Cited by 287Protein Structure and DynamicsGenomics and Chromatin DynamicsDNA and Nucleic Acid Chemistry

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The X-ray Structure of the GCN4-bZIP Bound to ATF/CREB Site DNA Shows the Complex Depends on DNA Flexibility

König, Peter, Richmond, Timothy J.·1993·Journal of Molecular Biology

DOI 10.1006/jmbi.1993.1490

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Abstract

The X-ray structure of the DNA binding domain of the yeast transcriptional activator protein GCN4 bound to a DNA fragment containing the sequence of the perfectly symmetrical ATF/CREB site has been solved to 3.0 A resolution. The architecture of this specific recognition complex supports the current model for bZIP proteins: a homodimer of parallel alpha-helices form an interhelix coiled-coil region via the leucine zipper, and the two N-terminal basic regions fit into the major groove of half sites on opposite sides of the DNA double helix. The structure shows that DNA flexibility plays the predominant role in the preservation of protein contacts with the symmetric ATF/CREB site (ATGACGTCAT) as compared to the pseudo-symmetric AP-1 target site (ATGACTCAT), overcoming the positional displacement of functional groups introduced by the additional G.C base-pair at the center of the ATF/CREB sequence.

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Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182
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The contribution of the methyl groups on thymine bases to binding specificity and affinity by alanine-rich mutants of the bZIP motif.
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Dissection of the basic subdomain of the c-Jun oncoprotein: a structural analysis of two peptide fragments by CD, Fourier-transform infrared and NMR.
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Plus ça change, plus c'est la même chose
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Dual DNA recognition codes of a short peptide derived from the basic leucine zipper protein EmBP1.
Hirata, A., Ueno, M., Aizawa, Y., Ohkubo, K., Morii, T., & Yoshikawa, S. (2005) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2005.02.052 · Cited by 4
Crystallization of bFGF-DNA aptamer complexes using a Sparse Matrix designed for protein–nucleic acid complexes
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Solution Structure of O-glycosylated C-terminal Leucine Zipper Domain of Human Salivary Mucin (MUC7)
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Towards a mutant analysis of the tertiary structures of functional DNA‐binding motifs
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Solution structure of the ATF-2 recognition site and its interaction with the ATF-2 peptide.
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NMR spectroscopy and X-ray crystallography provide complementary information on the structure and dynamics of leucine zippers.
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Simultaneous binding of a polyamide dimer and an oligonucleotide in the minor and major grooves of DNA.
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Structural characterization of a short peptide fragment that mediates estrogen-receptor dimerization.
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DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains.
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Molecular recognition: monomer of the yeast transcriptional activator GCN4 recognizes its dimer DNA binding target sites specifically
Cao, W.-G., Liu, L., Lai, L., & Tang, Y. (2000) · doi:10.1007/bf02969492 · Cited by 3
“the two optimal GCN4 target sites, and the X-ray crystal structures of the complexes of GCN4 with them have confirmed that([6,7]) GCN4 dimerizes via the leucine zipper regions to form a Yshaped dimer.”
Background
STUDIES ON THE FORMATION OF DNA.PROTEIN INTERFACES: DNA SPECIFICITY AND STRAIGHTENING BY CREB
Hamm, M., & Schepartz, A. (1995) · doi:10.1016/0960-894x(95)00266-v · Cited by 3
Deactivation of a dimeric DNA-binding peptide through a palladium-mediated self-immolative cleavage
Rodríguez, J., Pérez-González, C., Martínez-Calvo, M., Mosquera, J., & Mascareñas, J. (2022) · RSC Advances · doi:10.1039/d1ra09180h · Cited by 2
The bZIP Targets Overlapping DNA Subsites within a Half-Site, Resulting in Increased Binding Affinities
Chan, I.-S., Shahravan, S. H., Fedorova, A., & Shin, J.-M. A. (2008) · Biochemistry · doi:10.1021/bi800355t · Cited by 2
“In the symmetric CRE complex, the GCN4 bZIP makes a hybrid of the interactions made to AP-1: Arg243 forms a single H-bond to G1′ and direct and water-mediated interactions with the phosphodiester backbone (4, 5).”
BackgroundMethod
The monomer of the yeast transcriptional activator GCN4 recognizes its dimer binding DNA target sites without dimerization
Cao, W.-G., Liu, L., Klein, D., Wei, L.-Y., & Lai, L. (2000) · doi:10.1016/s0040-6031(00)00538-4 · Cited by 2
Sequence-specific DNA binding by short peptides
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Authors: König, P., & Richmond, T. J.
Affiliations: ETH Zurich (CH)
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1993-09
Volume: 233
Issue: 1
Pages: 139-154
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.1993.1490
OpenAlex: W2056115277
Cited by: 287
References: 0
Citations by year: 2026: 2 · 2025: 1 · 2022: 2 · 2021: 2 · 2020: 3 · 2019: 5 · 2018: 2 · 2017: 3 · 2016: 2 · 2015: 3 · 2014: 4 · 2013: 5 · 2012: 8
FWCI: 9.52
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords: GCN4, bZIP transcription factors, DNA-binding domain, DNA flexibility, protein-DNA complex structure, leucine zipper, coiled coil, AP-1 binding site, major groove binding
MeSH terms: Amino Acid Sequence, Base Sequence, Binding Sites, Blood Proteins, Crystallization, DNA-Binding Proteins, Fungal Proteins, Genes, Synthetic, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Peptide Fragments, Plant Proteins, Protein Conformation, Protein Kinases, Recombinant Proteins, Regulatory Sequences, Nucleic Acid, Transcription Factors, X-Ray Diffraction, Leucine Zippers, Cyclic AMP Response Element-Binding Protein, Protein Structure, Secondary, Saccharomyces cerevisiae Proteins, Macromolecular Substances, Basic-Leucine Zipper Transcription Factors, Activating Transcription Factors, G-Box Binding Factors

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The X-ray Structure of the GCN4-bZIP Bound to ATF/CREB Site DNA Shows the Complex Depends on DNA Flexibility

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