A STAT protein domain that determines DNA sequence recognition suggests a novel DNA-binding domain.

The nuclear receptors constitute a large family of ligand-inducible transcription factors. The control of many genetic pathways requires the assembly of these nuclear receptors in defined transcription-activating complexes within control regions of ligand-responsive genes. An essential step is the interaction of the receptors with specific DNA sequences, called hormone-response elements (HREs). These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. HREs are bipartite elements that are composed of two hexameric core half-site motifs. The identity of the response elements resides in three features: the nucleotide sequence of the two core motif half-sites, the number of base pairs separating them and the relative orientation of the motifs. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension. Residues in the first module determine the specificity of the DNA recognition, while residues in the second module are involved in dimerization. Indeed, nuclear receptors bind to their HREs as either homodimers or heterodimers. Depending on the type of receptor, the C-terminal extension plays a role in sequence recognition, dimerization, or both. The DNA-binding domain is furthermore involved in several other functions including nuclear localization, and interaction with transcription factors and co-activators. It is also the target of post-translational modifications. The DNA-binding domain therefore plays a central role, not only in the correct binding of the receptors to the target genes, but also in the control of other steps of the action mechanism of nuclear receptors.

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Characterization of the target DNA sequence for the DNA-binding domain of zinc finger protein 191

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/40.8.704 ◽

2008 ◽

Vol 40 (8) ◽

pp. 704-710 ◽

Cited By ~ 8

Author(s):

H. Wang ◽

R. Sun ◽

G. Liu ◽

M. Yao ◽

J. Fei ◽

...

Keyword(s):

Dna Binding ◽

Dna Sequence ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Binding Domain ◽

Dna Binding Domain ◽

Finger Protein ◽

Target Dna

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Characterization of two Arabidopsis thaliana myb-like proteins showing affinity to telomeric DNA sequence

Genome ◽

10.1139/g03-136 ◽

2004 ◽

Vol 47 (2) ◽

pp. 316-324 ◽

Cited By ~ 44

Author(s):

Petra Schrumpfová ◽

Milan Kuchař ◽

Gabriela Miková ◽

Lenka Skříšovská ◽

Tatiana Kubičárová ◽

...

Keyword(s):

Amino Acids ◽

Arabidopsis Thaliana ◽

Dna Binding ◽

Dna Sequence ◽

Binding Proteins ◽

Binding Domain ◽

Dna Binding Domain ◽

Telomeric Dna ◽

Telomeric Repeats ◽

Two Hybrid

Telomere-binding proteins participate in forming a functional nucleoprotein structure at chromosome ends. Using a genomic approach, two Arabidopsis thaliana genes coding for candidate Myb-like telomere binding proteins were cloned and expressed in E. coli. Both proteins, termed AtTBP2 (accession Nos. T46051 (protein database) and GI:638639 (nucleotide database); 295 amino acids, 32 kDa, pI 9.53) and AtTBP3 (BAB08466, GI:9757879; 299 amino acids, 33 kDa, pI 9.88), contain a single Myb-like DNA-binding domain at the N-terminus, and a histone H1/H5-like DNA-binding domain in the middle of the protein sequence. Both proteins are expressed in various A. thaliana tissues. Using the two-hybrid system interaction between the proteins AtTBP2 and AtTBP3 and self interactions of each of the proteins were detected. Gel-retardation assays revealed that each of the two proteins is able to bind the G-rich strand and double-stranded DNA of plant telomeric sequence with an affinity proportional to a number of telomeric repeats. Substrates bearing a non-telomeric DNA sequence positioned between two telomeric repeats were bound with an efficiency depending on the length of interrupting sequence. The ability to bind variant telomere sequences decreased with sequence divergence from the A. thaliana telomeric DNA. None of the proteins alone or their mixture affects telo merase activity in vitro. Correspondingly, no interaction was observed between any of two proteins and the Arabidopsis telo merase reverse transcriptase catalytic subunit TERT (accession No. AF172097) using two-hybrid assay.Key words: plant telomere-binding protein, two-hybrid assay, protein expression, telomerase.

