A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats

Leucine rich repeats (LRRs) are present in over 430 000 proteins from viruses to eukaryotes. The LRRs are 20 to 30 residues long and occur in tandem. Individual LRRs are separated into a highly conserved segment with the consensus of LxxLxLxxNxL or LxxLxLxxNxxL (HCS) and a variable segment (VS). In LRRs parallel stacking of short beta-strands (at positions 3-5 in HCS) form a super helix arrangement called a solenoid structure. Many classes have been recognized. All three classes of Plant specific, Leptospira-like, and SDS22-like LRRs which are 24, 23, and 22 residues long, respectively, form a 3(10)-helix in the VS part. To get a deeper understanding of sequence, structure correlations in LRR structures, we utilized secondary structure assignment and HELFIT analysis (calculating helix axis, pitch, radius, residues per turn, and handedness) based on the atomic coordinates in crystal structures of 43 LRR proteins. We also defined three structural parameters using the three unit vectors of the helix axes of 3(10)-helix, beta-turn, and LRR-domain calculated by HELFIT. The combination of the secondary structure assignment and HELFIT reveals that their LRRs adopt unique super secondary structures consisting of a 3(10)-helix and one or two Type I beta-turns. We propose one structural parameter as a geometrical invariant of LRR solenoid structures. The common LxxLxxL sequence (where L is Leu, Ile, Val, Phe or Cys) in the three classes is an essential determinant for the super secondary structures providing a medium range interaction.