TY - JOUR. T1 - Crystallographic studies of a novel DNA-binding domain from the yeast transcriptional activator Ndt80. AU - Montano, Sherwin P.. AU - Pierce, Michael. AU - Coté, Marie L.. AU - Vershon, Andrew K.. AU - Georgiadis, Millie. PY - 2002/12/1. Y1 - 2002/12/1. N2 - The Ndt80 protein is a transcriptional activator that plays a key role in the progression of the meiotic divisions in the yeast Saccharomyces cerevisiae. Ndt80 is strongly induced during the middle stages of the sporulation pathway and binds specifically to a promoter element called the MSE to activate transcription of genes required for the meiotic divisions. Here, the preliminary structural and functional studies to characterize the DNA-binding activity of this protein are reported. Through deletion analysis and limited proteolysis studies of Ndt80, a novel 32 kDa DNA-binding domain that is sufficient for DNA-binding in vitro has been defined. Crystals of the DNA-binding domain of Ndt80 in two distinct lattices have been ...
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences (k-mers). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other ...
p53 is an allosterically regulated protein with a latent DNA-binding activity. Posttranslational modification of a carboxy-terminal regulatory site in vitro, by casein kinase II and protein kinase C, can activate the sequence-specific DNA-binding function of the wild-type protein. The latent form of...
DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of
Members of the ARID (AT-rich interaction domain) (see ,PDOC51011,) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. Bright/ARID3a and the other two members (Bdp/ARID3b and Bright-like/ARID3c) have been described as the extended or eARID subfamily, having additional conserved sequences at both the N and C termini of the core ARID domain. In addition to the conserved regions immediately adjacent to the core ARID, the eARID proteins also share a conserved motif C-terminal to the ARID, named the REKLES domain after a conserved amino acid motif. The REKLES domain has not been found in any non-ARID proteins. REKLES consists of two subdomains: a modestly conserved N-terminal REKLESα and a highly conserved C-terminal REKLESβ. REKLES is a multifunctional domain that as co-evolved with and regulates functional properties of the eARID DNA-binding domain. REKLESα and -β are required, respectively, for nuclear entry and export of Bright during its ...
The manipulation of DNA by proteins is central to the life of a cell. It is critical for processes ranging from replication and recombination to transcription and the repair of DNA damage. Introduction to Protein-DNA Interactions, written by Gary Stormo, provides an up-to-date and interdisciplinary perspective on protein-DNA interactions, with an emphasis on DNA-binding proteins…
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a DNA-binding protein with a gcm-motif (glial cell missing motif). The encoded protein is a homolog of the Drosophila glial cells missing gene (gcm). This protein binds to the GCM-motif (A/G)CCCGCAT, a novel sequence among known targets of DNA-binding proteins. The N-terminal DNA-binding domain confers the unique DNA-binding activity of this protein. [provided by RefSeq, Jul 2008 ...
XRCC genes (X-ray cross-complementing group) were discovered mainly for their roles in protecting mammalian cells against damage caused by ionizing radiation. Studies determined that these genes are important in the genetic stability of DNA. Although the loss of some of these genes does not necessarily confer high levels of sensitivity to radiation, they have been found to represent ... more ...
IRF-4 binds with LANA through its DNA-binding domain in vitro.(A) IRF-4 binds to C-terminal domain of LANA in vitro. The 35S-radiolabeled in vitro-translated pr
iDNA-Prot,dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid ...
Lachke, Salil A.; OConnell, Daniel J.; Aboukhalil, Anton; Choe, Sung E.; Turbe-Doan, Annick; Robertson, Erin A.; Amendt, Brad A. et al. (PLoS ONE, 2012) Link to Published Version ...
DDB1 was originally identified as a large subunit of damaged DNA-binding protein (DDB), which plays a role in DNA repair. DDB1 also functions as an adaptor molecule of Cul4/DDB1 ubiquitin E3 ligase and participates in various cellular processes. ...
Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5-AGGTCTC-3 sequence within the…
Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5-AGGTCTC-3 sequence within the…
Fig 5: regulation of transcription : which evidence code should be used? kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a) kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IMP has_regulation_target: tbx5b ...
