SUPERFAMILY 1.75 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] (376)
Fold:   ssDNA-binding transcriptional regulator domain [ 54446]
Superfamily:   ssDNA-binding transcriptional regulator domain [ 54447] (4)
Families:   Transcriptional coactivator PC4 C-terminal domain [ 54448]
  Plant transcriptional regulator PBF-2 [ 75375]
  PMN2A0962/syc2379c-like [ 143038] (2)
  Guide RNA binding protein gBP [ 143043] (2)


Superfamily statistics
Genomes (548) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,106 1,327 6
Proteins 1,052 1,284 6


Functional annotation
General category Regulation
Detailed category DNA-binding

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 metabolic process0.0003920.0008566Least InformativeDirect
Biological Process (BP)regulation of cellular process0.007110.02518Least InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.0000059910.00002192Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process0.0000041060.04908Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.0000023160.04316Moderately InformativeInherited
Molecular Function (MF)binding0.042020.0007804Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.0000055740.00000003037Moderately InformativeDirect
Molecular Function (MF)DNA binding0.00000012760.0000000003065InformativeDirect
Molecular Function (MF)structure-specific DNA binding0.00000000014970.003051Highly 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 metabolic process 0.0008566 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.02518 Least Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00002192 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.04908 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.04316 Moderately Informative Inherited
Molecular Function (MF) binding 0.0007804 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000003037 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.0000000003065 Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.003051 Highly Informative Inherited

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDNA damage0.0001628Moderately InformativeDirect
Cellular componentNucleus0.00000000000007714Least InformativeDirect
DomainTransit peptide0.00000003021Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect

Document: KW annotation of SCOP domains

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

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · 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 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]