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

The DOI matches its Crossref record.

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

Open this paper in CoChat — free account

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.

Integrity signals

Registry

Crossref · 10.1006/jmbi.1993.1490

Cites

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Sorted by citations

Coiled coils: a highly versatile protein folding motif.
Burkhard, P., Stetefeld, J., & Strelkov, S. (2001) · Trends in Cell Biology · doi:10.1016/s0962-8924(00)01898-5 · Cited by 1,055
Crystal structure of the heterodimeric bZIP transcription factor c-Fos–c-Jun bound to DNA
Glover, J. N. M., & Harrison, S. C. (1995) · Nature · doi:10.1038/373257a0 · Cited by 734
Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA
Chen, L., Glover, J. N. M., Hogan, P. G., Rao, A., & Harrison, S. C. (1998) · Nature · doi:10.1038/32100 · Cited by 521
“AP-1 The segments of Fos and Jun are each single α-helices, and the heterodimer forks across the DNA major groove, just as in the DNA complexes of other bZIP protein”
Background
Structure of serum response factor core bound to DNA
Pellegrini, L., Tan, S., & Richmond, T. (1995) · Nature · doi:10.1038/376490a0 · Cited by 347
Self-citation
Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions
Fernandes, L., Rodrigues-Pousada, C., & Struhl, K. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.12.6982 · Cited by 337
“Biochemical and crystallographic analysis has defined the optimal AP-1 site (TGACTCA), the structure of the Gcn4-DNA complex at atomic resolution, and many of the protein-DNA contacts that mediate specific binding to AP-1 sites (10, 19, 29, 31, 42).”
Background
The Crystal Structure of the DNA-Binding Domain of Yeast RAP1 in Complex with Telomeric DNA
König, P., Giraldo, R., Chapman, L., & Rhodes, D. (1996) · Cell · doi:10.1016/s0092-8674(00)81088-0 · Cited by 308
“(König and Richmond, 1993).”
Self-citation
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
Luscombe, N., & Thornton, J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00571-5 · Cited by 272
A thermodynamic scale for leucine zipper stability and dimerization specificity: e and g interhelical interactions.
Krylov, D., Mikhailenko, I., & Vinson, C. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06579.x · Cited by 269
Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? 1 1Edited by R. Ebright
Pabo, C. O., & Nekludova, L. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3918 · Cited by 232
Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles.
Mandel-Gutfreund, Y., Schüler, O., & Margalit, H. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0559 · Cited by 212
Structural basis for the diversity of DNA recognition by bZIP transcription factors
Fujii, Y., Shimizu, T., Toda, T., Yanagida, M., & Hakoshima, T. (2000) · Nature Structural Biology · doi:10.1038/82822 · Cited by 198
bZIPs and WRKYs: two large transcription factor families executing two different functional strategies
Llorca, C. M., Potschin, M., & Zentgraf, U. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00169 · Cited by 202
Plant bZIP G-box binding factors. Modular structure and activation mechanisms.
Sibéril, Y., Doireau, P., & Gantet, P. (2001) · European Journal of Biochemistry · doi:10.1046/j.0014-2956.2001.02552.x · Cited by 189
Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA.
Bracken, C., Carr, P., Cavanagh, J., & Palmer, A. G. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2429 · Cited by 184
Crystal structure of ATF‐2/c‐Jun and IRF‐3 bound to the interferon‐β enhancer
Panne, D., Maniatis, T., & Harrison, S. (2004) · EMBO Journal · doi:10.1038/sj.emboj.7600453 · Cited by 182
“A bZIP element includes a DNA-binding region containing basic amino-acid residues and a dimerization domain containing coiled-coil heptad repeats (Ellenberger et al, 1992; Konig and Richmond, 1993).”
Background
The Structure of a CREB bZIP·Somatostatin CRE Complex Reveals the Basis for Selective Dimerization and Divalent Cation-enhanced DNA Binding