The ssb gene, coding for single-stranded-DNA-binding protein (SSB), was cloned from four marine Shewanella strains that differed in their temperature and pressure optima and ranges of growth. All four Shewanella ssb genes complemented Escherichia coli ssb point and deletion mutants, with efficiencies that varied with temperature and ssb gene source. The Shewanella SSBs are the largest bacterial SSBs identified to date (24.9-26.3 kDa) and may be divided into conserved amino- and carboxy-terminal regions and a highly variable central region. Greater amino acid sequence homology was observed between the Shewanella SSBs as a group (72-87%) than with other bacterial SSBs (52-69%). Analysis of the amino acid composition of the Shewanella SSBs revealed several features that could correlate with pressure or temperature adaptation. SSBs from the three low-temperature-adapted Shewanella strains were an order of magnitude more hydrophilic than that from the mesophilic strain, and differences in the distribution of
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Looking for online definition of DNA-binding protein RFX8 in the Medical Dictionary? DNA-binding protein RFX8 explanation free. What is DNA-binding protein RFX8? Meaning of DNA-binding protein RFX8 medical term. What does DNA-binding protein RFX8 mean?
Summary Evidence is presented here which indicates that the adenovirus DNA-binding protein (DBP) is phosphorylated at a tyrosine residue early in infection. This was suggested by the discovery that a proportion of the label in 32P-labelled DBP was resistant to alkali, and was substantiated by acid hydrolysis of DBP immunoprecipitates and by immunoblotting with a monoclonal antibody against phosphotyrosine. Treatment of [35S] methionine-labelled DBPs with chymotrypsin produced fragments of apparent M r 45K and 39K whereas digestion of 32P-labelled DBP resulted in fragments of 45K and 26K. Consideration of the distribution of 32P label and its alkali stability in these fragments suggested that chymotrypsin cleaved populations of DBP at different sites depending on their phosphorylation states. The conservation, in all of the seven adenovirus serotypes sequenced, of a tyrosine residue (at amino acid 195 in adenovirus type 2) together with its surrounding residues, suggests that phosphorylation
The human transcription enhancer factor-1 (TEF-1) belongs to a family of evolutionarily conserved proteins that have a DNA binding TEA domain. TEF-1 shares a 98% homology with Drosophila scalloped (sd) in the DNA binding domain and a 50% similarity in the activation domain. We have expressed human TEF-1 in Drosophila under the hsp-70 promoter and find that it can substitute for Sd function. The transformants rescue the wingblade defects as well as the lethality of loss-of-function alleles. Observation of reporter activity in the imaginal wing discs of the enhancer-trap alleles suggests that TEF-1 is capable of promoting sd gene regulation. The functional capability of the TEF-1 product was assessed by comparing the extent of rescue by heat shock (hs)-TEF-1 with that of hs-sd. The finding that TEF-1 can function in vivo during wingblade development offers a potent genetic system for the analysis of its function and in the identification of the molecular partners of TEF-1.. ...
The molecular determinants necessary and sufficient for recognition of its specific DNA target are contained in the C-domain (H-NSctd) of nucleoid-associated protein H-NS. H-NSctd protects from DNaseI cleavage a few short DNA segments of the H-NS-sensitive hns promoter whose sequences closely match the recently identified H-NS consensus motif (tCGt/aTa/tAATT) and, ... read more alone or fused to the protein oligomerization domain of phage λ CI repressor, inhibits transcription from the hns promoter in vitro and in vivo. The importance of H-NS oligomerization is indicated by the fact that with an extended hns promoter construct (400 bp), which allows protein oligomerization, DNA binding and transcriptional repression are highly and almost equally efficient with native H-NS and H-NSctd::λCI and much less effective with the monomeric H-NSctd. With a shorter (110 bp) construct, which does not sustain extensive protein oligomerization, transcriptional repression is less effective, but native H-NS, ...
