Sphingomonas sp. KT‑1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydrolysis

Poly­(aspartic acid) (PAA) is a common water-soluble polycarboxylate used in a broad range of applications. PAA biodegradation and environmental assimilation were first identified in river water bacterial strains, Sphingomonas sp. KT-1 and Pedobacter sp. KP-2. Within Sphingomonas sp. KT-1, PahZ1KT‑1 cleaves β-amide linkages to oligo­(aspartic acid) and then is degraded by PahZ2KT‑1. Recently, we reported the first structure for PahZ1KT‑1. Here, we report novel structures for PahZ2KT‑1 bound to either Gd3+/Sm3+ or Zn2+ cations in a dimeric state consistent with M28 metallopeptidase family members. PahZ2KT‑1 monomers include a dimerization domain and a catalytic domain with dual Zn2+ cations. MD methods predict the putative substrate binding site to span across the dimerization and catalytic domains, where NaCl promotes the transition from an open conformation to a closed conformation that positions the substrate adjacent to catalytic zinc ions. Structural knowledge of PahZ1KT‑1 and PahZ2KT‑1 will allow for protein engineering endeavors to develop novel biodegradation reagents.