Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A

Science ◽  
1991 ◽  
Vol 252 (5007) ◽  
pp. 809-817 ◽  
Author(s):  
N. Pavletich ◽  
C. Pabo
Keyword(s):  
Crystal Structure ◽  
Zinc Finger ◽  
Dna Recognition ◽  
Dna Complex

scholarly journals New Insights on DNA Recognition by ets Proteins from the Crystal Structure of the PU.1 ETS Domain-DNA Complex

1996 ◽  
Vol 271 (38) ◽  
pp. 23329-23337 ◽  
Author(s):  
Frédéric Pio ◽  
Ramadurgam Kodandapani ◽  
Chao-Zhou Ni ◽  
William Shepard ◽  
Michael Klemsz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Recognition ◽  
Ets Proteins ◽  
Ets Domain ◽  
Dna Complex

The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition

Nature ◽  
1993 ◽  
Vol 366 (6454) ◽  
pp. 483-487 ◽  
Author(s):  
Louise Fairall ◽  
John W. R. Schwabe ◽  
Lynda Chapman ◽  
John T. Finch ◽  
Daniela Rhodes
Keyword(s):  
Crystal Structure ◽  
Zinc Finger ◽  
Dna Recognition ◽  
Zinc Finger Peptide

scholarly journals New insights on DNA recognition by ets proteins from the crystal structure of the PU.1 ETS domain-DNA complex

1996 ◽  
Vol 271 (51) ◽  
pp. 33156
Author(s):  
Frédéric Pio ◽  
Ramadurgam Kodandapani ◽  
Chao-Zhou Ni ◽  
William Shepard ◽  
Michael Klemsz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Recognition ◽  
Ets Proteins ◽  
Ets Domain ◽  
Dna Complex

The crystal structure of the Sox4 HMG domain–DNA complex suggests a mechanism for positional interdependence in DNA recognition

2012 ◽  
Vol 443 (1) ◽  
pp. 39-47 ◽  
Author(s):  
Ralf Jauch ◽  
Calista K. L. Ng ◽  
Kamesh Narasimhan ◽  
Prasanna R. Kolatkar
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Dna Recognition ◽  
High Mobility ◽  
Mobility Shift ◽  
Binding Motifs ◽  
Binding Interface ◽  
Structural Mechanisms ◽  
Electrophoretic Mobility Shift Assays ◽  
Dna Complex

It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.

Crystal Structure of E47−NeuroD1/Beta2 bHLH Domain−DNA Complex:  Heterodimer Selectivity and DNA Recognition†,‡

Biochemistry ◽  
2008 ◽  
Vol 47 (1) ◽  
pp. 218-229 ◽  
Author(s):  
Antonella Longo ◽  
Gerald P. Guanga ◽  
Robert B. Rose
Keyword(s):  
Crystal Structure ◽  
Dna Recognition ◽  
Bhlh Domain ◽  
Dna Complex
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