In contrast to Myc, Max can form homodimers that bind tightly to DNA. However, the hydrogen bonds in the minor groove can be formed equally well to an A-T base pair or to a T-A base pair, because 02 of thymine and N3 of adenine occupy nearly stereochemically equivalent positions, and it is sufficient, therefore, for the consensus sequence of the TATA box to be quasi-palindromic. The consensus TATA-box sequence has an A-T base pair at position 4, but either a T-A or an A-T base pair at the symmetry-related position 5, and the sequence is, therefore, not strictly palindromic. By analogy with the symmetric binding of a dimeric repressor molecule to a palindromic sequence described in Chapter 8, the two motifs of TBP form symmetric sequence-specific hydrogen bonds to the quasi-palindromic DNA sequence at the center of the TATA box.
Like Thr 124 and Thr 215, the Asn 69 and Asn 159 residues occupy equivalent positions in the two homologous motifs of TBP. This sequence pattern can be used to search for possible two-sheet p structures in databases of amino acid sequences of proteins of unknown structure. The loops are stabilized by calcium ions which bind to the Asp residue (Figure S.28). The first six residues form the loop and the last three form a p strand with the side chain of U involved in the hydrophobic packing of the two p sheets. A specific amino acid sequence pattern identifies this unit namely a double repeat of a nine-residue consensus sequence Gly-Gly-X-Gly-X-Asp-X-U-X where X is any amino acid and U is large, hydrophobic and frequently leucine. The basic structural unit of these two-sheet p helix structures contains 18 amino acids, three in each p strand and six in each loop. In addition, any sequences of homologous proteins that lack both redox potentials and structures should be examined, because residues important in defining the redox potential are likely to have semi- sequence conservation of a few key amino acid types. These differences can then be correlated with any other sequence- redox potential data for proteins that lack crystal or NMR structures. The results for homologous proteins should be examined for differences in the contributions to ( ) per residue that correlate with observed redox potential differences. An effective method for localizing causes of redox potentials is to plot the total backbone and side chain contributions to ( ) per residue for homologous proteins as functions of the residue number using a consensus sequence, with insertions treated by summing the contribution of the entire insertion as one residue.
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