TY - JOUR. T1 - A proteolytic fragment from the central region of p53 has marked sequence-specific DNA-binding activity when generated from wild-type but not from oncogenic mutant p53 protein. AU - Bargonetti, Jill. AU - Manfredi, James J.. AU - Chen, Xinbin. AU - Marshak, Daniel R.. AU - Prives, Carol. PY - 1993. Y1 - 1993. N2 - p53 is a sequence-specific DNA-binding oligomeric protein that can activate transcription from promoters bearing p53-binding sites. Whereas the activation region of p53 has been identified within the amino terminus, the location of the specific DNA-binding domain has not been reported. Thermolysin treatment of p53 protein generates a stable protease-resistant fragment that binds with marked specificity to p53 DNA-binding sites. Amino-terminal sequencing of the fragment located the thennolysin cleavage site to residue 91. Because the fragment does not contain the cdc2 phosphorylation site at Ser-315, we conclude that the the site-specific DNA-binding domain of p53 spans ...
TY - JOUR. T1 - Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. AU - Senear, D. F.. AU - Brenowitz, M.. PY - 1991/9/9. Y1 - 1991/9/9. N2 - We have investigated the question of whether the gel mobility-shift assay can provide data that are useful to the demonstration of cooperativity in the site-specific binding of proteins to DNA. Three common patterns of protein-DNA interaction were considered: (i) the cooperative binding of a protein to two sites (illustrated by the Escherichia coli Gal repressor); (ii) the cooperative binding of a bidentate protein to two sites (illustrated by the E. coli Lac repressor); and (iii) the cooperative binding of a protein to three sites (illustrated by the λcI repressor). A simple, rigorous, and easily extendable statistical mechanical approach to the derivation of the binding equations for the different patterns is presented. Both stimulated and experimental data for each case are ...
Naturally elaborated membrane bleb fractions BI and BII of Neisseria gonorrhoeae contain both linear and circular DNAs. Because little is known about the interactions between DNA and blebs, studies were initiated to identify specific proteins that bind DNA in elaborated membrane blebs. Western immunoblots of whole-cell and bleb proteins from transformation-competent and DNA-uptake-deficient (dud) mutants were probed with single- or double-stranded gonococcal DNA, pBR322, or synthetic DNA oligomers containing intact or altered gonococcal transformation uptake sequences. The specificity and sensitivity of a nonradioactive DNA-binding protein assay was evaluated, and the assay was used to visualize DNA-protein complexes on the blots. The complexes were then characterized by molecular mass, DNA-binding specificity, and expression in bleb fractions. The assay effectively detected blotted DNA-binding proteins. At least 17 gonococcal DNA-binding proteins were identified; unique subsets occurred in BI ...
Purpose To evaluate the prognostic significance of DNA excision repair gene polymorphisms, excision repair cross-complementation group 1 ( ERCC1) and X-ray repair complementing defective repair in...
An inducible program of inflammatory gene expression is a hallmark of antimicrobial defenses. This response is controlled by a collaboration involving signal-dependent activation of transcription factors, transcriptional co-regulators, and chromatin-modifying factors. Here we have identified a highly conserved Zinc finger DNA binding protein CNBP (also called ZNF9) upregulated in myeloid cells exposed to lipopolysaccharide. CNBP resides primarily in the cytosol and upon TLR4 engagement, CNBP translocate to the nucleus. To investigate the functional consequences of these events, we generated mice lacking CNBP and characterized the role of CNBP in controlling the inducible transcriptional program using a combination of RNA-sequencing and multiplex gene expression analysis (Nanostring). In response to an array of signals such as LPS, CNBP-deficient macrophages were impaired in their ability to induce important immune genes including IL12p40 and IL6 amongst others. CNBP-deficient cells showed normal ...
