6SSN

RNASE 3/1 version3

Summary for 6SSN

• Entry DOI: 10.2210/pdb6ssn/pdb
• Descriptor: RNase 3/1 version3, GLYCEROL, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: rnase 3/1 version3, hydrolase, pancreatic ribonuclease
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 31841.56

Authors

Fernandez-Millan, P.,Prats-Ejarque, G.,Vazquez-Monteagudo, S.,Boix, E. (deposition date: 2019-09-08, release date: 2021-10-06, Last modification date: 2024-10-23)

Primary citation

Fernandez-Millan, P.,Vazquez-Monteagudo, S.,Boix, E.,Prats-Ejarque, G.
Exploring the RNase A scaffold to combine catalytic and antimicrobial activities. Structural characterization of RNase 3/1 chimeras.
Front Mol Biosci, 9:964717-964717, 2022

PubMed Abstract: Design of novel antibiotics to fight antimicrobial resistance is one of the first global health priorities. Novel protein-based strategies come out as alternative therapies. Based on the structure-function knowledge of the RNase A superfamily we have engineered a chimera that combines RNase 1 highest catalytic activity with RNase 3 unique antipathogen properties. A first construct (RNase 3/1-v1) was successfully designed with a catalytic activity 40-fold higher than RNase 3, but alas in detriment of its anti-pathogenic activity. Next, two new versions of the original chimeric protein were created showing improvement in the antimicrobial activity. Both second generation versions (RNases 3/1-v2 and -v3) incorporated a loop characteristic of RNase 3 (L7), associated to antimicrobial activity. Last, removal of an RNase 1 flexible loop (L1) in the third version enhanced its antimicrobial properties and catalytic efficiency. Here we solved the 3D structures of the three chimeras at atomic resolution by X-ray crystallography. Structural analysis outlined the key functional regions. Prediction by molecular docking of the protein chimera in complex with dinucleotides highlighted the contribution of the C-terminal region to shape the substrate binding cavity and determine the base selectivity and catalytic efficiency. Nonetheless, the structures that incorporated the key features related to RNase 3 antimicrobial activity retained the overall RNase 1 active site conformation together with the essential structural elements for binding to the human ribonuclease inhibitor (RNHI), ensuring non-cytotoxicity. Results will guide us in the design of the best RNase pharmacophore for anti-infective therapies.

PubMed: 36188223
DOI: 10.3389/fmolb.2022.964717

Experimental method

X-RAY DIFFRACTION (1.511 Å)