Schumacher, M. A., Goodman, R. H., & Brennan, R. G. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m007293200 · Cited by 172
Mechanism of DNA-binding enhancement by the human T-cell leukaemia virus transactivator Tax
Baranger, A., Palmer, C., Hamm, M., Giebler, H., Brauweiler, A., Nyborg, J., & Schepartz, A. (1995) · Nature · doi:10.1038/376606a0 · Cited by 175
γ‐Peptides Forming More Stable Secondary Structures than α‐Peptides: Synthesis and helical NMR‐solution structure of the γ‐hexapeptide analog of H‐(Val‐Ala‐Leu)2‐OH
Hintermann, T., Gademann, K., Jaun, B., & Seebach, D. (1998) · doi:10.1002/hlca.19980810514 · Cited by 164
Predicting the kinetics of peptide-antibody interactions using a multivariate experimental design of sequence and chemical space
Andersson, K., Choulier, L., H�m�l�inen, M. D., Regenmortel, M. H. V. V., Altschuh, D., & Malmqvist, M. (2001) · Journal of Molecular Recognition · doi:10.1002/1099-1352(200101/02)14:1 · Cited by 37
A role for CH…O interactions in protein-DNA recognition
Mandel‐Gutfreund, Y., Margalit, H., Jernigan, R. L., & Zhurkin, V. B. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1660 · Cited by 176
α-Helical Protein Assembly Motifs
Kohn, W. D., Mant, C. T., & Hodges, R. S. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.5.2583 · Cited by 187
Combinatorial bZIP dimers display complex DNA-binding specificity landscapes
Rodríguez‐Martínez, J. A., Reinke, A. W., Bhimsaria, D., Keating, A. E., & Ansari, A. Z. (2017) · eLife · doi:10.7554/elife.19272 · Cited by 179
Electrostatic mechanisms of DNA deformation.
Williams, L., & Maher, L. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.497 · Cited by 158
A novel oxidative stress-inducible peroxidase promoter from sweetpotato: molecular cloning and characterization in transgenic tobacco plants and cultured cells
Kim, K., Kwon, S.-Y., Lee, H.-S., Hur, Y., Bang, J., & Kwak, S. (2003) · Plant Molecular Biology · doi:10.1023/a:1023045218815 · Cited by 156
“This element is known to be involved in oxidative stress in animal cells (Hilson et al., 1990; Konig and Richmond, 1993).”
Background
Cell-type-specific binding of the transcription factor CREB to the cAMP-response element
Cha‐Molstad, H., Keller, D. M., Yochum, G. S., Impey, S., & Goodman, R. H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405587101 · Cited by 149
Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition.
Keller, W., König, P., & Richmond, T. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0645 · Cited by 149
“The interaction between Asn235 and the purine A −5 via a water interaction demonstrates how the fixed asparagine side - chain extends the specificity determination for this residue to three base - pairs .”
BackgroundMethodResultInfluentialSelf-citation
The Yap family and its role in stress response
Rodrigues‐Pousada, C., Menezes, R., & Pimentel, C. (2010) · Yeast · doi:10.1002/yea.1752 · Cited by 156
“In the Gcn4 basic domain, five residues (Asn235, Ala238, Ala239, Ser242 and Arg243) required for the basespecific contacts in Gcn4 and Jun/Fos are most highly conserved [8–10].”
Background
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes
Kanhere, A., & Bansal, M. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki627 · Cited by 147
“Many other transcription factors also facilitate the adoption of curved conformations by DNA molecules (36, 37 ).”
Background
Measurement of Interhelical Electrostatic Interactions in the GCN4 Leucine Zipper
Lumb, K. J., & Kim, P. S. (1995) · Science · doi:10.1126/science.7716550 · Cited by 156
Structural Basis for DNA Recognition by the Basic Region Leucine Zipper Transcription Factor CCAAT/Enhancer-binding Protein α
Miller, M., Shuman, J. D., Sebastian, T. B., Dauter, Z., & Johnson, P. F. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300417200 · Cited by 136
Antigen recognition by conformational selection
Berger, C., Weber-Bornhauser, S., Eggenberger, J., Hanes, J., Plückthun, A., & Bosshard, H. (1999) · FEBS Letters · doi:10.1016/s0014-5793(99)00458-5 · Cited by 133
Salt effects on protein stability: two-strandedα-helical coiled-coils containing inter- or intrahelical ion pairs
