zinc finger binding to DNA consensus sequence [AT]GATA[AG]
SMART accession number:SM00401
Interpro abstract (IPR000679):

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [(PUBMED:10529348), (PUBMED:15963892), (PUBMED:15718139), (PUBMED:17210253), (PUBMED:12665246)]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [(PUBMED:11179890)]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [(PUBMED:2249770)] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [(PUBMED:2776214), (PUBMED:8332909)]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed [(PUBMED:8332909)]. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain.

More information about these proteins can be found at Protein of the Month: Zinc Fingers [].

GO process:regulation of transcription, DNA-dependent (GO:0006355)
GO function:sequence-specific DNA binding (GO:0043565), zinc ion binding (GO:0008270), sequence-specific DNA binding transcription factor activity (GO:0003700)
Family alignment:
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There are 1511 ZnF_GATA domains in 1176 proteins in SMART's nrdb database.

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