SUPERFAMILY 1.73 HMM library and genome assignments server


ssDNA-binding transcriptional regulator domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (334)
  Mainly antiparallel beta sheets (segregated alpha and beta regions)
Fold:   ssDNA-binding transcriptional regulator domain [ 54446]
  helix-swapped dimer of beta(4)-alpha motifs
Superfamily:   ssDNA-binding transcriptional regulator domain [ 54447] (4)
Families:   Transcriptional coactivator PC4 C-terminal domain [ 54448]
  dimer of two separate motifs
  Plant transcriptional regulator PBF-2 [ 75375]
  single-chain domain formed by a tandem repeat of two motifs
  PMN2A0962/syc2379c-like [ 143038] (2)
  Pfam 08848; DUF1818; specific to cyanobacteria; single-chain domain made of two repeats of this structural motif
  Guide RNA binding protein gBP [ 143043] (2)
  includes PfamB 080318 and PB073991; forms heterooligomers; similar subunit and oligomeric structures to the Plant transcriptional regulator family


Superfamily statistics
Genomes (277) UniProt 15.0 PDB chains (SCOP 1.73)
Domains 426 267 6
Proteins 407 264 6


Functional annotation
General category Regulation
Detailed category DNA-binding

Function annotation of SCOP domain superfamilies
InterPro annotation
Cross references IPR009044 SSF54447 Protein matches
Abstract

This entry represents a ssDNA-binding transcriptional regulator domain consisting of a helix-swapped dimer of beta(4)-alpha motifs. This domain is found as a C-terminal domain in the transciptional co-activator PC4 (where it is a dimer of two separate motifs), and in the plant transciprional regulator PBF-2 (where it is a single chain domain formed by a tandem repeat of two motifs).

Transcriptional regulators play a critical role in controlling the level of transcription from specific genes in response to different stimuli. Members of this family of transcriptional regulators, which preferentially bind single-stranded DNA, include PBF-2 from plants, the mammalian nuclear factor 1-X (NF1-X), and positive cofactor 4 (PC4). These proteins are structurally similar, consisting of a helix-swapped dimer of beta(4)-alpha motifs.

The plant defence transcription factor PBF-2 is comprised of four p24 subunits that interact through a helix-loop-helix motif to produce a central pore [PubMed12080340]. PBF-2 functions as part of the plant¿s defence system in response to the detection of a pathogen. Upon stimulation, PBF-2 induces several signal transduction pathways leading to changes in the expression of defence genes, including the pathogenesis-related (PR) genes.

NF1-X is one of several NF1 proteins that function as transcription factors. NF1-X consists of two functionally distinct domains: a conserved N-terminal DNA-binding domain and a C-terminal transcriptional regulatory domain. NF1-X binds to the promoter for the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase gene [PubMed10432316].

PC4 (or P15) possess the ability to co-activate and suppress transcription via its DNA-binding activity. PC4 has been shown to stimulate transcription in vitro with diverse activators, including VP16, thyroid hormone receptor, BRCA-1, often involving TFIIA. PC4 and TFIIA are thought to facilitate the assembly of the pre-initiation complex. The repressive activity of PC4 can be alleviated by the transcription factor TFIIH, which protects promoters from PC4 repression [PubMed12590132]. PC4 consists of two domains: an N-terminal regulatory domain and a C-terminal cryptic DNA-binding domain. The protein acts as a dimer with two ssDNA binding channels running in opposite directions to each other [PubMed9360603].


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

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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 6 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 ssDNA-binding transcriptional regulator domain 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 6 hidden Markov models representing the ssDNA-binding transcriptional regulator domain 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 · Internal database links ]