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

Abstract

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, PahZ1_KT-1 cleaves β-amide linkages to oligo(aspartic acid) and then is degraded by PahZ2_KT-1. Recently, we reported the first structure for PahZ1_KT-1. Here, we report novel structures for PahZ2_KT-1 bound to either Gd³⁺/Sm³⁺ or Zn²⁺ cations in a dimeric state consistent with M28 metallopeptidase family members. PahZ2_KT-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 PahZ1_KT-1 and PahZ2_KT-1 will allow for protein engineering endeavors to develop novel biodegradation reagents.