Author Summary The main role of transcription factors is to modulate the expression levels of functionally related genes in response to environmental and cellular cues. For this process to be precise, the transcription factor needs to locate and bind specific DNA sequences in the genome and needs to bind these sites with a strength that appropriately adjusts the amount of gene expressed. Both specific protein-DNA interactions and transcription factor activity are intimately coupled, because they are both dependent upon the biochemical properties of the DNA-binding domain. Here we experimentally probe how variable these properties are using a novel in vivo selection assay. We observed that the specific binding preferences for the transcription factor MarA and its transcriptional activity can be altered over a large range with a few mutations and that selection on one function will impact the other. This work helps us to better understand the mechanism of transcriptional regulation and its evolution, and
Cervical cancer is a public health problem and the molecular mechanisms underlying radioresistance are still poorly understood. Here, we evaluated the modulation of key molecules involved in cell proliferation, cell cycle and DNA repair in cervical cancer cell lines (CASKI and C33A) and in malignant tissues biopsied from 10 patients before and after radiotherapy. The expression patterns of epidermal growth factor receptor (EGFR), excision repair cross-complementation group 1 (ERCC1) and p53 were evaluated in cancer cell lines by quantitative PCR and western blotting, and in human malignant tissues by immunohistochemistry. The mutation status of TP53 gene was evaluated by direct sequencing. Among cell lines, absent or weak modulations of EGFR, ERCC1 and p53 ...
Genome replication and maintenance occurs through the collective action of proteins that operate on single-stranded DNA (ssDNA). All cells express single-stranded DNA binding proteins (SSBs), which prevent errors by sequestering ssDNA with high-affinity, keeping it free from transient structures and protecting it from unwanted chemical modification. SSBs must be easily repositioned, or else risk stalling DNA replication and repair processes. How does a protein simulataneously bind DNA tightly yet diffuse rapidly?. Through a set of extensive all-atom molecular dynamics (MD) simulations, we have elucidated the molecular mechanism of SSB association with ssDNA. First, we showed that the same SSB-ssDNA complex can both spontaneously rearrange its structure and maintain its stable conformation depending on whether it is surrounded by physiological solution or a protein-crystal environment. Next, we probed the local interaction between ssDNA and SSB through simulations of mechanical unraveling of the ...
XPB antibody (excision repair cross-complementation group 3) for IHC-P, WB. Anti-XPB pAb (GTX55844) is tested in Human, Mouse, Rat samples. 100% Ab-Assurance.
TY - JOUR. T1 - Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. AU - Kalodimos, Charalampos G.. AU - Biris, Nikolaos. AU - Bonvin, Alexandre M.J.J.. AU - Levandoski, Marc M.. AU - Guennuegues, Marc. AU - Boelens, Rolf. AU - Kaptein, Robert. PY - 2004/7/16. Y1 - 2004/7/16. N2 - Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient ...
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Binding of transcriptional activators to a promoter is a prerequisite process in transcriptional activation. It is well established that the efficiency of activator binding to a promoter is determined by the affinity of direct interactions between the DNA-binding domain of an activator and its specific target sequences. However, I describe here that activator binding to a promoter is augmented in vivo by the effects of two other determinants that have not been generally appreciated: (i) the number of activator binding sites present in a promoter and (ii) the potency of activation domains of activators. Multiple sites within a promoter can cooperatively recruit cognate factors regardless of whether they contain an effective activation domain. This cooperativity can result in the synergistic activation of transcription. The second effect is the enhancement of activator binding to a promoter by the presence of activation domains. In this case, activation domains are not simply tethered to the ...
The hns gene is a member of the cold-shock regulon, indicating that the nucleoid-associated, DNA-binding protein H-NS plays an important role in the adaptation of Escherichia coli to low temperatures. We show here that the ability to cope efficiently with a cold environment (12 degrees C and 25 degr …
Genes expressed in erythroid cells contain binding sites for a cell-specific nuclear factor, GF-1 (NF-E1, Eryf 1), believed to be an important transcriptional regulator. Previously we characterized murine GF-1 as a 413-amino acid polypeptide containing two cysteine-cysteine regions reminiscent of zinc-finger DNA-binding domains. By cross-hybridization to the finger domain of murine GF-1 we have isolated cDNA encoding the human homolog. Peptide sequencing of purified human GF-1 confirmed the authenticity of the human cDNA. The predicted primary sequence of human GF-1 is highly similar to that of murine GF-1, particularly in the DNA-binding region. Although the DNA-binding domains of human, murine, and chicken proteins are remarkably conserved, the mammalian polypeptides are strikingly divergent from the avian counterpart in other regions, most likely those responsible for transcriptional activation. By hybridization to panels of human-rodent DNAs we have assigned the human GF-1 locus to Xp21-11. ...
