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

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Sphingomonas sp. KT-1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydrolysis.

Brambley, C.A.Yared, T.J.Gonzalez, M.Jansch, A.L.Wallen, J.R.Weiland, M.H.Miller, J.M.

(2021) J Phys Chem B 125: 5722-5739

  • DOI: https://doi.org/10.1021/acs.jpcb.1c01216
  • Primary Citation of Related Structures:  
    7LJH, 7LJI

  • 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, 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.

  • Organizational Affiliation

    Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, Tennessee 37132, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly(Aspartic acid) hydrolase
A, B
425Sphingomonas sp. KT-1Mutation(s): 0 
Gene Names: pahZ2
Find proteins for Q769D3 (Sphingomonas sp. KT-1)
Explore Q769D3 
Go to UniProtKB:  Q769D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ769D3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.399α = 90
b = 146.174β = 90
c = 197.238γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release