6KBR

Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex

Summary for 6KBR

• Entry DOI: 10.2210/pdb6kbr/pdb
• Descriptor: Kallikrein-4, K41043, GLYCEROL, ... (4 entities in total)
• Functional Keywords: protein engineering, cystine knot protein, protease inhibitor, structural analysis, protein binding, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 34400.10

Authors

Kawaguchi, Y.,Nishimiya, D. (deposition date: 2019-06-26, release date: 2019-07-17, Last modification date: 2024-10-23)

Primary citation

Nishimiya, D.,Kawaguchi, Y.,Kodama, S.,Nasu, H.,Yano, H.,Yamaguchi, A.,Tamura, M.,Hashimoto, R.
A protein scaffold, engineered SPINK2, for generation of inhibitors with high affinity and specificity against target proteases.
Sci Rep, 9:11436-11436, 2019

PubMed Abstract: Proteases are one of attractive therapeutic targets to play key roles in pharmacological action. There are many protease inhibitors in nature, and most of them structurally have cystine knot motifs. Their structures are favorable for recognition of active pockets of proteases, leading to the potent inhibition. However, they also have drawbacks, such as broad cross-reactivity, on the therapeutic application. To create therapeutic proteins derived from a disulfide-rich scaffold, we selected human serine protease inhibitor Kazal type 2 (SPINK2) through a scaffold screening, as a protein scaffold with requirements for therapeutic proteins. We then constructed a diverse library of the engineered SPINK2 by introducing random mutations into its flexible loop region with the designed method. By phage panning against four serine proteases, we isolated potent inhibitors against each target with picomolar K and sub-nanomolar K values. Also, they exhibited the desired specificities against target proteases without inhibiting non-target proteases. The crystal structure of kallikrein related peptidase 4 (KLK4)-engineered SPINK2 complex revealed the interface with extensive conformational complementarity. Our study demonstrates that engineered SPINK2 can serve as a scaffold to generate therapeutic molecules against target proteins with groove structures.

PubMed: 31391482
DOI: 10.1038/s41598-019-47615-5

Experimental method

X-RAY DIFFRACTION (2 Å)