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Differential protein binding in lymphocytes to a sequence in the enhancer of the mouse retrovirus SL3-3.

Molecular and Cellular Biology ◽

10.1128/mcb.8.4.1625 ◽

1988 ◽

Vol 8 (4) ◽

pp. 1625-1637 ◽

Cited By ~ 46

Author(s):

A Thornell ◽

B Hallberg ◽

T Grundström

Keyword(s):

T Cell ◽

Dna Binding ◽

Electrophoretic Mobility ◽

Dna Sequence ◽

Cell Lines ◽

T Lymphocyte ◽

Binding Domain ◽

Dna Binding Domain ◽

Dna Motifs ◽

Lymphocyte Cell

An electrophoretic mobility shift assay was used to characterize interactions of nuclear proteins with a DNA segment in the enhancer element of the leukemogenic murine retrovirus SL3-3. Mutation of a DNA sequence of the 5'-TGTGG-3' type decreased transcription in vivo specifically in T-lymphocyte cell lines. Extracts of nuclei from different T-lymphocyte cell lines or cells from lymphoid organs resulted in much higher amounts of complexes in vitro with this DNA sequence than did extracts from other cell lines or organs tested. Differences were also found in the sets of complexes obtained with extracts from the different types of cells. The DNA sequence specificities of the different SL3-3 enhancer factor 1 (SEF1) protein complexes were found to be distinct from those of several other previously identified DNA motifs of the TGTGG type because of differences in several nucleotides critical for binding and because these other DNA motifs could not compete with the identified DNA sequence for binding of SEF1. Limited treatment with several different proteases cleaved the SEF1 proteins such that their DNA-binding domain(s) remained and created complexes with decreased and nondistinguishable electrophoretic mobility shifts and with new properties. These results indicate that the SEF1 proteins have a structure with a flexible and relatively vulnerable hinge region linking a DNA-binding domain(s) to a more variable domain(s) with other functions. We suggest that the binding of SEF1 is an essential factor for the T-cell tropism of SL3-3 and the ability of this virus to cause T-cell lymphomas.

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Structural basis of DNA sequence recognition by the response regulator PhoP

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314085908 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1409-C1409

Author(s):

Xiaoyuan He ◽

Shuishu Wang

Keyword(s):

Crystal Structure ◽

Dna Binding ◽

Dna Sequence ◽

Response Regulator ◽

Direct Repeat ◽

Regulatory Domain ◽

Response Regulators ◽

Sequence Recognition ◽

Repeat Dna ◽

Dna Sequence Recognition

The PhoP-PhoR two-component system plays a key role in regulating virulence of Mycobacterium tuberculosis. The response regulator PhoP is a transcription regulator, and it regulates expression of more than 100 genes. PhoP belongs to the OmpR/PhoB subfamily of response regulators. Despite extensive research in recent years, the molecular mechanism of DNA sequence recognition by this large subfamily of response regulators is not fully understood, especially the role of the N-terminal regulatory domain on DNA binding of the effector domain. Here we present a crystal structure of the full-length PhoP in complex with a direct-repeat DNA sequence. PhoP binds to DNA as a dimer. The two effector domains bind in tandem, each interacting with a half site of the direct repeat DNA. The DNA recognition helix inserts into the major groove, reading the sequence of a 7-bp motif. The wing residues interact with the downstream sequence, with a conserved arginine side chain inserting into the minor groove. Surprisingly, the regulatory domain also forms a tandem arrangement, instead of the anticipated symmetric dimer. The regulatory domain of the upstream protomer interacts with both domains of the downstream protomer. The structural elements of the alpha4-beta5-alpha5 face, which often found to be involved in dimer interface of the regulatory domain, play important roles in the interactions between the protomers. The crystal structure explains why PhoP recognizes direct repeats of two 7-bp motifs with a strict spacing of 4 bp and the highly cooperative binding of the two monomers. Detailed analysis of the structure along with analysis of the DNA sequence requirements and ITC measurements of protein-DNA binding interactions will be presented.

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