Type I beta turns make a new twist in pentapeptide repeat proteins: Crystal structure of Alr5209 from Nostoc sp. PCC 7120 determined at 1.7 angström resolution

Current Understanding of the Structure and Function of Pentapeptide Repeat Proteins

“…The alr5209 gene from Nostoc sp. st. PCC7120 encodes a 129 amino acid protein that contains 16 tandem PRs [ 21 ]. Zhang et al determined the three-dimensional structure of Alr5209 in 2019 [ 21 ] revealing that it was composed of four complete Rfr coils of a β helix that was capped by a nine-residue α helix at the N-terminus and by a four-reside α helix at the C-terminus ( Figure 15 ).…”

“…PCC 7120 [ 12 , 13 ], Cyanothece 51142 [ 14 , 15 ], Arabidopsis thaliana [ 16 ], Enterococcus faecalis [ 17 ], K. pneumonia [ 18 ], Xanthomonas albilineans [ 19 ], Aeromonas hydrophila [ 20 ], and M. tuberculosis [ 6 ]. In 2019, Zhang et al updated the PR consensus sequence to (A/C/S/V/T/L/I)/(D/N/S/K/E/I/R)/(L/F)/(S/T/R/E/Q/K/V/D)/(G/D/E/N/R/Q/K) based on the consideration of several newly available PRP crystal structures [ 21 ]. By 2020, the number of PRPs in the PF00805 Pfam had increased to 38,000 sequences in over 3300 species reported in a study by Xu and Kennedy that characterized the protein dynamics in PRPs [ 22 ].…”

Structural dynamics of pentapeptide repeat proteins

“…A single coil is formed by four pentapeptide repeats, and each pentapeptide repeat occupies one face of the coil. Proteins in the PRP family are recognized as containing at least eight tandem repeats with each repeat consisting of the consensus (A/C/S/V/T/L/I)(D/N/S/K/E/I/R)(L/F)(S/T/R/E/Q/K/V/D)(G/D/E/N/R/Q/K) 1,27 . Each coil contains 20 amino acids to complete a revolution, which traverses 4.8 Å along the β‐helix axis.…”

“…The five amino acids in the pentapeptide repeat are designated i − 2, i − 1, i , i + 1, i + 2, with site i being the central residue and “−” and “+” representing amino acids previous and following the central i residue. Based on the main chain (Φ, ψ) dihedral values of the i + 1 and i + 2 residues in a β turn, which also correspond to the i + 1 and i + 2 residues of the pentapeptide repeat sequence, respectively, type II and type IV β‐turns had previously been suggested to be the two universal motifs that shape the Rfr fold of PRP family, 21 although more recently, type I β turns have also been found in PRPs 27 . The two predominant main‐chain conformations observed for pentapeptide repeat sequences result from different orientations of the peptide bond between the i and i + 1 residues of a β turn.…”

“…The ψ‐torsion angle of i and the Φ‐torsion angle of i + 1 differ by about 90° between type II and type IV β turns. Such a rotation in the peptide conformation between the residue i and residue i + 1 results in different intercoil and intracoil hydrogen (H) bonding networks within the Rfr fold 21,27 . In type II β turns, the carbonyl of the i residue forms an intracoil H‐bond with the i − 2 residue of the following pentapeptide repeat ( i + 3 residue of the β turn), and the rest of the amide and carbonyl groups of amino acids form intercoil H‐bonds with the amino acids of the pentapeptide repeat amino acids in the coils above and below it.…”