A common pentapeptide conformation occurs in viral acid proteases and other proteins.
We found a pentapeptide conformation, termed a type I twist, which has a strikingly high propensity (56%) for aspartic acid in the first position. Type I twists include the active site loops from cellular and viral aspartic proteases, with the catalytic Asp in the first position. Fifteen other type I twists, from non-homologous proteins, were found among high-resolution structures in the Protein Data Bank using a comparison method based on main-chain torsion angles. We propose that the Asp affects electrostatic interactions and thus plays a major structural role in the formation of this recurring motif, in addition to its catalytic role in the aspartic proteases.
Karpen
M E
ME
Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106.
Neet
K E
KE
de Haseth
P L
PL
D000595:Amino Acid Sequence; D016208:Databases, Factual; D010450:Endopeptidases / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012689:Sequence Homology, Nucleic Acid; D014764:Viral Proteins / Q000235:genetics*; D014780:Viruses / Q000201:enzymology / Q000235:genetics*
D014764:Viral Proteins; D010450:Endopeptidases