9O5B
RNase A in complex with N1-Methylpseudouridine Vanadate and decavanadates
Summary for 9O5B
| Entry DOI | 10.2210/pdb9o5b/pdb |
| Descriptor | Ribonuclease pancreatic, 5-[(2S,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione, DECAVANADATE, ... (5 entities in total) |
| Functional Keywords | ribonuclease, rna, n1-methylpseudouridine vanadate, decavanadate, hydrolase |
| Biological source | Bos taurus (domestic cattle) |
| Total number of polymer chains | 2 |
| Total formula weight | 31571.41 |
| Authors | Gutierrez, C.S.,Lim, D.C.,Silkenath, B.,Kojasoy, V.,Raines, R.T. (deposition date: 2025-04-09, release date: 2025-09-24, Last modification date: 2025-10-29) |
| Primary citation | Gutierrez, C.S.,Silkenath, B.,Kojasoy, V.,Pich, J.A.,Lim, D.C.,Raines, R.T. Pseudouridine residues as substrates for serum ribonucleases. Rna, 31:1542-1556, 2025 Cited by PubMed Abstract: In clinical uses, RNA must maintain its integrity in serum that contains ribonucleases (RNases), especially RNase 1, which is a human homolog of RNase A. These omnipresent enzymes catalyze the cleavage of the P-O bond on the 3' side of pyrimidine residues. Pseudouridine (Ψ) is the most abundant modified nucleoside in natural RNA. The substitution of uridine (U) with Ψ or ‑methylpseudouridine (mΨ) reduces the immunogenicity of mRNA and increases ribosomal translation, and these modified nucleosides are key components of RNA-based vaccines. Here, we assessed the ability of RNase A and RNase 1 to catalyze the cleavage of the P-O bond on the 3' side of Ψ and mΨ. We find that these enzymes catalyze the cleavage of UpA up to 10‑fold more efficiently than the cleavage of ΨpA or mΨpA. X-ray crystallography of enzyme-bound nucleoside 2',3'‑cyclic vanadate complexes and molecular dynamics simulations of enzyme·dinucleotide complexes show that U, Ψ, and mΨ bind to RNase A and RNase 1 in a similar manner. Quantum chemistry calculations suggested that the higher reactivity of UpA is intrinsic, arising from an inductive effect that decreases the p of the 2'‑hydroxy group of U and enhances its nucleophilicity toward the P-O bond. Experimentally, we found that UpA does indeed undergo spontaneous hydrolysis faster than does mΨpA. Our findings inform the continuing development of RNA-based vaccines and therapeutic agents. PubMed: 40835455DOI: 10.1261/rna.080404.125 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.71 Å) |
Structure validation
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