6GNL

Zr(IV)-substituted Keggin directly binding to the side chain of Hen Egg-White Lysozyme (HEWL)

Summary for 6GNL

• Entry DOI: 10.2210/pdb6gnl/pdb
• Related: 4XYY 5FHW
• Descriptor: Lysozyme C, ZIRCONIUM(IV) PHOSPHOTUNGSTATE KEGGIN, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: lysozyme, co-crystal, hydrolysis, catalysis, hydrolase
• Biological source: Gallus gallus (Chicken)
• Total number of polymer chains: 1
• Total formula weight: 19976.36

Authors

Vandebroek, L.,Van Meervelt, L.,Parac-Vogt, T.N. (deposition date: 2018-05-31, release date: 2018-10-31, Last modification date: 2024-10-16)

Primary citation

Vandebroek, L.,Van Meervelt, L.,Parac-Vogt, T.N.
Direct observation of the ZrIVinteraction with the carboxamide bond in a noncovalent complex between Hen Egg White Lysozyme and a Zr-substituted Keggin polyoxometalate.
Acta Crystallogr C Struct Chem, 74:1348-1354, 2018

PubMed Abstract: The successful cocrystallization of the noncovalent complex formed between (EtNH)[{α-PWOZr-(μ-OH)(HO)}]·7HO Keggin polyoxometalate (2) and Hen Egg White Lysozyme (HEWL) protein is reported. The resulting structural model revealed interaction between monomeric [Zr(PWO)](1), which is a postulated catalytically active species, and the protein in two positions in the asymmetric unit. The first position (occupancy 36%) confirms the previously observed binding sites on the protein surface, whereas the second position (occupancy 14%) provides novel insights into the hydrolytic mechanisms of Zr-substituted polyoxometalates. The new interaction site occurs at the Asn65 residue, which is directly next to the Asp66-Gly67 peptide bond that was identified recently as a cleavage site in the polyoxometalate-catalysed hydrolysis of HEWL. Furthermore, in this newly discovered binding site, the monomeric polyoxometalate 1 is observed to bind directly to the side chain of the Asn65 residue. This binding of Zr as a Lewis-acid metal to the carbonyl O atom of the Asn65 side chain is very similar to the intermediate state proposed in density functional theory (DFT) studies in which Zr activates the peptide bond via interaction with its carbonyl O atom, and can be thus regarded as a model for interaction between Zr and a peptide bond.

PubMed: 30398187
DOI: 10.1107/S2053229618010690

Experimental method

X-RAY DIFFRACTION (1.23 Å)