The initiation of transcription is accomplished via interactions of many different proteins with common and gene-specific regulatory motifs. Clearly, sequence-specific transcription factors play a crucial role in the specificity of transcription initiation. A group of sequence-specific DNA-binding proteins, related to the transcription factor Sp1, has been implicated in the regulation of many different genes, since binding sites for these transcription factors (GC/GT boxes) are a recurrent motif in regulatory sequences such as promoters, enhancers and CpG islands of these genes. The simultaneous occurrence of several homologous GC/GT box-binding factors precludes a straightforward deduction of their role in transcriptional regulation. In this review, we focus on the connection between functional specificity and biochemical properties including glycosylation, phosphorylation and acetylation of Sp1-related factors.. ...
The human ERYF1 gene (summary) NF-E1 DNA-binding protein GATA1, locus Xp11.23 [§§; †] containing 2 finger motifs referred to as ERYF1 of an erythroid-specific gene. The cDNA for the human ERYF1 gene is almost identical to that of chicken and mouse GATA1 gene consisting of 2 zinc finger type motifs its activator domain contains the binding…
Tumor protein p53, encoded in humans by the TP53 gene, was originally identified based on its interaction with the large T antigen of simian virus 40 (SV40). p53 is expressed at low levels in most cell types but is upregulated in many transformed (cancer) cell lines. In response to cellular stress, p53 regulates over 100 target genes that control cell cycle arrest, apoptosis, senescence, DNA repair, and metabolic changes. p53 protein has multiple domains that include DNA-binding, transactivation, and oligomerization activities. Mutations in the TP53 gene cause loss of tumor suppression activity and are found in more than 50% of human tumors. Multiple isoforms of p53 are known, with distinct DNA-binding and transcriptional activation properties. p53 is also known as cellular tumor antigen p53, p53 tumor suppressor, transformation-related protein 53, BCC7, LFS1, TRP53, and antigen NY-CO-13.. ...
Single stranded binding protein (SSB) is a prokaryotic DNA protein that binds to single stranded DNA during times when the DNA is rendered from its double stranded form during times of genetic recombination or DNA damage in order to stabilize and protect it from further unnecessary harm. The protein exists as a tetramer with each monomer being made of an N-terminal and Cterminal domain. The C-terminal domain is made of two smaller sub-domains, both of which have yet to resolve properly in a crystal structure, named the intrinsically disordered linker and the acidic tip, with limited understanding on how they function and relate to other proteins and SSB itself. Due to the disordered nature of its C-terminal domain limiting the ability to yield a concise crystal structure, much of the function and nearly all of the structure of the C-terminal domain has yet to be identified. While some function has been determined for these disordered regions, its relationship with other binding partners, DNA, ...
DNA-binding proteins from starved cells (DPS) are proteins that belong to the ferritin superfamily and are characterized by strong similarities but also distinctive differences with respect to canonical ferritins. DPS proteins are part of a complex bacterial defence system that protects DNA against oxidative damage and are distributed widely in the bacterial kingdom. DPS are highly symmetrical dodecameric proteins of 200 kDa characterized from a shell-like structure of 2:3 tetrahedral symmetry assembled from identical subunits with an external diameter of ~ 9 nm and a central cavity of ~ 4.5 nm in diameter. Dps proteins belong to the ferritin superfamily and the DNA protection is afforded by means of a double mechanism: The first was discovered in Escherichia coli Dps in 1992 and has given the name to the protein family; during stationary phase, Dps binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and ...
Zinc finger proteins contain DNA-binding domains and have a wide variety of functions, most of which encompass some form of transcriptional activation or repression. The majority of zinc finger proteins contain a Krueppel-type DNA binding domain and a KRAB domain, which is thought to interact with KAP1, thereby recruiting histone modifying proteins. Zinc finger protein 75 (ZNF75), also known as ZNF82, is a 289 amino acid member of the Krueppel C2H2-type zinc finger protein family. Localized to the nucleus, ZNF75 contains five C2H2- type zinc fingers and one KRAB domain through which it is thought to be involved in DNA-binding and transcriptional regulation ...