Kohn, W. D., Kay, C. M., & Hodges, R. S. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0930 · Cited by 117
Yeast activator proteins and stress response: an overview
Rodrigues‐Pousada, C., Nevitt, T., Menezes, R., Azevedo, D., Pereira, J. A. M., & Amaral, C. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.03.119 · Cited by 116
De novo design of α-helical proteins: basic research to medical applications
Hodges, R. S. (1996) · Biochemistry and Cell Biology · doi:10.1139/o96-015 · Cited by 155
Getting a grip on DNA recognition: structures of the basic region leucine zipper, and the basic region helix-loop-helix DNA-binding domains
Ellenberger, T. (1994) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(94)90054-x · Cited by 124
EUKARYOTIC TRANSCRIPTION FACTOR-DNA COMPLEXES
Patikoglou, G. A., & Burley, S. K. (1997) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.26.1.289 · Cited by 133
The leucine zipper domain controls the orientation of AP-1 in the NFAT·AP-1·DNA complex
Erlanson, D. A., Chytil, M., & Verdine, G. L. (1996) · Chemistry & Biology · doi:10.1016/s1074-5521(96)90165-9 · Cited by 126
The importance and identification of regulatory polymorphisms and their mechanisms of action
Buckland, P. R. (2005) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2005.10.004 · Cited by 107
Kinetic studies of sequence-specific binding of GCN4-bZIP peptides to DNA strands immobilized on a 27-MHz quartz-crystal microbalance.
Okahata, Y., Niikura, K., Sugiura, Y., Sawada, M., & Morii, T. (1998) · Biochemistry · doi:10.1021/bi980037k · Cited by 111
A framework for the DNA–protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules
Suzuki, M. (1994) · Structure · doi:10.1016/s0969-2126(00)00033-2 · Cited by 114
Structural model for the cooperative assembly of HIV-1 Rev multimers on the RRE as deduced from analysis of assembly-defective mutants.
Jain, C., & Belasco, J. (2001) · Molecules and Cells · doi:10.1016/s1097-2765(01)00207-6 · Cited by 106
“…of tail-to-tail and head-to the RRE is reminiscent of the yeast DNA binding protein Gcn4p and related bZip transcription factors to-head interactions (Figure 4B), it might seem puzzling that mutants with a defective head surface were identi-(Konig and Richmond, 1993; Glover and Harrison, 1995).”
Crystal Structure of the CCAAT Box/Enhancer-binding Protein β Activating Transcription Factor-4 Basic Leucine Zipper Heterodimer in the Absence of DNA
Podust, L. M., Krezel, A. M., & Kim, Y. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m005594200 · Cited by 93
Crystal structure of a PUT3–DNA complex reveals a novel mechanism for DMA recognition by a protein containing a Zn2Cys6 binuclear cluster
Swaminathan, K., Flynn, P., Reece, R. J., & Marmorstein, R. (1997) · Nature Structural Biology · doi:10.1038/nsb0997-751 · Cited by 92
Orientation, positional, additivity, and oligomerization-state effects of interhelical ion pairs in α-helical coiled-coils
Kohn, W. D., Kay, C. M., & Hodges, R. S. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2125 · Cited by 95
Use of a heterodimeric coiled-coil system for biosensor application and affinity purification
Chao, H., Bautista, D. L., Litowski, J. R., Irvin, R. T., & Hodges, R. S. (1998) · Journal of Chromatography B Biomedical Sciences and Applications · doi:10.1016/s0378-4347(98)00172-8 · Cited by 101
Buried asparagines determine the dimerization specificities of leucine zipper mutants
Zeng, X., Herndon, A., & Hu, J. C. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.8.3673 · Cited by 92
High Resolution NMR Solution Structure of the Leucine Zipper Domain of the c-Jun Homodimer
Junius, F. K., O’Donoghue, S. I., Nilges, M., Weiss, A. S., & King, G. F. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.23.13663 · Cited by 97
Yeast AP-1 like transcription factors (Yap) and stress response: a current overview
Rodrigues‐Pousada, C., Devaux, F., Caetano, S. M., Pimentel, C., da Silva, S. M., Gaspar‐Cordeiro, A., & Amaral, C. (2019) · Microbial Cell · doi:10.15698/mic2019.06.679 · Cited by 112
