scholarly journals Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4

2021 ◽  
Vol 77 (7) ◽  
Author(s):  
Alessandro Agnarelli ◽  
Kamel El Omari ◽  
Ramona Duman ◽  
Armin Wagner ◽  
Erika J. Mancini
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Protein Complexes ◽  
Interferon Regulatory Factor ◽  
Dna Binding Proteins ◽  
Binding Domain ◽  
Anomalous Scattering ◽  
Dna Binding Domain ◽  
Regulatory Factor ◽  
Interferon Regulatory Factor 4

Pivotal to the regulation of key cellular processes such as the transcription, replication and repair of DNA, DNA-binding proteins play vital roles in all aspects of genetic activity. The determination of high-quality structures of DNA-binding proteins, particularly those in complexes with DNA, provides crucial insights into the understanding of these processes. The presence in such complexes of phosphate-rich oligonucleotides offers the choice of a rapid method for the routine solution of DNA-binding proteins through the use of long-wavelength beamlines such as I23 at Diamond Light Source. This article reports the use of native intrinsic phosphorus and sulfur single-wavelength anomalous dispersion methods to solve the complex of the DNA-binding domain (DBD) of interferon regulatory factor 4 (IRF4) bound to its interferon-stimulated response element (ISRE). The structure unexpectedly shows three molecules of the IRF4 DBD bound to one ISRE. The sole reliance on native intrinsic anomalous scattering elements that belong to DNA–protein complexes renders the method of general applicability to a large number of such protein complexes that cannot be solved by molecular replacement or by other phasing methods.

scholarly journals Subunit of an alpha-interferon-responsive transcription factor is related to interferon regulatory factor and Myb families of DNA-binding proteins.

1992 ◽  
Vol 12 (8) ◽  
pp. 3315-3324 ◽  
Author(s):  
S A Veals ◽  
C Schindler ◽  
D Leonard ◽  
X Y Fu ◽  
R Aebersold ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Recognition ◽  
Interferon Regulatory Factor ◽  
Dna Binding Proteins ◽  
Alpha Interferon ◽  
Cdna Clones ◽  
Regulatory Factor ◽  
Amino Terminal ◽  
Sequence Similarities

Alpha interferon stimulates transcription by converting the positive transcriptional regulator ISGF3 from a latent to an active form. This receptor-mediated event occurs in the cytoplasm, with subsequent translocation of the activated factor to the nucleus. ISGF3 has two components, termed ISGF3 alpha and ISGF3 gamma. ISGF3 gamma serves as the DNA recognition subunit, while ISGF3 alpha, which appears to consist of three polypeptides, is a target for alpha interferon signaling and serves as a regulatory component whose activation is required to form ISGF3. ISGF3 gamma DNA-binding activity was identified as a 48-kDa polypeptide, and partial amino acid sequence has allowed isolation of cDNA clones. ISGF3 gamma translated in vitro from recombinant clones bound DNA with a specificity indistinguishable from that of ISGF3 gamma purified from HeLa cells. Sequencing of ISGF3 gamma cDNA clones revealed significant similarity to the interferon regulatory factor (IRF) family of DNA binding proteins in the amino-terminal 117 residues of ISGF3 gamma. The other IRF family proteins bind DNA with a specificity related to but distinct from that of ISGF3 gamma. We note sequence similarities between the related regions of IRF family proteins and the imperfect tryptophan repeats which constitute the DNA-binding domain of the c-myb oncoprotein. These sequence similarities suggest that ISGF3 gamma and IRF proteins and the c-myb oncoprotein use a common structural motif for DNA recognition. Recombinant ISGF3 gamma, like the natural protein, interacted with HeLa cell ISGF3 alpha to form the mature ISGF3 DNA-binding complex. We suggest that other IRF family members may participate in signaling pathways by interacting with as yet unidentified regulatory subunits analogous to ISGF3 alpha.

scholarly journals Secondary structure and folding topology of the DNA binding domain of interferon regulatory factor 2, as revealed by NMR spectroscopy

FEBS Letters ◽  
1995 ◽  
Vol 359 (2-3) ◽  
pp. 184-188 ◽  
Author(s):  
Koichi Uegaki ◽  
Masahiro Shirakawa ◽  
Hisashi Harada ◽  
Tadatsugu Taniguchi ◽  
Yoshimasa Kyogoku
Keyword(s):  
Nmr Spectroscopy ◽  
Secondary Structure ◽  
Dna Binding ◽  
Interferon Regulatory Factor ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Regulatory Factor

scholarly journals Unique Structure of the DNA Binding Domain of Interferon Regulatory Factor 2 Determined by NMR Spectroscopy.

1994 ◽  
Vol 70 (10) ◽  
pp. 200-204
Author(s):  
Koichi UEGAKI ◽  
Masahiro SHIRAKAWA ◽  
Hisashi HARADA ◽  
Tadatsugu TANIGUCHI ◽  
Yoshimasa KYOGOKU
Keyword(s):  
Nmr Spectroscopy ◽  
Dna Binding ◽  
Interferon Regulatory Factor ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Regulatory Factor ◽  
Unique Structure

Crystallographic Characterization of the DNA-Binding Domain of Interferon Regulatory Factor-2 Complexed with DNA

1998 ◽  
Vol 121 (3) ◽  
pp. 363-366 ◽  
Author(s):  
Masahiro Kusumoto ◽  
Yoshifumi Fujii ◽  
Yuko Tsukuda ◽  
Takeshi Ohira ◽  
Yoshimasa Kyougoku ◽  
...  
Keyword(s):  
Dna Binding ◽  
Interferon Regulatory Factor ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Regulatory Factor

scholarly journals Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA-binding proteins.

