BSD domain

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

BSD
	solution structure of the bsd domain of human tfiih basal transcription factor complex p62 subunit
Identifiers
Symbol	BSD
Pfam	PF03909
InterPro	IPR005607
Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Last updated March 12, 2019

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. 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]

A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins.

In the nervous system, a synapse is a structure that permits a neuron to pass an electrical or chemical signal to another neuron or to the target effector cell.

In taxonomy, Homo sapiens is the only extant human species. The name is Latin for "wise man" and was introduced in 1758 by Carl Linnaeus.

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]

A helix, plural helixes or helices, is a type of smooth space curve, i.e. a curve in three-dimensional space. It has the property that the tangent line at any point makes a constant angle with a fixed line called the axis. Examples of helices are coil springs and the handrails of spiral staircases. A "filled-in" helix – for example, a "spiral" (helical) ramp – is called a helicoid. Helices are important in biology, as the DNA molecule is formed as two intertwined helices, and many proteins have helical substructures, known as alpha helices. The word helix comes from the Greek word ἕλιξ, "twisted, curved".

Phenylalanine is an essential α-amino acid with the formula C^₉H^₁₁NO^₂. It can be viewed as a benzyl group substituted for the methyl group of alanine, or a phenyl group in place of a terminal hydrogen of alanine. This essential amino acid is classified as neutral, and nonpolar because of the inert and hydrophobic nature of the benzyl side chain. The L-isomer is used to biochemically form proteins, coded for by DNA. Phenylalanine is a precursor for tyrosine, the monoamine neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline), and the skin pigment melanin. It is encoded by the codons UUU and UUC.

Tryptophan is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a non-polar aromatic amino acid. It is essential in humans, meaning the body cannot synthesize it: it must be obtained from the diet. Tryptophan is also a precursor to the neurotransmitter serotonin, the hormone melatonin and vitamin B3. It is encoded by the codon UGG.

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, involved in single-copy DNA replication and ubiquitination.
Drosophila synapse-associated protein SAP47.
Mammalian SYAP1.
Various Arabidopsis thaliana (mouse-ear cress) hypothetical proteins.

In molecular biology, a transcription factor (TF) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The function of TFs is to regulate—turn on and off—genes in order to make sure that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Groups of TFs function in a coordinated fashion to direct cell division, cell growth, and cell death throughout life; cell migration and organization during embryonic development; and intermittently in response to signals from outside the cell, such as a hormone. There are up to 2600 TFs in the human genome.

Protein complex A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthet

A protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Different polypeptide chains may have different functions. This is distinct from a multienzyme complex, in which multiple catalytic domains are found in a single polypeptide chain.

General transcription factor IIH subunit 1 is a protein that in humans is encoded by the GTF2H1 gene.

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The ribosome is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules. Ribosomes consist of two major components: the small ribosomal subunits, which read the RNA, and the large subunits, which join amino acids to form a polypeptide chain. Each subunit comprises one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.

The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor is an ionotropic transmembrane receptor for glutamate that mediates fast synaptic transmission in the central nervous system (CNS). It has been traditionally classified as a non-NMDA-type receptor, along with the kainate receptor. Its name is derived from its ability to be activated by the artificial glutamate analog AMPA. The receptor was first named the "quisqualate receptor" by Watkins and colleagues after a naturally occurring agonist quisqualate and was only later given the label "AMPA receptor" after the selective agonist developed by Tage Honore and colleagues at the Royal Danish School of Pharmacy in Copenhagen. AMPARs are found in many parts of the brain and are the most commonly found receptor in the nervous system. The AMPA receptor GluA2 (GluR2) tetramer was the first glutamate receptor ion channel to be crystallized.

EGR-1 also known as Zif268 or NGFI-A is a protein that in humans is encoded by the EGR1 gene.

In molecular biology, a CCAAT box is a distinct pattern of nucleotides with GGCCAATCT consensus sequence that occur upstream by 60–100 bases to the initial transcription site. The CAAT box signals the binding site for the RNA transcription factor, and is typically accompanied by a conserved consensus sequence. It is an invariant DNA sequence at about minus 70 base pairs from the origin of transcription in many eukaryotic promoters. Genes that have this element seem to require it for the gene to be transcribed in sufficient quantities. It is frequently absent from genes that encode proteins used in virtually all cells. This box along with the GC box is known for binding general transcription factors. Both of these consensus sequences belong to the regulatory promoter. Full gene expression occurs when transcription activator proteins bind to each module within the regulatory promoter. Protein specific binding is required for the CCAAT box activation. These proteins are known as CCAAT box binding proteins/CCAAT box binding factors.

