TAL effector: Difference between revisions

Sequence-specific contacts of PthXo1 to the DNA are made exclusively by the second residue in each RVD to the corresponding base on the sense strand. In contrast, the side chain at the first position of each RVD contacts the backbone carbonyl oxygen of position 8 in each repeat, constraining the RVD-containing loop (Figure 3). Additional, nonspecific contacts to the DNA are made by a lysine and glutamine found at positions 16 and 17.  

‘HD’ RVDs:

the aspartate residue makes van der Waals contacts with the edge of the corresponding cytosine base and a hydrogen bond to the cytosine N4 atom.  

‘NG’ and ‘HG’RVDs:

make a contact in which the backbone alpha carbon of the glycine residue forms a nonpolar van der Waals interaction with the methyl group of the opposing thymine base (average distance ~ 3.3 Å). At the one position where an NG is aligned opposite a cytosine base, the backbone carbonyl and alpha-carbon of the same glycine residue displays a less favorable, far more distant contact (~ 6 Å).

‘NN’ RVDs:

is positioned to make a hydrogen bond with the N7 nitrogen of an opposing guanine base. This RVD associates with either guanosine or adenine with roughly equal frequency (3, 4, 14); the availability of an N7 nitrogen in either purine ring appears to explain that observation (13).

‘N*’RVDs:

PthXo1 contains two 33 residue (7 and 22). Since RVDs are followed immediately by two conserved glycine residues, this repeat is equivalent to an ‘NG’ repeat in which one of those glycine residues is missing. The crystal structure indicates that the deletion results in a truncated RVD loop that extends less deeply into the DNA major groove, with the glycine at position 13 located a considerable distance (over 6 Å)

‘NI’ RVDs:

Occurs seven times in PthXo1, and displays an unusual contact pattern to adenosine or cytosine bases. The aliphatic side chain of the isoleucine residue is observed to make non-polar van der Waals contacts to C8 (and N7) of the adenine purine ring, or to C5 of the cytosine pyrimidine ring.