Based on the type of DNA binding domain, regulators have been classified into several families basic leucine zipper (bZIP), cysteine rich zinc finger, helix-loop-helix (HLH), homeobox, and so forth.
Indeed, serine 273 phosphorylation affects the stability of RXR α, mostly in the zinc-finger helix which is in contact with DNA's major groove.
The five structural superclasses are: (1) basic domain (basic domain), (2) zinc-coordinating DNA-binding domains (zinc finger), (3) helix-turn-helix (helix-turn-helix), (4) beta-scaffold factors with minor groove contacts (beta-scaffold) and (5) other transcription factors (others).
MyTH4, Myosin tail homology 4; Band, Band 4.1; CC, Coiled-coil; CH, Calponin homology; HTH, Helix-turn-helix; ZF, Zinc Finger; HHH, Helix-hairpin-helix; ARM, Armadillo repeat; KR, Kinesin related; UG, Ungrouped; N, N-terminal; I, Internal; C, C-terminal.
Non-HTH motif predictions such as zinc fingers, helix-loop-helix, beta-sheet antiparallel or RNA binding domains are available in the generalist DNA Binding Domain Database [ 54].
Bowman, J. L. & Smyth, D. R. CRABS CLAW, a gene that regulates carpel and nectary development in Arabidopsis, encodes a novel protein with zinc finger and helix-loop-helix domains.
The respective average absolute errors (AAEs) on the test datasets are: basic domain: 0.093, zinc finger: 0.087, helix-turn-helix: 0.098, beta-scaffold: 0.080 and others 0.137.
The results of these tests indicate a linear relationship between the predicted and the measured PFM similarity scores (see Figure 4), where the Pearson correlation coefficients are: basic domain: 0.77, zinc finger: 0.80, helix-turn-helix: 0.77, beta-scaffold: 0.64 and others: 0.69.
The list of specifically activated transcription factors in PMA included four transcription factors (DRD1, ZOS2-03-C2H2 zinc finger, a helix-loop-helix, and a MYB transcription factor).
