| Literature References | 1. REEVES, R. AND NISSEN, M.S.
The A.T-DNA-binding domain of mammalian high mobility group-I chromosomal
proteins - a novel peptide motif for recognizing DNA-structure.
J.BIOL.CHEM. 265 8573-8582 (1990).
2. FRIEDMANN, M., HOLTH, L.T., ZOGHBI H.Y. AND REEVES, R.
Organization, inducible-expression and chromosome localization of the human
HMG-I(Y) nonhistone protein gene.
NUCLEIC ACIDS RES. 21 4259-4267 (1993).
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| Documentation | High mobility group (HMG)I proteins bind preferentially to the minor groove
of A.T-rich regions in double-stranded DNA [1,2]. DNA-binding of these, and
several related, proteins is effected by an 11-residue domain known as an
A.T-hook [1].
Within known HMG-I proteins are found three highly conserved regions,
closely related to the consensus sequence TPKRPRGRPKK [1]. A synthetic
oligopeptide with this sequence specifically binds to substrate DNA in a
manner reminiscent of intact HMG-I proteins. Structure predictions suggest
that the peptide has a secondary structure similar to the anti-tumour and
anti-viral drugs netropsin and distamycin, and to the dye Hoechst 33258 [1].
These ligands, which also preferentially bind to A.T-rich DNA, effectively
compete with both the synthetic peptide and the HMG-I proteins for DNA
binding [1]. The peptide also contains novel structural features such as a
predicted Asx bend, or "hook", at its N-terminus, and laterally-projecting
cationic Arg/Lys "bristles", which may play a role in the binding of HMG-I
proteins [1]. The predicted peptide structure, the A.T-hook, is a previously
undescribed DNA-binding motif [1].
ATHOOK is a 3-element fingerprint that provides a signature for AT-hook-like
domains. The fingerprint was derived from an initial alignment of 5
sequences: the motifs were drawn from 3 consecutive hook regions. Two
iterations on OWL30.2 were required to reach convergence, at which point
a true set comprising 20 sequences was identified. Several partial matches
were also found, all of which are DNA-binding proteins with regions of
sequence showing strong similarity to the hook domain. Note that the motifs
in this fingerprint are short and of low complexity. The fingerprint is
therefore not highly diagnostic, and results should therefore be treated
with a degree of caution.
An update on SPTR37_9f identified a true set of 24 sequences, and 2
partial matches.
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