scholarly journals Structural view on the role of WT1’s zinc finger 1 in DNA binding

2018 ◽  
Author(s):  
Raymond K. Yengo ◽  
Elmar Nurmemmedov ◽  
Marjolein M Thunnissen
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Fingers ◽  
Binding Specificity ◽  
Regulatory Elements ◽  
Regulatory Function ◽  
Gene Promoters ◽  
Binding Behavior ◽  
Dna Binding Specificity

AbstractThe WT1 protein is a transcription factor that controls genes involved in cell proliferation, differentiation and apoptosis. It has become increasing apparent that WT1 can act both as a tumor suppressor and oncogene in a tissue specific manner. This opposing role of WT1 is linked to its underlying transcriptional regulatory function, which involves the specific binding to its regulatory elements on gene promoters. WT1 binds DNA using it C-terminal domain made up of 4 C2H2-typ zinc fingers. This same zinc finger domain is used to bind RNA and proteins and it is still not clear how each zinc finger contributes to this promiscuous binding behavior. The molecular details of DNA binding by zinc finger 2 to 4 have been described but it remains to be determined whether or not zinc finger 1 binds DNA and if so whether it exhibits any DNA binding specificity. We present the X-ray structures of zinc finger 1 to 3 bound to a 9 bp and an 8 bp DNA. The two structures refined to 1.7 Å, show no DNA binding specificity for zinc finger 1. The only DNA interactions involving zinc finger 1 are crystal-packing interactions with a symmetry related molecule. In the structure of zinc finger 1 to 3 bound to the 9 bp DNA we observe a shift in the DNA binding positions for zinc fingers 2 and 3. These structures provide molecular detail into the WT1-DNA interaction showing that zinc finger 1 only modestly contributes to DNA binding affinity through transient interactions. The dislocation of zinc finger 2 and 3 emphasizes the importance of zinc finger 4 for maintaining gene transcriptional specificity.

scholarly journals The geometric influence on the Cys2His2 zinc finger domain and functional plasticity

2020 ◽  
Vol 48 (11) ◽  
pp. 6382-6402
Author(s):  
April L Mueller ◽  
Carles Corbi-Verge ◽  
David O Giganti ◽  
David M Ichikawa ◽  
Jeffrey M Spencer ◽  
...  
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Fingers ◽  
Binding Specificity ◽  
Synthetic Approach ◽  
Dna Interactions ◽  
Dna Binding Specificity ◽  
Mechanistic Insight ◽  
Natural Geometry ◽  
Protein Dna Interactions

Abstract The Cys2His2 zinc finger is the most common DNA-binding domain expanding in metazoans since the fungi human split. A proposed catalyst for this expansion is an arms race to silence transposable elements yet it remains poorly understood how this domain is able to evolve the required specificities. Likewise, models of its DNA binding specificity remain error prone due to a lack of understanding of how adjacent fingers influence each other's binding specificity. Here, we use a synthetic approach to exhaustively investigate binding geometry, one of the dominant influences on adjacent finger function. By screening over 28 billion protein–DNA interactions in various geometric contexts we find the plasticity of the most common natural geometry enables more functional amino acid combinations across all targets. Further, residues that define this geometry are enriched in genomes where zinc fingers are prevalent and specificity transitions would be limited in alternative geometries. Finally, these results demonstrate an exhaustive synthetic screen can produce an accurate model of domain function while providing mechanistic insight that may have assisted in the domains expansion.

scholarly journals The C6 zinc finger and adjacent amino acids determine DNA-binding specificity and affinity in the yeast activator proteins LAC9 and PPR1.

1990 ◽  
Vol 10 (10) ◽  
pp. 5128-5137 ◽  
Author(s):  
M M Witte ◽  
R C Dickson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Dna Binding ◽  
Zinc Finger ◽  
Binding Specificity ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Transcription Activator ◽  
Activator Proteins ◽  
Dna Binding Specificity

