Structure of the SPXX motif

Abstract

To understand the structure of the DNA-binding SPXX motif, an analysis of Ser1-Pro2-X3-X4 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 beta-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 X4 (a standard beta-turn type), and the other between OH of (Ser or Thr) and NH of X3 (which we name the sigma type). Within the beta-turn of the TPXX sequence, another type of hydrogen bond (which we name the tau type) occurs between OH of Thr and NH of X4 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 beta-turn stabilized by a side-chain-main-chain interaction, which may be suitable to fit into the groove of DNA.