1996 ◽  
Vol 16 (3) ◽  
pp. 792-799 ◽  
Author(s):  
S L Gregory ◽  
R D Kortschak ◽  
B Kalionis ◽  
R Saint
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
The Dead

We reported the identification of a new family of DNA-binding proteins from our characterization of the dead ringer (dri) gene of Drosophila melanogaster. We show that dri encodes a nuclear protein that contains a sequence-specific DNA-binding domain that bears no similarity to known DNA-binding domains. A number of proteins were found to contain sequences homologous to this domain. Other proteins containing the conserved motif include yeast SWI1, two human retinoblastoma binding proteins, and other mammalian regulatory proteins. A mouse B-cell-specific regulator exhibits 75% identity with DRI over the 137-amino-acid DNA-binding domains of these proteins, indicating a high degree of conservation of this domain. Gel retardation and optimal binding site screens revealed that the in vitro sequence specificity of DRI is strikingly similar to that of many homeodomain proteins, although the sequence and predicted secondary structure do not resemble a homeodomain. The early general expression of dri and the similarity of DRI and homeodomain in vitro DNA-binding specificity compound the problem of understanding the in vivo specificity of action of these proteins. Maternally derived dri product is found throughout the embryo until germ band extension, when dri is expressed in a developmentally regulated set of tissues, including salivary gland ducts, parts of the gut, and a subset of neural cells. The discovery of this new, conserved DNA-binding domain offers an explanation for the regulatory activity of several important members of this class and predicts significant regulatory roles for the others.

Heteronuclear Strategies for the Assignment of Larger protein/DNA complexes: Application to the 37 kDa trp Represser-Operator Complex

1997 ◽  
Author(s):  
M.J. Revington ◽  
W. Lee
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Nmr Studies ◽  
Dna Complexes ◽  
Dna Binding Domains ◽  
Binding Domains

The sequence-specific DNA binding function of many proteins is recognized as one of the central mechanisms of regulating transcription and DNA replication and repair. The ability of these proteins to select a short (usually 10 to 20 basepair) sequence out of the entire genome with which to form a stable complex is a prime example of molecular recognition. Atomic resolution structural studies using NMR and X-ray crystallography have emerged as essential techniques in understanding the basis of specificity and stability in these systems. While NMR studies of small DNA-binding domains of proteins have become almost routine (see Kaptein, 1993 for a review) relatively few NMR studies of protein-DNA complexes have been reported. These include the lac repressor headpiece complex (Chuprina et al., 1993). the Antennapedia homeodomain complex (Billetere et al., 1993), the GATA-1 complex (Omichinski et al., 1993). and the Myb DNA binding domain complex (Ogata et al., 1993); all of these complexes are smaller than 20 kDa. In most cases, size limitations have meant that only the DNA binding domain of the protein in complex with a single binding element have been studied. In vivo, however, most DNA binding proteins are much larger than these domains and often function as oligomers. The decrease in quality and increase in complexity of spectra as the molecular weight of the sample increases, limits the number of systems amenable to study using NMR and influences the decision to focus on single domains of multidomain proteins. However, since many DNA-binding proteins are regulated by the binding of ligands, other proteins or phosphorylation, often at sites distal from the DNA-binding domain, it is preferable to study as much of the intact protein as possible in order to characterize allosteric and regulatory mechanisms (Pabo and Sauer, 1992). E. coli trp repressor is a 25 kDa homodimer that regulates operons involved in tryptophan biosynthesis. The dimer is one of the smallest intact proteins that binds sequence specifically to DNA and whose affinity is modulated by an effector (L-tryptophan).

Subunit of an alpha-interferon-responsive transcription factor is related to interferon regulatory factor and Myb families of DNA-binding proteins

1992 ◽  
Vol 12 (8) ◽  
pp. 3315-3324
Author(s):  
S A Veals ◽  
C Schindler ◽  
D Leonard ◽  
X Y Fu ◽  
R Aebersold ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Recognition ◽  
Interferon Regulatory Factor ◽  
Dna Binding Proteins ◽  
Alpha Interferon ◽  
Cdna Clones ◽  
Regulatory Factor ◽  
Amino Terminal ◽  
Sequence Similarities

Alpha interferon stimulates transcription by converting the positive transcriptional regulator ISGF3 from a latent to an active form. This receptor-mediated event occurs in the cytoplasm, with subsequent translocation of the activated factor to the nucleus. ISGF3 has two components, termed ISGF3 alpha and ISGF3 gamma. ISGF3 gamma serves as the DNA recognition subunit, while ISGF3 alpha, which appears to consist of three polypeptides, is a target for alpha interferon signaling and serves as a regulatory component whose activation is required to form ISGF3. ISGF3 gamma DNA-binding activity was identified as a 48-kDa polypeptide, and partial amino acid sequence has allowed isolation of cDNA clones. ISGF3 gamma translated in vitro from recombinant clones bound DNA with a specificity indistinguishable from that of ISGF3 gamma purified from HeLa cells. Sequencing of ISGF3 gamma cDNA clones revealed significant similarity to the interferon regulatory factor (IRF) family of DNA binding proteins in the amino-terminal 117 residues of ISGF3 gamma. The other IRF family proteins bind DNA with a specificity related to but distinct from that of ISGF3 gamma. We note sequence similarities between the related regions of IRF family proteins and the imperfect tryptophan repeats which constitute the DNA-binding domain of the c-myb oncoprotein. These sequence similarities suggest that ISGF3 gamma and IRF proteins and the c-myb oncoprotein use a common structural motif for DNA recognition. Recombinant ISGF3 gamma, like the natural protein, interacted with HeLa cell ISGF3 alpha to form the mature ISGF3 DNA-binding complex. We suggest that other IRF family members may participate in signaling pathways by interacting with as yet unidentified regulatory subunits analogous to ISGF3 alpha.

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