“These residues are highly conserved in the Jun/Fos bZIP proteins found in mammals [4-6].”
Background
Structural Basis of Alternative DNA Recognition by Maf Transcription Factors
Kurokawa, H., Motohashi, H., Sueno, S., Kimura, M., Takagawa, H., Kanno, Y., Yamamoto, M., & Tanaka, T. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.00708-09 · Cited by 83
“This observation agrees well with the previously reported solution structure of monomeric MafG(1-76) (21).”
BackgroundMethodResultInfluential
The transcriptional activator GvpE for the halobacterial gas vesicle genes resembles a basic region leucine-zipper regulatory protein.
Krüger, K., Hermann, T., Armbruster, V., & Pfeifer, F. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1795 · Cited by 83
RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease
Dai, S., Zhang, Z., Chen, S., & Beachy, R. N. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307687100 · Cited by 72
The Human T-cell Leukemia Virus-1 Transcriptional Activator Tax Enhances cAMP-responsive Element-binding Protein (CREB) Binding Activity through Interactions with the DNA Minor Groove
Lundblad, J. R., Kwok, R. P. S., Laurance, M. E., Huang, M., Richards, J. P., Brennan, R. G., & Goodman, R. H. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.30.19251 · Cited by 73
Complilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae
Svetlov, V. V., & Cooper, T. (1995) · Yeast · doi:10.1002/yea.320111502 · Cited by 78
DNA-Binding Specificity of the PAR Basic Leucine Zipper Protein VBP Partially Overlaps Those of the C/EBP and CREB/ATF Families and Is Influenced by Domains That Flank the Core Basic Region
Haas, N. B., Cantwell, C. A., Johnson, P. F., & Burch, J. B. E. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.4.1923 · Cited by 66
“, essentially core bZIP) forms of GCN4 (7, 15), it was of interest to examine in a systematic fashion the possibility that additional domains might be relevant to the interactions of at least some bZIP factors with their respective binding sites.”
BackgroundInfluential
Stabilization of bzip Peptides through Incorporation of Fluorinated Aliphatic Residues
Son, S.-H., Tanrikulu, I. C., & Tirrell, D. (2006) · ChemBioChem · doi:10.1002/cbic.200500420 · Cited by 70
Specific Regions of Contact between Human T-cell Leukemia Virus Type I Tax Protein and DNA Identified by Photocross-linking*
Kimzey, A., & Dynan, W. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.22.13768 · Cited by 70
DNA-binding specificity of the homeodomain-leucine zipper domain.
Sessa, G., Morelli, G., & Ruberti, I. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1408 · Cited by 70
DNA-binding specificity of PAR and C/EBP leucine zipper proteins: a single amino acid substitution in the C/EBP DNA-binding domain confers PAR-like specificity to C/EBP.
Falvey, E., Marcacci, L., & Schibler, U. (1996) · Biological chemistry · doi:10.1515/bchm3.1996.377.12.797 · Cited by 70
Towards an understanding of protein-DNA recognition
Rhodes, D., Schwabe, J. W. R., Chapman, A. C., & Fairall, L. (1996) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1996.0048 · Cited by 69
Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun.
Leonard, D. A., Rajaram, N., & Kerppola, T. K. (1997) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.94.10.4913 · Cited by 69
The Sko1p Repressor and Gcn4p Activator Antagonistically Modulate Stress-Regulated Transcription inSaccharomyces cerevisiae
Pascual-Ahuir, A., Serrano, R. L., & Proft, M. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.1.16-25.2001 · Cited by 65
Certain bZIP peptides bind DMA sequentially as monomers and dimerize on the DMA
Metallo, S. J., & Schepartz, A. (1997) · Nature Structural Biology · doi:10.1038/nsb0297-115 · Cited by 63
Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.
Siggers, T., Silkov, A., & Honig, B. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.11.010 · Cited by 63
Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers.
Wolfe, S., Ramm, E. I., & Pabo, C. (2000) · Structure · doi:10.1016/s0969-2126(00)00161-1 · Cited by 63
Pharmacological interference with protein-protein interactions mediated by coiled-coil motifs.
