31vj | pdb_000031vj
Alcalase/CI-2A(M59P) complex at 100K
Structural highlights
FunctionPublication Abstract from PubMedSerine proteases catalyze peptide-bond hydrolysis through a conserved catalytic triad and an extensive network of hydrogen bonds that facilitate proton transfer and stabilization of reaction intermediates. Despite decades of study, the nature of the hydrogen-bonding interactions within the catalytic machinery remains incompletely understood. Here, we report ultra-high-resolution crystal structures of alcalase, a subtilisin-family serine protease, in complex with native chymotrypsin inhibitor 2A (CI-2 A) and with a low-affinity M59P inhibitor variant. The cryogenic structures were determined at 0.74 A resolution, while an additional 4 degrees C (277 K) structure of the native complex was determined at 1.05 A resolution. The data allowed visualization and refinement of numerous hydrogen atoms within the active site and at the enzyme-inhibitor interface. Comparison of the 4 degrees C and cryogenic structures revealed a systematic shortening of hydrogen-bond donor-acceptor distances upon cooling, consistent with the global lattice contraction. A notable exception was the hydrogen bond between the catalytic residues Ser221 and His64, which remained unusually short at both temperatures. In the 4 degrees C structure, the corresponding hydrogen atom is associated with weak and diffuse electron density, suggesting increased proton mobility within this interaction. The structures further reveal temperature-dependent differences in interactions involving the scissile peptide bond of the inhibitor and the conserved backbone carbonyl oxygen of Ser125. These observations support a model in which Ser125 participates in a concerted hydrogen-bond network coupled to proton transfer within the catalytic triad. Together, the results provide atomic-level insights into hydrogen bonding, protonation equilibria, and catalytic mechanism in subtilisin-like serine proteases. Catalytic hydrogen bonds in alcalase-CI-2A complexes revealed by ultra-high-resolution crystallography.,Raczynska JE, Jedrzejczak R, Dauter M, Ostergaard PR, Wilson KS, Rypniewski W J Struct Biol. 2026 Sep 25;218(4):108377. doi: 10.1016/j.jsb.2026.108377. PMID:42790760[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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