Two-hybrid screening is a molecular biology technique used to discover protein–protein interactions (PPIs) and protein–DNA interactions by testing for physical interactions between two proteins or a single protein and a DNA molecule, respectively.

The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters..

In molecular biology, SWI/SNF, is a nucleosome remodeling complex found in eukaryotes. In simpler terms, it is a group of proteins that associate to remodel the way DNA is packaged. It is composed of several proteins – products of the SWI and SNF genes as well as other polypeptides. It possesses a DNA-stimulated ATPase activity and can destabilise histone-DNA interactions in reconstituted nucleosomes in an ATP-dependent manner, though the exact nature of this structural change is unknown.

In molecular biology and genetics, transcription coregulators are proteins that interact with transcription factors to either activate or repress the transcription of specific genes. Transcription coregulators that activate gene transcription are referred to as coactivators while those that repress are known as corepressors. The mechanism of action of transcription coregulators is to modify chromatin structure and thereby make the associated DNA more or less accessible to transcription. In humans several dozen to several hundred coregulators are known, depending on the level of confidence with which the characterisation of a protein as a coregulator can be made. One class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP dependent class modifies the conformation of chromatin.

Transcription factor II Human is an important protein complex, having roles in transcription of various protein-coding genes and DNA nucleotide excision repair (NER) pathways. TFIIH first came to light in 1989 when general transcription factor-δ or basic transcription factor 2 was characterized as an indispensable transcription factor in vitro. This factor was also isolated from yeast and finally named as TFIIH in 1992.

Myocyte-specific enhancer factor 2C also known as MADS box transcription enhancer factor 2, polypeptide C is a protein that in humans is encoded by the MEF2C gene. MEF2C is a transcription factor in the Mef2 family.

Transcription initiation factor TFIID subunit 4 is a protein that in humans is encoded by the TAF4 gene.

General transcription factor IIH subunit 2 is a protein that in humans is encoded by the GTF2H2 gene.

General transcription factor IIF subunit 2 is a protein that in humans is encoded by the GTF2F2 gene.

Mediator of RNA polymerase II transcription subunit 26 is an enzyme that in humans is encoded by the MED26 gene. It forms part of the Mediator complex.

RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins.

In molecular biology, the adaptor complexes medium subunit domain is a protein domain found at the C-terminus of the mu subunit from various clathrin adaptor protein complexes and muniscins. The C-terminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle.

In molecular biology, the Ubiquitin-Interacting Motif (UIM), or 'LALAL-motif', is a sequence motif of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA, UBX, ENTH domain, EH, VHS, SH3 domain, HECT, VWFA, EF-hand calcium-binding, WD-40, F-box, LIM, protein kinase, ankyrin, PX, phosphatidylinositol 3- and 4-kinase, C2 domain, OTU, DnaJ domain, RING-finger or FYVE-finger. UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs.

The transactivation domain or trans-activating domain (TAD) is a transcription factor scaffold domain which contains binding sites for other proteins such as transcription coregulators. These binding sites are frequently referred to as activation functions (AFs). TADs are named after their amino acid composition. These amino acids are either essential for the activity or simply the most abundant in the TAD. Transactivation by the Gal4 transcription factor is mediated by acidic amino acids, whereas hydrophobic residues in Gcn4 play a similar role. Hence, the TADs in Gal4 and Gcn4 are referred to as acidic or hydrophobic The activation domains, respectively. Nine-amino-acid transactivation domain (9aaTAD) defines a novel domain common to a large superfamily of eukaryotic transcription factors represented by Gal4, Oaf1, Leu3, Rtg3, Pho4, Gln3, Gcn4 in yeast and by p53, NFAT, NF-κB and VP16 in mammals.

Gcn4 is a transcription factor and a “master regulator” for gene expression which regulates close to one tenth of the yeast genome. In a study by Razaghi et al, amino acid starvation activated the transcription factor Gcn4p, resulting in transcriptional induction of almost all genes involved in amino acid biosynthesis, including HIS4. Thus involvement of Gcn4 in regulation of both histidinol dehydrogenase HIS4 and interferon gamma hIFNγ was hypothesised as a scenario explaining the increased level of hIFNγ under amino acid starvation.

The Gal4 transcription factor is a positive regulator of gene expression of galactose-induced genes.

References

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 2 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. doi:10.1016/s0968-0004(01)02042-4. PMID 11943536.

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[pmid11943536-1] 1 2 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. doi:10.1016/s0968-0004(01)02042-4. PMID 11943536.