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4  structures 308  species 0  interactions 1184  sequences 18  architectures

Family: BSD (PF03909)

Summary: BSD domain

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BSD domain Edit Wikipedia article

BSD
PDB 2dii EBI.jpg
solution structure of the bsd domain of human tfiih basal transcription factor complex p62 subunit
Identifiers
Symbol BSD
Pfam PF03909
InterPro IPR005607

In molecular biology, the BSD domain is an approximately 60 amino acid long protein domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain or the U-box in multidomain proteins. The function of the BSD domain is as yet unknown.[1]

Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain.[1]

Some proteins known to contain one or two BSD domains are listed below:

  • Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.

References[edit]

BSTA Promotes mTORC2-Mediated Phosphorylation of Akt1 to Suppress Expression of FoxC2 and Stimulate Adipocyte Differentiation. Yao Y, Suraokar M, Darnay BG, Hollier BG, Shaiken TE, Asano T, Chen CH, Chang BH, Lu Y, Mills GB, Sarbassov D, Mani SA, Abbruzzese JL, Reddy SA. Sci Signal. 2013 Jan 8;6(257):ra2. doi: 10.1126/scisignal.2003295. PMID 23300339

  1. ^ a b Doerks T, Huber S, Buchner E, Bork P (April 2002). "BSD: a novel domain in transcription factors and synapse-associated proteins". Trends Biochem. Sci. 27 (4): 168–70. PMID 11943536. 

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BSD domain Provide feedback

This domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function.

Literature references

  1. Doerks T, Huber S, Buchner E, Bork P; , Trends Biochem Sci 2002;27:168-170.: BSD: a novel domain in transcription factors and synapse-associated proteins. PUBMED:11943536 EPMC:11943536


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005607

The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see PROSITEDOC) or the U-box in multidomain proteins. The function of the BSD domain is yet unknown [PUBMED:11943536].

Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain [PUBMED:11943536].

Some proteins known to contain one or two BSD domains are listed below:
  • Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1).
  • Yeast RNA polymerase II transcription factor B 73 kDa subunit (TFB1), the homologue of BTF2.
  • Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination.
  • Drosophila synapse-associated protein SAP47.
  • Mammalian SYAP1.
  • Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.
  • Domain organisation

    Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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    Alignments

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      Seed
    (81)
    Full
    (1184)
    Representative proteomes NCBI
    (1161)
    Meta
    (12)
    RP15
    (250)
    RP35
    (448)
    RP55
    (674)
    RP75
    (822)
    Alignment:
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      Seed
    (81)
    Full
    (1184)
    Representative proteomes NCBI
    (1161)
    Meta
    (12)
    RP15
    (250)
    RP35
    (448)
    RP55
    (674)
    RP75
    (822)
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    Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

    You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

    External links

    MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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    Trees

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    Curation and family details

    This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

    Curation View help on the curation process

    Seed source: [1]
    Previous IDs: none
    Type: Domain
    Author: Yeats C
    Number in seed: 81
    Number in full: 1184
    Average length of the domain: 60.20 aa
    Average identity of full alignment: 21 %
    Average coverage of the sequence by the domain: 16.77 %

    HMM information View help on HMM parameters

    HMM build commands:
    build method: hmmbuild -o /dev/null HMM SEED
    search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
    Model details:
    Parameter Sequence Domain
    Gathering cut-off 20.4 20.4
    Trusted cut-off 20.7 20.6
    Noise cut-off 20.3 20.2
    Model length: 62
    Family (HMM) version: 12
    Download: download the raw HMM for this family

    Species distribution

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    Structures

    For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the BSD domain has been found. There are 4 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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