Structure of the SPXX motif

Abstract

To understand the structure of the DNA -binding SPXX motif, an analysis of Ser₄—Pro₂—X₃—X 4 and Thr₁-Pro₂- X₃- X₄ structures observed in proteins is presented. About half (43-46 %) of the (S or T) PXX sequences fold into a (3-turn of type (I) or one of a few closely related turn structures. The turn structure has either or both of two compatible hydrogen bonds, one between CO of (Ser or Thr) and NH of X 4 (a standard P-turn type), and the other between OH of (Ser or Thr) and NH of X 3 (which we name the a type). Within the P-turn of the TPXX sequence, another type of hydrogen bond (which we name the I type) occurs between OH of Thr and NH of X 4 with the frequency of 72 %. These observations support a previous proposal that the (S or T) PXX sequences of DNA -binding proteins fold into a compact P-turn stabilized by a side-chain-main-chain interaction, which may be suitable to fit into the groove of DNA.