Abstract
MED-1 is a member of a group of divergent GATA-type zinc finger proteins recently identified in several species of Caenorhabditis. The med genes are transcriptional regulators that are involved in the specification of the mesoderm and endoderm precursor cells in nematodes. Unlike other GATA-type zinc fingers that recognize the consensus sequence (A/C/T)GATA(A/G), the MED-1 zinc finger (MED1zf) binds the larger and atypical site GTATACT(T/C)(3). We have examined the basis for this unusual DNA specificity using a range of biochemical and biophysical approaches. Most strikingly, we show that although the core of the MED1zf structure is similar to that of GATA-1, the basic tail C-terminal to the zinc finger unexpectedly adopts an alpha-helical structure upon binding DNA. This additional helix appears to contact the major groove of the DNA, making contacts that explain the extended DNA consensus sequence observed for MED1zf. Our data expand the versatility of DNA recognition by GATA-type zinc fingers and perhaps shed new light on the DNA-binding properties of mammalian GATA factors.
Highlights
Members of the GATA family of transcription factors contain either one or two type IV zinc fingers [1]
Our data indicate that a single arginine residue in the core zinc finger domain drives a specificity switch from AGATA to GTATA and that, unexpectedly, the C-terminal basic tail of MED-1 zinc finger (MED1zf) forms an additional well ordered ␣-helix that interacts with the 3Ј-pyrimidine-rich extension in the DNA consensus sequence
MED-type Zinc Fingers Recognize a Different Consensus Sequence— the MED-1 zinc finger has a substantial degree of sequence similarity to the mammalian GATA-type zinc fingers, we previously demonstrated that MED1zf recognized the variant consensus sequence GTATACT(T/C)3 [17]
Summary
C-finger, C-terminal zinc finger; MED1zf, MED-1 zinc finger; ITC, isothermal titration calorimetry; RDCs, residual dipolar couplings; HSQC, heteronuclear single quantum coherence; NOESY, nuclear Overhauser effect spectroscopy; dsDNA, double-stranded DNA; DTT, dithiothreitol.
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