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.

doi:10.1006/jmbi.1993.1490

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

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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In crystal structures of GCN4 homodimers and Jun-Fos heterodimers, g-e' intersubunit salt bridges are seen between oppositely charged residues at positions gi and e/+5.
“In the crystal structures of GCN4 homodimers and Jun-Fos heterodimers, g-e' intersubunit salt bridges are visible between oppositely charged amino acids in the gi and e/+5 positions (O'Shea et al., 1991; Ellenberger et al., 1992; Konig & Richmond, 1993; Glover & Harrison, 1995).”
From Oligomerization properties of GCN4 leucine zipper e and g position mutants (1997) · cites this paper as Konig & Richmond, 1993

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de Viedma, D. G., Giraldo, R., Rivas, G., Fernández-Tresguerres, E., & Dı́az-Orejas, R. (1996) · EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00427.x · Cited by 47 · see citing works
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Thermodynamic signature of GCN4-bZIP binding to DNA indicates the role of water in discriminating between the AP-1 and ATF/CREB sites.
Dragan, A., Frank, L., Liu, Y.-Y., Makeyeva, E., Crane-Robinson, C., & Privalov, P. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.08.101 · Cited by 45 · see citing works
Diffusion‐controlled DNA recognition by an unfolded, monomeric bZIP transcription factor
Berger, C., Piubelli, L., Haditsch, U., & Bosshard, H. R. (1998) · FEBS Letters · doi:10.1016/s0014-5793(98)00156-2 · Cited by 45 · see citing works
SKN-1 domain folding and basic region monomer stabilization upon DNA binding.Preprint
Carroll, A. S., Gilbert, D., Liu, X.-Y., Cheung, J. W., Michnowicz, J. E., Wagner, G., Ellenberger, T., & Blackwell, T. K. (1997) · Genes & Development · doi:10.1101/gad.11.17.2227 · Cited by 44 · see citing works
“A critical prediction of this model is that residues on the BR back side, which do not contact DNA (Ellenberger et al. 1992; König and Richmond 1993; Glover and Harrison 1995; Keller et al. 1995), would be important for binding because they would be involved directly in critical packing…”
Background
DNA-binding motifs from eukaryotic transcription factors
Burley, S. K. (1994) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(94)90053-1 · Cited by 37 · see citing works
The role of helix stabilizing residues in GCN4 basic region folding and DNA binding
Hollenbeck, J. J., McClain, D. L., & Oakley, M. G. (2002) · Protein Science · doi:10.1110/ps.0211102 · Cited by 42 · see citing works
“In the presence of DNA, the bZip domain forms a dimer of uninterrupted -helices (Ellenberger et al. 1992; König and Richmond 1993; Keller et al. 1995).”
Background
Distribution of labor among bZIP segments in the control of DNA affinity and specificity.
Metallo, S. J., & Schepartz, A. (1994) · Chemistry and Biology · doi:10.1016/1074-5521(94)90004-3 · Cited by 42 · see citing works
An Intrahelical Salt Bridge within the Trigger Site Stabilizes the GCN4 Leucine Zipper*
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General and Cross-Pathway Controls of Amino Acid Biosynthesis
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Ang II and EGF synergistically induce COX‐2 expression via CREB in intestinal epithelial cells
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“Competition with dsDNA containing the AP-1-consensus partially decreased the CRE-specific band, possibly due to partial sequence affinity for CREB binding (Konig and Richmond, 1993).”
Background
Inhibition of major-groove-binding proteins by pyrrole-imidazole polyamides with an Arg-Pro-Arg positive patch.
Bremer, R., Baird, E. E., & Dervan, P. (1998) · Chemistry and Biology · doi:10.1016/s1074-5521(98)90057-6 · Cited by 40
Stimuli-responsive selection of target DNA sequences by synthetic bZIP peptides
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Response: How Much Solar Radiation Do Clouds Absorb?
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DNA-binding domains of Fos and Jun do not induce DNA curvature: an investigation with solution and gel methods.
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The GCN4 leucine zipper can functionally substitute for the heat shock transcription factor’s trimerization domain
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DNA binding of Jun and Fos bZip domains: homodimers and heterodimers induce a DNA conformational change in solution.
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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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