A Dynamics-enabled Structural Characterization of a Set of Poly(aspartic acid) Hydrolases from Sphingomonas sp. KT-1

Abstract

Polymers of aspartic acid (PAA) belong to a class of water-soluble polycarboxylates (WSP) with widespread usage in a variety of commercial applications. Given increasing evidence that such WSPs may pose environmental risks via leeching and accumulation into ground and surface water, the need to develop an effective means of degradation and bioremediation is clear. Biodegradation of PAA has most recently been made possible by the discovery of a collection of PAA hydrolases isolated from river water bacteria, Sphingomonas sp. KT-1 and Pedobacter sp. KP-2. PAA-hydrolase-1 (PahZ1) was identified in both species, while a subsequent PAA-hydrolase-2 (PahZ2) was found only in Sphingomonas sp. KT-1. The two enzymes have previously been shown to cooperatively carry out the hydrolysis of PAA as part of a multi-step catalytic mechanism. PahZ1KT-1 targets β-amide linkages to yield oligo(aspartic acid)(OAA), which is in turn further degraded by PahZ2KT-1. Here, we present a collection of dynamics focused structural characterizations of both enzymes. We additionally report a machine-learning strategy to model the structure and motions of a putative chimeric enzyme engineered to include both PahZ1KT-1 and PahZ2KT-1 functional domains.