8RTK image
Deposition Date 2024-01-26
Release Date 2025-02-12
Last Version Date 2025-07-16
Entry Detail
PDB ID:
8RTK
Keywords:
Title:
X-ray structure of lysozyme obtained upon reaction with [VIVO(8-HQ)2] in sodium formate
Biological Source:
Source Organism:
Gallus gallus (Taxon ID: 9031)
Method Details:
Experimental Method:
Resolution:
1.21 Å
R-Value Free:
0.19
R-Value Work:
0.17
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Lysozyme C
Gene (Uniprot):LYZ
Chain IDs:A (auth: AAA)
Chain Length:129
Number of Molecules:1
Biological Source:Gallus gallus
Primary Citation
Protein-Protein Stabilization in V IV O/8-Hydroxyquinoline-Lysozyme Adducts.
Chemistry 30 e202401712 e202401712 (2024)
PMID: 38923243 DOI: 10.1002/chem.202401712

Abstact

The binding of the potential drug [VIVO(8-HQ)2], where 8-HQ is 8-hydroxyquinolinato, with hen egg white lysozyme (HEWL) was evaluated through spectroscopic (electron paramagnetic resonance, EPR, and UV-visible), spectrometric (electrospray ionization-mass spectrometry, ESI-MS), crystallographic (X-ray diffraction, XRD), and computational (DFT and docking) studies. ESI-MS indicates the interaction of [VIVO(8-HQ)(H2O)]+ and [VIVO(8-HQ)2(H2O)] species with HEWL. Room temperature EPR spectra suggest both covalent and non-covalent binding of the two different V-containing fragments. XRD analyses confirm these findings, showing that [VIVO(8-HQ)(H2O)]+ interacts covalently with the solvent exposed Asp119, while cis-[VIVO(8-HQ)2(H2O)] non-covalently with Arg128 and Lys96 from a symmetry mate. The covalent binding of [VIVO(8-HQ)(H2O)]+ to Asp119 is favored by a π-π contact with Trp62 and a H-bond with Asn103 of a symmetry-related molecule. Additionally, the covalent binding of VVO2 + to Asp48 and non-covalent binding of other V-containing fragments to Arg5, Cys6, and Glu7 are revealed. Molecular docking indicates that, in the absence of the interactions occurring at the protein-protein interface close to Asp119, the covalent binding to Glu35 or Asp52 should be preferred. Such a protein-protein stabilization could be more common than what believed up today, at least in the solid state, and should be considered in the characterization of metal-protein adducts.

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