Strauss, H., & Keller, S. (2008) · Handbook of Experimental Pharmacology · doi:10.1007/978-3-540-72843-6_19 · Cited by 63
“... vital functions of these proteins – that is, dimerization and ensuing DNA binding – are reflected in the structure of their bZip domain, which is about 60–80 amino acid residues long and consists of two distinct regions (Vinson et al. 1989): an N-terminal basic region responsible for binding to the major groove of…”
Background
Design of a C/EBP-specific, Dominant-negative bZIP Protein with Both Inhibitory and Gain-of-function Properties
Olive, M., Williams, S. C., Dezan, C., Johnson, P. F., & Vinson, C. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.4.2040 · Cited by 57
Nuclear Magnetic Resonance Characterization of the Jun Leucine Zipper Domain: Unusual Properties of Coiled-Coil Interfacial Polar Residues
Junius, F. K., Mackay, J. P., Bubb, W. A., Jensen, S. A., Weiss, A. S., & King, G. F. (1995) · Biochemistry · doi:10.1021/bi00018a020 · Cited by 64
Synthesis and Characterization of Iron Silasesquioxane Phosphane Complexes
Liu, F., John, K. D., Scott, B. L., Baker, R. T., Ott, K. C., & Tumas, W. (2000) · Angewandte Chemie · doi:10.1002/1521-3757(20000901)112:17 · Cited by 6
Zen and the art of Fos and Jun
Kerppola, T., & Curran, T. (1995) · Nature · doi:10.1038/373199a0 · Cited by 56
DNA targets for certain bZIP proteins distinguished by an intrinsic bend.
Paolella, D. N., Palmer, C., & Schepartz, A. (1994) · Science · doi:10.1126/science.8178171 · Cited by 55
Crystal structure of the amino-terminal coiled-coil domain of the APC tumor suppressor 1 1Edited by I. A. Wilson
Day, C. L., & Alber, T. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3895 · Cited by 52
DNA sequence‐dependent folding determines the divergence in binding specificities between Maf and other bZIP proteins
Dlakić, M., Grinberg, A. V., Leonard, D. A., & Kerppola, T. K. (2001) · The EMBO Journal · doi:10.1093/emboj/20.4.828 · Cited by 52
LSF and NTF-1 Share a Conserved DNA Recognition Motif yet Require Different Oligomerization States to Form a Stable Protein-DNA Complex*
Shirra, M., & Hansen, U. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.30.19260 · Cited by 53
Differential Gene Regulation by Selective Association of Transcriptional Coactivators and bZIP DNA-Binding Domains
Miotto, B., & Struhl, K. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.00696-06 · Cited by 47
“Upon binding to DNA, the previously unfolded basic region becomes -helical (36, 38, 54) such that five conserved amino acid residues are positioned to contact specific base pairs in the target sites (12, 26).”
Background
Bipartite determinants of DNA-binding specificity of plant basic leucine zipper proteins
Niu, X.-P., Renshaw-Gegg, L., Miller, L., & Guiltinan, M. (1999) · Plant Molecular Biology · doi:10.1023/a:1006206011502 · Cited by 51
“One explanation for this is that the basic regions of these GCN4 mutants may bifurcate at a wider angle from the dimerization domain to accommodate the CRE site which has two central base pairs for half-site spacing (König and Richmond, 1993; Keller et al., 1995).”
MethodInfluential
Specific interaction of the tomato bZIP transcription factor VSF-1 with a non-palindromic DNA sequence that controls vascular gene expression
Ringli, C., & Keller, B. (1998) · Plant Molecular Biology · doi:10.1023/a:1006030007333 · Cited by 51
“In the fully palindromic ATF/CRE site, both arginines of GCN4 establish one hydrogen bond with a central guanine and a backbone phosphate [ 30 ].”
Background
Characterization of IDI‐4, a bZIP transcription factor inducing autophagy and cell death in the fungus Podospora anserina
Dementhon, K., Saupe, S., & Clavé, C. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04235.x · Cited by 50
“In the prototypical Gcn4p bZIP factor this conserved residue makes DNAcontacts (Ellenberger et al., 1992; Konig and Richmond, 1993) and substitution of this residue by a serine alleviates DNA-binding in vitro and Gcn4p activity in vivo (Tzamarias et al., 1992; Suckow et al., 1994).”
