Crystal structure of aspartyl dipeptidase from Xenopus laevis revealed ligand binding induced loop ordering and catalytic triad assembly

Abstract

Gene encoding aspartyl dipeptidase from Xenopus levies (PepExl) is upregulated by thyroid hormone and is proposed to play a significant role in resorption of tadpole tail during metamorphosis. However, the importance of peptidase activity for the resorption of the tail remain elusive. Here we report the crystal structures of first eukaryotic S51 peptidase, PepExl, in its ligand‐free and Asp‐bound states at 1.4 and 1.8 Å resolutions, respectively. The active site is located at dimeric interface and the catalytic triad is found to be dissembled in ligand‐free and assembled in Asp‐bound state. Structural comparison and molecular dynamic simulations of ligand‐free and Asp‐bound states shows that distinct loop (loop‐A) plays an important role in active site shielding, substrate binding and enzyme activation. This study illuminates the Asp‐X dipeptide binding in PepExl is associated with ordering of the loop‐A and assembly of residues of catalytic triad in active conformation for enzymatic activity.

Characterization and functional evidence for Orf2 of Streptomyces sp. 139 as a novel dipeptidase E

“…Slightly different with aspartyl dipeptidase E (PepE) from Salmonella typhimurium and Xenopus laevis (Lassy and Miller 2000 ), Orf2 displays a higher relative activity with Asp-Gly-Gly and isoAsp-Leu substrates and only moderate-level activity with Asp-Leu and Asp-His. The active site of Orf2 contains a Ser-His-Asp catalytic triad, which is incompletely similar to eukaryotic PepE from Xenopus laevis and prokaryotic PepE from Salmonella typhimurium with a Ser-His-Glu catalytic triad (Kumar et al 2022 ; Lassy and Miller 2000 ). In addition, the Asp147 residue of Orf2 is also proven to be critical for the enzyme’s activity through point mutation.…”

“…PCC6803, which can hydrolyze cyanophycin (multi-L-arginyl-poly-L-aspartic acid) into Asp-Arg (Richter et al 1999 ). Subsequently, homologous dipeptidase E has been identified in other species, such as Escherichia coli (Conlin et al 1994 ), Listeria monocytogenes , Deinococcus radiodurans (Yadav et al 2019 ), Xenopus laevis (Kumar et al 2022 ), and Lactococcus lactis (Kuerman et al 2023 ). In this study, the characterization of Orf2 aims to elucidate its biological function in S sp.…”