LAC9 is a DNA-binding protein that regulates transcription of the lactose-galactose regulon in Kluyveromyces lactis. The DNA-binding domain is composed of a zinc finger and nearby amino acids (M. M. Witte and R. C. Dickson, Mol. Cell. Biol. 8:3726-3733, 1988). The single zinc finger appears to be structurally related to the zinc finger of many other fungal transcription activator proteins that contain positively charged residues and six conserved cysteines with the general form Cys-Xaa2-Cys-Xaa6-Cys-Xaa6-9-Cys-Xaa2-Cys-Xaa 6-Cys, where Xaan indicates a stretch of the indicated number of any amino acids (R. M. Evans and S. M. Hollenberg, Cell 52:1-3, 1988). The function(s) of the zinc finger and other amino acids in DNA-binding remains unclear. To determine which portion of the LAC9 DNA-binding domain mediates sequence recognition, we replaced the C6 zinc finger, amino acids adjacent to the carboxyl side of the zinc finger, or both with the analogous region from the Saccharomyces cerevisiae PPR1 or LEU3 protein. A chimeric LAC9 protein, LAC9(PPR1 34-61), carrying only the PPR1 zinc finger, retained the DNA-binding specificity of LAC9. However, LAC9(PPR1 34-75), carrying the PPR1 zinc finger and 14 amino acids on the carboxyl side of the zinc finger, gained the DNA-binding specificity of PPR1, indicating that these 14 amino acids are necessary for specific DNA binding. Our data show that C6 fingers can substitute for each other and allow DNA binding, but binding affinity is reduced. Thus, in a qualitative sense C6 fingers perform a similar function(s). However, the high-affinity binding required by natural C6 finger proteins demands a unique C6 finger with a specific amino acid sequence. This requirement may reflect conformational constraints, including interactions between the C6 finger and the carboxyl-adjacent amino acids; alternatively or in addition, it may indicate that unique, nonconserved amino acid residues in zinc fingers make sequence-specifying or stabilizing contacts with DNA.

scholarly journals Origins of DNA-binding specificity: Role of protein contacts with the DNA backbone

1999 ◽  
Vol 96 (3) ◽  
pp. 811-817 ◽  
Author(s):  
J. F. Schildbach ◽  
A. W. Karzai ◽  
B. E. Raumann ◽  
R. T. Sauer
Keyword(s):  
Dna Binding ◽  
Binding Specificity ◽  
Dna Binding Specificity ◽  
Dna Backbone

scholarly journals Re-programming DNA-binding specificity in zinc finger proteins for targeting unique address in a genome

2010 ◽  
Vol 4 (4) ◽  
pp. 323-329 ◽  
Author(s):  
Abhinav Grover ◽  
Akshay Pande ◽  
Krishna Choudhary ◽  
Kriti Gupta ◽  
Durai Sundar
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Binding Specificity ◽  
Zinc Finger Proteins ◽  
Dna Binding Specificity ◽  
A Genome

scholarly journals The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks

2008 ◽  
Vol 379 (3) ◽  
pp. 627-643 ◽  
Author(s):  
Irma Lozada-Chávez ◽  
Vladimir Espinosa Angarica ◽  
Julio Collado-Vides ◽  
Bruno Contreras-Moreira
Keyword(s):  
Dna Binding ◽  
Regulatory Networks ◽  
Binding Specificity ◽  
Dna Binding Specificity

scholarly journals Segments of the POU domain influence one another's DNA-binding specificity.

1992 ◽  
Vol 12 (2) ◽  
pp. 455-467 ◽  
Author(s):  
R Aurora ◽  
W Herr
Keyword(s):  
Dna Binding ◽  
Sequence Similarity ◽  
Binding Specificity ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Surprising Result ◽  
Pou Domain ◽  
Dna Binding Specificity ◽  
Octamer Motif ◽  
Better Than

The ubiquitously expressed mammalian POU-domain protein Oct-1 specifically recognizes two classes of cis-acting regulatory elements that bear little sequence similarity, the octamer motif ATGCAAAT and the TAATGARAT motif. The related pituitary-specific POU protein Pit-1 also recognizes these two motifs but, unlike Oct-1, binds preferentially to the TAATGARAT motif. Yet in our assay, Pit-1 still binds octamer elements better than does the octamer motif-binding protein Oct-3. The POU domain is responsible for recognizing these diverse regulatory sequences through multiple DNA contacts that include the two POU subdomains, the POU-specific region, and the POU homeodomain. The DNA-binding properties of 10 chimeric POU domains, in which different POU-domain segments are derived from either Oct-1 or Pit-1, reveal a high degree of structural plasticity; these hybrid proteins all bind DNA well and frequently bind particular sites better than does either of the parental POU domains. In these chimeric POU domains, the POU-specific A and B boxes and the hypervariable POU linker can influence DNA-binding specificity. The surprising result is that the influence a particular segment has on DNA-binding specificity can be greatly affected by the origin of other segments of the POU domain and the sequence of the binding site. Thus, the broad but selective DNA-binding specificity of Oct-1 is conferred both by multiple DNA contacts and by dynamic interactions within the DNA-bound POU domain.

scholarly journals A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity

2015 ◽  
Vol 43 (19) ◽  
pp. 9147-9157 ◽  
Author(s):  
Michael Garton ◽  
Hamed S. Najafabadi ◽  
Frank W. Schmitges ◽  
Ernest Radovani ◽  
Timothy R. Hughes ◽  
...  
Keyword(s):  
Dna Binding ◽  
Zinc Fingers ◽  
Binding Specificity ◽  
Structural Approach ◽  
Dna Binding Specificity
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