Background
Oligomerization properties of GCN4 leucine zipper e and g position mutants
Zeng, X., Zhu, H., Lashel, H. A., & Hu, J. C. (1997) · Protein Science · doi:10.1002/pro.5560061016 · Cited by 50
cAMP Response Element-binding Protein Monomers Cooperatively Assemble to Form Dimers on DNA*
Wu, X.-L., Spiro, C., Owen, W. G., & McMurray, C. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.33.20820 · Cited by 49
The transcription activation domains of Fos and Jun induce DNA bending through electrostatic interactions
Kerppola, T., & Curran, T. (1997) · EMBO Journal · doi:10.1093/emboj/16.10.2907 · Cited by 48
“…site (Oakley MI 48109-0650 and 2Department of Developmental Neurobiology, and Dervan, 1990; O’Neil et al., 1990; Talanian et al.,St Jude Children’s Research Hospital, Memphis, TN 38105-2794, USA 1990; O’Shea et al., 1991; Konig and Richmond, 1993;1Corresponding author Glover and Harrison, 1995).”
Background
A leucine zipper motif determines different functions in a DNA replication protein.
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
Thermodynamics of sequence-specific protein-DNA interactions.
Härd, T., & Lundbäck, T. (1996) · Biophysical Chemistry · doi:10.1016/s0301-4622(96)02197-7 · Cited by 46
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
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
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
“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
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
“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
An Intrahelical Salt Bridge within the Trigger Site Stabilizes the GCN4 Leucine Zipper*
Kammerer, R., Jaravine, V., Frank, S., Schulthess, T., Landwehr, R., Lustig, A., García-echeverría, C., Alexandrescu, A., Engel, J., & Steinmetz, M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m010492200 · Cited by 41
General and Cross-Pathway Controls of Amino Acid Biosynthesis
Sachs, M. (1996) · Biochemistry and Molecular Biology · doi:10.1007/978-3-662-10367-8_14 · Cited by 41
Ang II and EGF synergistically induce COX‐2 expression via CREB in intestinal epithelial cells
Pham, H., Chong, B., Vincenti, R., & Slice, L. (2008) · Journal of Cellular Physiology · doi:10.1002/jcp.21167 · Cited by 40
“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
Mosquera, J., Jiménez-Balsa, A., Dodero, V., Vázquez, M. E., & Mascareñas, J. (2013) · Nature Communications · doi:10.1038/ncomms2825 · Cited by 37
Response : Interhelical Salt Bridges, Coiled-Coil Stability, and Specificity of Dimerization
Lumb, K. J., & Kim, P. S. (1996) · Science · doi:10.1126/science.271.5252.1137 · Cited by 46
Reversible supramolecular assembly at specific DNA sites: nickel-promoted bivalent DNA binding with designed peptide and bipyridyl-bis(benzamidine) components.
Sánchez, M. I., Mosquera, J., Vázquez, M., & Mascareñas, J. (2014) · Angewandte Chemie · doi:10.1002/anie.201405726 · Cited by 36
DNA-binding domains of Fos and Jun do not induce DNA curvature: an investigation with solution and gel methods.
Sitlani, A., & Crothers, D. (1998) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.95.4.1404 · Cited by 34
The GCN4 leucine zipper can functionally substitute for the heat shock transcription factor’s trimerization domain
Drees, B., Grotkopp, E., & Nelson, H. C. M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1283 · Cited by 33
DNA binding of Jun and Fos bZip domains: homodimers and heterodimers induce a DNA conformational change in solution.
John, M., Leppik, R., Busch, S. J., Granger-Schnarr, M., & Schnarr, M. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.22.4487 · Cited by 34
Deconstruction of GCN4/GCRE into a monomeric peptide-DNA complex
Stanojević, D., & Verdine, G. (1995) · Nature Structural Biology · doi:10.1038/nsb0695-450 · Cited by 34
DNA recognition by structure-selective nucleases
Suck, D. (1997) · Biopolymers · doi:10.1002/(sici)1097-0282(1997)44:4 · Cited by 41

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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cited by

Metadata

Record

About these checks