Open AccessSphingomonas sp. KT-1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydrolysis
Author(s) -
Chad A. Brambley,
Tarah J. Yared,
Marriah Gonzalez,
Amanda L. Jansch,
Jamie R. Wallen,
Mitch H. Weiland,
Justin M. Miller
Publication year - 2021
Publication title -
the journal of physical chemistry. b
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.864
H-Index - 392
eISSN - 1520-6106
pISSN - 1520-5207
DOI - 10.1021/acs.jpcb.1c01216
Subject(s) - chemistry , monomer , hydrolysis , catalysis , aspartic acid , amide , substrate (aquarium) , peptide , sphingomonas , peptide bond , stereochemistry , protein structure , molecular dynamics , amino acid , biochemistry , organic chemistry , computational chemistry , biology , polymer , ecology , 16s ribosomal rna , gene
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 Gd 3+ /Sm 3+ or Zn 2+ 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 Zn 2+ 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.