As a commentator up-thread noted, any slip-and-slide model of sequence-specific DNA binding activity by transcription factors fails the sniff test: how is the activator (or repressor) able to effectively scan the nucleotide side-groups to achive site-specificity when the latter are coated with histones (in most eukaryotes) and with other attendant DNA-binding molecules (in all organisms). The notion that the chromosomal DNA molecule exists in all of its double-helical beauty for all proteins to probe seems rather tired and readily debunked to my mind. Ive been a hesitant skeptic of the histone code as anything other than correlative observations, but given the ubiquitous habit of histone compaction of large chromosomal segments, some portions of which obviously remain accessible to transcription factors, it seems clear to me that were missing some vital pieces of the puzzle.. Delete ...
Recent analysis of a Gal4 mutant (Gap71) carrying three point mutations (S22D, K23Q and K25F) in its DNA-binding domain (DBD), has demonstrated that it cannot occupy GAL promoters efficiently in cells and that it is not mono-ubiquitylated, suggesting a functional link between this modification and stable DNA binding in cells. The mechanistic underpinning of this phenotype is that this protein is hypersensitive to a newly discovered activity of the proteasomal ATPases--their ability to actively dissociate transcription factor-DNA complexes after direct interaction with the activation domain. In this paper, we examine the roles of each of the three point mutations contained in Gap71 individually. These experiments have revealed that serine 22 is a site of phosphorylation in the Gal4 DBD and that lysine 23 is essential for S22 phosphorylation, possibly acting as part of the kinase recognition site. Mutation of either residue blocks Gal4 DBD phosphorylation, its subsequent ubiquitylation and ...
DNA binding capacity of Orf8 and Orf16 by electrophoretic mobility shift assays (EMSAs). Preparation of DNA substrate is graphically shown in panel A. US8 and U
Progression through the cell cycle is essential for the continued existence of all uni- and multicellular organisms. It is crucial for the survival of a cell that its DNA is correctly replicated. In mammals, the onset of DNA replication is regulated by the activity of the heterodimeric E2F-DP transcription factor. The mammalian E2F family contains six proteins (E2F1, E2F2, E2F3, E2F4, E2F5 and E2F6) (Trimarchi and Lees, 2002). All E2Fs have an N-terminally located DNA-binding domain immediately followed by a dimerization domain, allowing them to pair with a dimerization partner (DP1 or DP2). Dimerization of E2F with DP is a prerequisite for high affinity, sequence-specific binding to the E2F consensus DNA-binding site. E2F activity is negatively regulated by retinoblastoma (Rb), which binds to the transcriptional activation domain of the E2F-DP factor, rendering it inactive. Moreover, the recruitment by Rb of DNA-modifying enzymes, such as histone deacetylases and polycomb proteins, leads to ...
Enhancer factor C, EFC, EF-C, MHC class II regulatory factor RFX, MHC class II regulatory factor RFX1, regulatory factor X, 1 (influences HLA class II expression), Regulatory factor X 1, RFX, trans-acting regulatory factor 1, Transcription factor ...
The TET2 DNA dioxygenase regulates gene expression by catalyzing demethylation of 5-methylcytosine, thus epigenetically modulating the genome. TET2 does not contain a sequence-specific DNA-binding domain, and how it is recruited to specific genomic sites is not fully understood. Here we carried out a mammalian two-hybrid screen and identified multiple transcriptional regulators potentially interacting with TET2. The SMAD nuclear interacting protein 1 (SNIP1) physically interacts with TET2 and bridges TET2 to bind several transcription factors, including c-MYC. SNIP1 recruits TET2 to the promoters of c-MYC target genes, including those involved in DNA damage response and cell viability. TET2 protects cells from DNA damage-induced apoptosis dependending on SNIP1. Our observations uncover a mechanism for targeting TET2 to specific promoters through a ternary interaction with a co-activator and many sequence-specific DNA-binding factors. This study also reveals a TET2-SNIP1-c-MYC pathway in ...
