9RUV image
Deposition Date 2025-07-05
Release Date 2025-08-13
Last Version Date 2025-08-13
Entry Detail
PDB ID:
9RUV
Keywords:
Title:
X-ray structure of the adduct formed upon reaction of dirhodium-tetraacetate with lysozyme at body temperature
Biological Source:
Source Organism:
Gallus gallus (Taxon ID: 9031)
Method Details:
Experimental Method:
Resolution:
2.12 Å
R-Value Free:
0.26
R-Value Work:
0.19
Space Group:
P 43 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
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
Dirhodium Tetraacetate Binding to Lysozyme at Body Temperature.
Int J Mol Sci 26 ? ? (2025)
PMID: 40724832 DOI: 10.3390/ijms26146582

Abstact

Paddlewheel dirhodium complexes are cytotoxic compounds that are also used as catalysts and in the formation of Rh-based artificial metalloenzymes. Low-temperature structures of adducts formed by the model protein hen egg white lysozyme (HEWL) with dirhodium tetraacetate ([Rh2(μ-O2CCH3)4]) when crystals of the protein were treated with the metal compound at 20 °C demonstrated that [Rh2(μ-O2CCH3)4] in part breaks down upon reaction with HEWL; dimeric Rh-Rh units bind the side chains of Asp18 and the C-terminal carboxylate, and monometallic fragments coordinate the side chains of Arg14 and His15 in 20% ethylene glycol, 0.100 M sodium acetate at pH 4.5 and 0.600 M sodium nitrate, while dimeric Rh-Rh units bind the side chains of Asn93 and Lys96, the C-terminal carboxylate and Asp101, with monometallic fragments that bind the side chains of Lys33 and His15 in 0.010 M HEPES pH 7.5 and 2.00 M sodium formate. To verify whether the binding of this metallodrug to proteins also occurs at body temperature, crystals of HEWL were grown in 0.010 M HEPES pH 7.5 and 2.00 M sodium formate at 37 °C and soaked with [Rh2(μ-O2CCH3)4] at the same temperature. X-ray diffraction data collected on these crystals at 37 °C demonstrate that [Rh2(μ-O2CCH3)4] reacts with proteins at body temperature. The structures of the Rh/HEWL adduct formed at 20 °C (obtained from data collected at 100 K) and at 37 °C under the same experimental conditions are very similar, with metal binding sites that are conserved. However, metal-containing fragment occupancy is higher in the structure obtained at 37 °C, suggesting a role of temperature in defining the protein metalation process.

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