Differential DNA-binding specificity of the engrailed homeodomain: The role of residue 50

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.

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The role of protein sequence and global conformation in DNA binding specificity of members of the Cro family

The FASEB Journal ◽

10.1096/fasebj.26.1_supplement.740.4 ◽

2012 ◽

Vol 26 (S1) ◽

Author(s):

Michael R Nelson ◽

Keith Olson ◽

Matthew H.J. Cordes

Keyword(s):

Dna Binding ◽

Protein Sequence ◽

Binding Specificity ◽

Dna Binding Specificity

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Functional specificity of the homeodomain protein fushi tarazu: the role of DNA-binding specificity in vivo.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.90.4.1450 ◽

1993 ◽

Vol 90 (4) ◽

pp. 1450-1454 ◽

Cited By ~ 22

Author(s):

A. F. Schier ◽

W. J. Gehring

Keyword(s):

Dna Binding ◽

Binding Specificity ◽

Homeodomain Protein ◽

Fushi Tarazu ◽

Functional Specificity ◽

Dna Binding Specificity

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Role of the PAS Domain in Regulation of Dimerization and DNA Binding Specificity of the Dioxin Receptor

Molecular and Cellular Biology ◽

10.1128/mcb.18.7.4079 ◽

1998 ◽

Vol 18 (7) ◽

pp. 4079-4088 ◽

Cited By ~ 73

Author(s):

Ingemar Pongratz ◽

Camilla Antonsson ◽

Murray L. Whitelaw ◽

Lorenz Poellinger

Keyword(s):

Dna Binding ◽

Target Genes ◽

Binding Specificity ◽

Pas Domain ◽

Bhlh Domain ◽

Dna Binding Specificity ◽

Dioxin Receptor

ABSTRACT The dioxin receptor is a ligand-regulated transcription factor that mediates signal transduction by dioxin and related environmental pollutants. The receptor belongs to the basic helix-loop-helix (bHLH)–Per-Arnt-Sim (PAS) family of factors, which, in addition to the bHLH motif, contain a PAS region of homology. Upon activation, the dioxin receptor dimerizes with the bHLH-PAS factor Arnt, enabling the receptor to recognize xenobiotic response elements in the vicinity of target genes. We have studied the role of the PAS domain in dimerization and DNA binding specificity of the dioxin receptor and Arnt by monitoring the abilities of the individual bHLH domains and different bHLH-PAS fragments to dimerize and bind DNA in vitro and recognize target genes in vivo. The minimal bHLH domain of the dioxin receptor formed homodimeric complexes, heterodimerized with full-length Arnt, and together with Arnt was sufficient for recognition of target DNA in vitro and in vivo. In a similar fashion, only the bHLH domain of Arnt was necessary for DNA binding specificity in the presence of the dioxin receptor bHLH domain. Moreover, the bHLH domain of the dioxin receptor displayed a broad dimerization potential, as manifested by complex formation with, e.g., the unrelated bHLH-Zip transcription factor USF. In contrast, a construct spanning the dioxin receptor bHLH domain and an N-terminal portion of the PAS domain failed to form homodimers and was capable of dimerizing only with Arnt. Thus, the PAS domain is essential to confer dimerization specificity of the dioxin receptor.

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