DNA-binding protein that preferentially recognizes a curved DNA sequence. It is probably a functional analog of DnaJ; displays overlapping activities with DnaJ, but functions under different conditions, probably acting as a molecular chaperone in an adaptive response to environmental stresses other than heat shock. Lacks autonomous chaperone activity; binds native substrates and targets them for recognition by DnaK. Its activity is inhibited by the binding of CbpM.
Predicted to have DNA-binding transcription factor activity and sequence-specific DNA binding activity. Involved in pericyte cell differentiation and vascular smooth muscle cell development. Predicted to localize to the nucleus. Is expressed in head mesenchyme; pharyngeal arch 1; and pharyngeal arch 2. Orthologous to human FOXF2 (forkhead box F2 ...
The present invention provides a process of transfecting a cell with a polynucleotide mixed with one or more amphipathic compounds and an effective amount of a DNA-binding protein. Exemplary and preferred DNA-binding proteins are H1, H2A, and H2B. Exemplary and preferred amphipathic compounds are cationic amphipathic compounds.
Vol 9: Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome.. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
HSSB, MSTP075, MST075, replication protein A 70 kDa DNA-binding subunit, replication protein A1 (70kD), replication protein A1, 70kDa, REPA1RF-A protein 1, Replication factor A protein 1, RF-A, RP-A, RPA70RP-A p70, Single-stranded DNA-binding ...
On the other hand, if the same series of reaction is done not on purified DNA, but rather on DNA that has been allowed to interact with extracts containing DNA-binding proteins, these DNA-binding proteins can, if condition are appropriate, bind specifically to regions of DNA. Such a binding will interfere both with the Maxam-Gilbert sequencing reactions and with the cleavage of DNA by the deoxyribonuclease. As a result, those fragments that are produced by cleavage near a protein-binding site will fail to be formed or be formed at a much lower level leaving a gap in the ladder of reaction products. Such a gap is called a footprint and is evidence for the existence of a specific DNA-binding complex. A similar logic allows the DNA binding regions to be determined by using the Exonuclease III protection* approach. Although the basic idea of doing a footprint is straight forward executing one in practice is more complex because of the difficulty of non-specific binding reactions. DNA is a highly ...
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Although bats are recognized as major reservoir hosts of emerging infectious diseases, Joffrin and colleagues highlight that a significant knowledge gap on transmission mechanisms remains and needs further exploration. They question whether bat bites are the exception rather than the rule, and ask whether other animals can transmit bat-borne pathogens. They conclude by questioning what we can learn from bat-to-bat transmission.. ...
Summary: The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for ,500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes.. Availability: http://bioinfo.wilmer.jhu.edu/PDI/. Contact: [email protected] ...
GT:ID BAD55361.1 GT:GENE BAD55361.1 GT:PRODUCT putative DNA-binding protein GT:DATABASE GIB00210CH01 GT:ORG nfar0 GB:ACCESSION GIB00210CH01 GB:LOCATION complement(531217..531633) GB:FROM 531217 GB:TO 531633 GB:DIRECTION - GB:PRODUCT putative DNA-binding protein GB:PROTEIN_ID BAD55361.1 LENGTH 138 SQ:AASEQ MADFAARLNKLFETVHPPGRKPHTNAEVAAALTASGHPISKPYLSQLRSGQRTNPSDETVAALAKFFKVKPDYFFNDIYAAKIDHDLELLSQLQGYGLRRLSSRAFDLSEESQNLLTSMAEKLRASEGLPEIPPDGTE GT:EXON 1,1-138:0, BL:SWS:NREP 1 BL:SWS:REP 1-,69,Y1416_COXBU,7e-04,37.9,58/100, RP:PDB:NREP 1 RP:PDB:REP 6-,104,2ao9A,3e-07,10.1,99/117, HM:PFM:NREP 1 HM:PFM:REP 33-,74,PF01381,4.7e-10,36.1,36/55,HTH_3, RP:SCP:NREP 1 RP:SCP:REP 6-,104,2ao9A1,2e-07,10.1,99/117,a.4.1.17, HM:SCP:REP 39-,77,2a6cA1,0.00055,33.3,39/0,a.35.1.13,1/1,lambda repressor-like DNA-binding domains, OP:NHOMO 42 OP:NHOMOORG 31 OP:PATTERN -------------------------------------------------------------------- ...
