/development0.06134Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)visible0InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)thoracic segment0Moderately InformativeDirect
Fly Anatomy (FA)adult segment0Moderately InformativeDirect
Fly Anatomy (FA)adult thorax0Moderately InformativeDirect
Fly Anatomy (FA)adult integumentary system0Moderately InformativeDirect
Fly Anatomy (FA)appendage0Moderately InformativeDirect
Fly Anatomy (FA)tagmatic subdivision of integument0Moderately InformativeDirect

Document: FA 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 phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor0InformativeDirect

Document: EC 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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]