A water molecule acts as a nucleophile along with aspartic acid to hydrolyze the scissile
peptide bond present at the center of the tunnel.
Lane, "Unraveling the scissile
bond: how ADAMTS13 recognizes and cleaves von Willebrand factor," Blood, vol.
2006); CL2 and CL3 have affinity for different hydrophobic amino acids in the amino-terminal side of the scissile
bond, CL3 for Leu and lie, whereas CL2 has preference for Pro, lie, and Val, in addition to affinity for hydrophobic amino acids and the CL1 cleavage in polar amino acids Gin and Thr too (Bibo-Verdugo et al.
RNA and DNA present only two types of phophodiester bonds for cleavage, 5' or 3' of a scissile
phosphate, and the fundamental chemistry is bimolecular nucleophilic substitution or [S.sub.N]2 in short.
Schmid, "Anatomy of lipase binding sites: the scissile
fatty acid binding site," Chemistry and Physics of Lipids, vol.
Lim et al., "An SRLLR motif downstream ofthe scissile
bond enhances enterokinase cleavage efficiency," Biochimie, vol.
Aspartic acid at conserved C-terminal "DG" sequence in these BPPhy sequences might act as a proton donor to the oxygen atom of the scissile
phosphomonoester bond and may play a role in catalytic mechanism of these enzymes.
group is able to attack the scissile
peptide bond nucleophilically in the initial stage of hydrolysis.
Oroszlan, "Substitution of proline with pipecolic acid at the scissile
bond converts a peptide substrate of HIV proteinase into a selective inhibitor," Biochemical and Biophysical Research Communications, vol.