High-resolution computational models of genome binding events. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
GT:ID BAD57449.1 GT:GENE BAD57449.1 GT:PRODUCT putative DNA-binding protein GT:DATABASE GIB00210CH01 GT:ORG nfar0 GB:ACCESSION GIB00210CH01 GB:LOCATION 2771120..2771977 GB:FROM 2771120 GB:TO 2771977 GB:DIRECTION + GB:PRODUCT putative DNA-binding protein GB:PROTEIN_ID BAD57449.1 LENGTH 285 SQ:AASEQ MQQAVAERGPTVLRIALGGQLRKLRESRNITREAAGDAIRGSHAKISRLELGRTGFKERDIRDLLTLYGVVDPAERESFLDLARRANEPGWWHRYSDLLPQWFGQYLGLEQAAWKIRTYEAHLVPGLLQTPDYARAVLALGSDDADTDRRVDVRRRRQEILRRPEPPIVWAVLDEAALHRPVGGVQVHRAQIEHLIELAALPNVTLQVLPYSAGEHAAAGASFSILRFAEAELPDVVYLEHLTSALYLDRTQDLALYRSVMDRLSVQALAPDKSVDWLKNFAAGL GT:EXON 1,1-285:0, SEG 143-,163,ddadtdrrvdvrrrrqeilrr, RP:PDB:NREP 1 RP:PDB:REP 3-,90,2csfA,5e-08,8.0,88/101, HM:PFM:NREP 1 HM:PFM:REP 21-,74,PF01381,6.3e-06,24.5,53/55,HTH_3, RP:SCP:NREP 1 RP:SCP:REP 17-,116,1s4kA,5e-07,20.8,96/120,a.35.1.6, HM:SCP:REP 9-,70,1y9qA1,1.7e-05,29.0,62/0,a.35.1.8,1/1,lambda repressor-like DNA-binding domains, OP:NHOMO 191 OP:NHOMOORG 14 OP:PATTERN ...
In living cells, DNA-binding proteins regulate the activity of various genes so that different cells carry out the right tasks at the right time. For this to work, the DNA-binding proteins need to find the right DNA site sufficiently quickly. The research team behind the new study has previously succeeded in determining that it takes only a few minutes for an individual protein molecule to look through the millions of nearly identical binding alternatives and find the right place to bind. This is nevertheless slower than what is predicted by the established theoretical model for how DNA-binding proteins find their way to the proper place by alternating between diffusing in the cell cytoplasm and along DNA strands ...
This motif was first noticed as a feature of the crystal structure of the bacteriophage l Cro protein. The structure of this small regulatory protein contained two a-helices separated by 34 Ã… - the pitch of a DNA double helix. Model building studies showed that these two a-helices would fit into two successive major grooves. As the structures of a number of other bacterial regulatory proteins (the CRP protein and the bacteriophage l cI repressor) were solved, the same structural motif - called a helix-turn-helix - was observed. It consists of two a-helices separated by a short turn (it is not a b turn). One helix binds to recognition elements within the major groove of DNA; the other helps to keep the binding helix properly positioned with respect to the rest of the molecule. This motif, common in bacterial DNA-binding proteins, also occurs in the eukaryotic homeobox proteins ...
1PER: THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES
The DNA triplets recognized by non-metazoan C2H2-ZF domains are also recognized by metazoan C2H2-ZFs based on experimental B1H data [16], often using identical basecontacting residues
Does anyone use DNA binding proteins expressed in rabbit reticulocyte lysates to do gel shift assays? This system would allow easy and quick expression of a suspected DNA binding protein that I could study (much easier than trying to express and purify the protein). I would specifically like to know if the other proteins in the system or maybe even the DNA added would somehow interfere in a gel shift assay (although I guess its no different than using cell/nuclear extracts). If anyone has experience with this or know of a reference could you please let me know? Thanks. -- Steve Some day I will get the hell out of Wisconsin Rodems Then I am here for the Lee family renioun ... shur-wajo-shur ...