A lack of peptide binding and decreased thermostability suggests that the CASKIN2 scaffolding protein SH3 domain may be vestigial.
CASKIN2 is a neuronal signaling scaffolding protein comprised of multiple ankyrin repeats, two SAM domains, and one SH3 domain. The CASKIN2 SH3 domain for an NMR structural determination because its peptide-binding cleft appeared to deviate from the repertoire of aromatic enriched amino acids that typically bind polyproline-rich sequences.



The structure demonstrated that two non-canonical basic amino acids (K290/R319) in the binding cleft were accommodated well in the SH3 fold. An K290Y/R319W double mutant restoring the typical aromatic amino acids found in the binding cleft resulted in a 20 °C relative increase in the thermal stability. Considering the reduced stability, we speculated that the CASKIN2 SH3 could be a nonfunctional remnant in this scaffolding protein.



While the NMR structure demonstrates that the CASKIN2 SH3 domain is folded, its cleft has suffered two substitutions that prevent it from binding typical polyproline ligands. This observation led us to additionally survey and describe other SH3 domains in the Protein Data Bank that may have similarly lost their ability to promote protein-protein interactions.
Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.|Present Address: McEwen Centre for Regenerative Medicine, Ontario Cancer Institute, 101 College Street, Toronto, ON, M5G 1L7, Canada.
Jamie J
JJ
Kwan
Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada. logand@yorku.ca.
Logan W
LW
Donaldson
D048868:Adaptor Proteins, Signal Transducing / Q000737:chemistry* / Q000378:metabolism*; D000595:Amino Acid Sequence; D006801:Humans; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism*; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000378:metabolism*; D011485:Protein Binding; D017510:Protein Folding; D055550:Protein Stability; D013696:Temperature; D018909:src Homology Domains
D048868:Adaptor Proteins, Signal Transducing; C499244:CASKIN2 protein, human; D009419:Nerve Tissue Proteins; D010455:Peptides; C011083:polyproline
Molecular modeling; NMR spectroscopy; SH3 domain