Primary Citation PubMed: 7500340
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The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes.
(2008) PLoS One 3
PubMed: 18698409 | PubMedCentral: PMC2492810 | DOI: 10.1371/journal.pone.0002944
The center of the tree depicts a typical bZIP dimer bound to DNA, representing the conserved bZIP domain (GCN4 from Saccharomyces cerevisiae ; Protein Data Bank entry 2DGC).
Publication Year: 2008
Assessment of the optimization of affinity and specificity at protein-DNA interfaces.
(2009) Nucleic Acids Res 37
PubMed: 19389725 | PubMedCentral: PMC2691843 | DOI: 10.1093/nar/gkp242
MATERIALS AND METHODS Structural data The following high-resolution crystal structures of protein–DNA complexes were modeled: Helical transcription factors: 1ig7 1k61 1puf 2hdd 1w0u 1e3o 2d5v ... zaa 1ubd 1g2f 1am9 1gd2 1gu4 1jnm 2dgc 1nkp 1lmb 2or1 1hcr 1ign 1tc3 1bl0 1zs4 2h27 1r71 1pp7 1bc8 1dp7 1f4k.
A) DNAse I (pdb code: 2DNJ), B) C2H2 zinc finger Zif268 (1ZAA), C) [β]-Zip GCN4 (2DGC), D) Eco RV (1B94), E) I- Mso I (1M5X).
β-Zip transcription factor GCN4 The transcription factor GCN4 (pdb code: 2DGC ( 20 )), shown in Figure 1 C, has a high density of amino acid side chains with direct contacts to DNA that extend from an α-helix nestled deeply into the DNA major groove, as also seen in zinc fingers, homeodomains and response regulators.
Publication Year: 2009
Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example.
(2010) Nucleic Acids Res 38
PubMed: 20685816 | PubMedCentral: PMC2995082 | DOI: 10.1093/nar/gkq683
Among all crystal structures of protein–DNA complexes, we selected Gcn4 bound to the ATF/CREB site (PDB id 2DGC) and the Jun/Fos heterodimer (PDB id 1FOS).
Publication Year: 2010
Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components.
(2011) Nucleic Acids Res 39
PubMed: 21071403 | PubMedCentral: PMC3074165 | DOI: 10.1093/nar/gkq984
of ionic contacts, Z Identity of contacting residues (Ref): PDB file CoreATH2 −2.1 (15) 3 K7,R8,K14 (14): 2EZD ATH3 −2.6 (15) 4 R33,K34,K41,K40 (14): 2EZF D74 −2.5 (17) 4 R7,K2... ,K60,K37/R44 (34): 1QRV LEF79 −3.4 (12) 5 K3,K14,R17,K27,R59 (35): 2LEF GCN4 −4.1 (11) 6 R232,R234,R240,R241,R243,R245 (36): 2DGC NHP6A −6.4 (12) 9 K16,K22,R36,R40,K53K60,K67,K78,K85 (37): 1LWA SRY −8.5 (12) 12 R4,R6,R17,R21,R31,K37,K44,K51,R66,K73,K79,K81 (38): 1J47 desNK2 −5.5 (13) 4 R31,K46,R53,K55 (39): 1NK3 MATα2 −5.8 (13) 5 K46,R53,R54,K55,K57 (40): 1APL desANTP −7.0 (13) 6 R28,R31,R43,R52,R53,K55 (42): 9ANT Engrailed −6.6 (13) 6 R31,K46,R53,K55,K57,K58 (41): 3HDD Release of anions specifically bound to these homeodomains upon association with DNA is not an exception and has been documented experimentally in the formation of several protein/DNA complexes ( 22–24 ).
Publication Year: 2011
Rationally designed coiled-coil DNA looping peptides control DNA topology.
(2013) Nucleic Acids Res 41
PubMed: 23825092 | PubMedCentral: PMC3783159 | DOI: 10.1093/nar/gkt553
The models were assembled from the GCN4 bZip:CREB DNA co-crystal [PDB ID 2DGC ( 38 )], a segment with coordinates taken from the structure of cortexillin to provide the peptide backbone between DNA-bi... ding helices [1D7M ( 41 )] and inverted portions of 2DGC to give the C-terminal structure.
Publication Year: 2013
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