9O7U

Structure Determination of Pedobacter sp. KP-2 PahZ1

Summary for 9O7U

• Entry DOI: 10.2210/pdb9o7u/pdb
• Descriptor: Poly(Aspartic acid) hydrolase-1 (2 entities in total)
• Functional Keywords: hydrolase
• Biological source: Pedobacter sp. KP-2
• Total number of polymer chains: 1
• Total formula weight: 32616.87

Authors

Wallen, J.R.,Miller, J.M. (deposition date: 2025-04-15, release date: 2026-03-11)

Primary citation

Marsee, J.D.,Brambley, C.A.,Ho, T.,Callaway, W.W.,Jansch, A.L.,Taylor, K.,Watson-Sanders, S.R.,Williams, B.,Wolvington, A.,Nguyen, C.T.,Khan, L.,Cabrera, C.,Cerna, M.V.C.,Wallen, J.R.,Weiland, M.H.,Miller, J.M.
Expansion of the known Poly(Aspartic Acid) Hydrolases through the Identification of Four New PahZ1 Homologs.
Protein Eng.Des.Sel., 2026

PubMed Abstract: Polyaspartic acid (PAA) is a biodegradable polymer with various industrial applications. To date there are only three known PAA hydrolases (from the gene PahZ) capable of degrading PAA . These enzymes are expressed in two different bacteria, Sphingomonas sp. KT-1 (PahZ1KT-1 and PahZ2KT-1) and Pedobacter sp. KP-2 (PahZ1KP-2). PahZ1KT-1 and PahZ2KT-1 form a two-component system degrading tPAA to oligoaspartic acid (OAA) and subsequently into aspartic acid. This study aims to expand the diversity of PAA hydrolases and inform efforts to improve PAA degradation. To further understand the known PahZ1 homologs, the X-ray crystal structure of PahZ1KP-2 was determined to examine its structural homology with PahZ1KT-1. Crystallographic analysis revealed PahZ1KP-2 is monomeric, contrasting with the dimeric PahZ1KT-1, yet both share a conserved serine protease catalytic triad. With the aim of expanding the PahZ1 family, four putative homologs were identified using bioinformatics and AI-based structural modeling, all of which retained the α/β hydrolase domain. Importantly, all homologs exhibited measurable PAA-degrading activity and each was classified as either monomer or dimer to further expand the diversity of PahZ1 enzymes and provide a broader toolbox for sustainable polymer degradation.

PubMed: 41761765
DOI: 10.1093/protein/gzag006

Experimental method

X-RAY DIFFRACTION (2 Å)