| Literature References | 1. YAMAMOTO, M., KO, L.J., LEONARD, M.W., BEUG, H., ORKIN, S.H. AND
ENGEL, J.D.
Activity and tissue-specific expression of the transcription factor NF-E1
multigene family.
GENES DEV. 4 1650-1662 (1990).
2. EVANS, T. AND FELSENFELD, G.
The erythroid-specific transcription factor Eryf1: a new finger protein.
CELL 58 877-885 (1989).
3. OMINCHINSKI, J.G., CLORE, G.M., SCHAAD, O., FELSENFELD, G., TRAINOR, C.,
APPELLA, E., STAHL, S.J. AND GRONENBORN, A.M.
NMR structure of a specific DNA complex of Zn-containing DNA binding domain
of GATA-1.
SCIENCE 261 438-446 (1993).
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| Documentation | A number of transcription factors (including erythroid-specific tran-
scription factor and nitrogen regulatory proteins), specifically bind the
DNA sequence (A/T)GATA(A/G) [1] in the regulatory regions of genes; they
are consequently termed GATA-binding transcription factors [2,3]. The
interactions occur via highly-conserved zinc finger domains in which the
zinc ion is coordinated by 4 cysteine residues [2,3].
NMR studies have shown the core of the zinc finger 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 [3]. 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 [3]. 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 [3].
Interactions between the zinc finger 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 [3].
GATAZNFINGER is a 2-element fingerprint that provides a signature for the
zinc finger domain of GATA-binding transcription factors. The fingerprint
was derived from an initial alignment of 6 sequences: the motifs were drawn
from the full finger domain, spanning the region encoded by PROSITE pattern
GATA_ZN_FINGER (PS00344). Two iterations on OWL28.3 were required to reach
convergence, at which point a true set comprising 59 sequences was
identified.
An update on SPTR37_9f identified a true set of 64 sequences.
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