7W2A

gliadinase Bga1903

Summary for 7W2A

• Entry DOI: 10.2210/pdb7w2a/pdb
• Descriptor: Peptidase, CALCIUM ION (3 entities in total)
• Functional Keywords: serine protease, celiac disease, lyase
• Biological source: Burkholderia gladioli pv. gladioli
• Total number of polymer chains: 2
• Total formula weight: 72652.00

Authors

Meng, M. (deposition date: 2021-11-23, release date: 2022-12-07, Last modification date: 2023-11-29)

Primary citation

Liu, Y.Y.,Lin, I.C.,Chen, P.C.,Lee, C.C.,Meng, M.
Crystal structure of a Burkholderia peptidase and modification of the substrate-binding site for enhanced hydrolytic activity toward gluten-derived pro-immunogenic peptides.
Int.J.Biol.Macromol., 222:2258-2269, 2022

PubMed Abstract: Celiac disease (CD) is a human autoimmune disease triggered by toxic gluten peptides. Recently, oral enzyme therapy has been proposed to ameliorate the health condition of CD patients based on the concept of removing pepsin-insensitive gluten-derived pro-immunogenic peptides. A Burkholderia peptidase, Bga1903, with promising gluten-degrading activity was characterized previously. Here, we report the crystal structure of Bga1903, in which the core has a α/β/α fold featured with a twisted six-stranded parallel β-sheet sandwiched between two layers of α-helices. The mutations at the substrate-binding pocket that might enhance the peptidase's affinity toward tetrapeptide PQPQ were predicted by FoldX. Accordingly, four single-substitution mutants, G351A, E380L, S386F, and S387L, were created. The specificity constant (k/K) of wild type toward chromogenic peptidyl substrates Z-HPK-pNA, Z-HPQ-pNA, Z-HPL-pNA, and Z-QPQ-pNA are 30.2, 7.9, 3.3, and 0.79 s·mM, respectively, indicating that the QPQ motif, which frequently occurs in pro-immunogenic peptides, is not favorable. Among the mutants, E380L loses the hydrolytic activity toward Z-HPK-pNA, suggesting a critical role of E380 in preferring a lysine residue at the P1 position. S387L shows a 17-fold increase in the specificity constant toward Z-QPQ-pNA and hydrolyzes the pro-immunogenic peptides more efficiently than the wild-type peptidase.

PubMed: 36209912
DOI: 10.1016/j.ijbiomac.2022.10.016

Experimental method

X-RAY DIFFRACTION (1.6 Å)