Sphingomonas sp. KT-1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydrolysis
| Autor: | Jamie R. Wallen, Chad A. Brambley, Amanda L. Jansch, Justin M. Miller, Mitch H. Weiland, Marriah Gonzalez, Tarah J. Yared |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
010304 chemical physics
Metallopeptidase Chemistry Stereochemistry Substrate (chemistry) Protein engineering 010402 general chemistry 01 natural sciences Article 0104 chemical sciences Surfaces Coatings and Films Catalysis Hydrolysis 0103 physical sciences Aspartic acid Materials Chemistry Peptide bond Physical and Theoretical Chemistry Binding site |
| Zdroj: | J Phys Chem B |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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