7LJH

Structure of poly(aspartic acid) hydrolase PahZ2 with Zn+2 bound

Summary for 7LJH

• Entry DOI: 10.2210/pdb7ljh/pdb
• Descriptor: Poly(Aspartic acid) hydrolase, ZINC ION (3 entities in total)
• Functional Keywords: serine protease, poly(aspartic acid) hydrolase, hydrolase
• Biological source: Sphingomonas sp. KT-1
• Total number of polymer chains: 2
• Total formula weight: 91717.80

Authors

Brambley, C.A.,Yared, T.J.,Gonzalez, M.,Jansch, A.L.,Wallen, J.R.,Weiland, M.H.,Miller, J.M. (deposition date: 2021-01-29, release date: 2021-12-08, Last modification date: 2024-05-22)

Primary citation

Brambley, C.A.,Yared, T.J.,Gonzalez, M.,Jansch, A.L.,Wallen, J.R.,Weiland, M.H.,Miller, J.M.
Sphingomonas sp. KT-1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydrolysis.
J.Phys.Chem.B, 125:5722-5739, 2021

PubMed 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, sp. KT-1 and sp. KP-2. Within sp. KT-1, PahZ1 cleaves β-amide linkages to oligo(aspartic acid) and then is degraded by PahZ2. Recently, we reported the first structure for PahZ1. Here, we report novel structures for PahZ2 bound to either Gd/Sm or Zn cations in a dimeric state consistent with M28 metallopeptidase family members. PahZ2 monomers include a dimerization domain and a catalytic domain with dual Zn 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 and PahZ2 will allow for protein engineering endeavors to develop novel biodegradation reagents.

PubMed: 34060838
DOI: 10.1021/acs.jpcb.1c01216

Experimental method

X-RAY DIFFRACTION (2.5 Å)