9ncs | pdb_00009ncs

RNase A in complex with Uridine Vanadate and decavanadates

spinqualitylabelsall models 9ncs, resolution 1.83Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9ncs is a 2 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.83Å Ligands: URI, VVO Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RNAS1_BOVIN Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA. Publication Abstract from PubMed 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(5) bond on the 3' side of pyrimidine residues. Pseudouridine (Psi) is the most abundant modified nucleoside in natural RNA. The substitution of uridine (U) with Psi or N (1)‑methylpseudouridine (m(1)Psi) 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(5) bond on the 3' side of Psi and m(1)Psi. We find that these enzymes catalyze the cleavage of UpA up to 10‑fold more efficiently than the cleavage of PsipA or m(1)PsipA. X-ray crystallography of enzyme-bound nucleoside 2',3'‑cyclic vanadate complexes and molecular dynamics simulations of enzyme.dinucleotide complexes show that U, Psi, and m(1)Psi 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 pK (a) of the 2'‑hydroxy group of U and enhances its nucleophilicity toward the P-O(5) bond. Experimentally, we found that UpA does indeed undergo spontaneous hydrolysis faster than does m(1)PsipA. Our findings inform the continuing development of RNA-based vaccines and therapeutic agents. Pseudouridine Residues as Substrates for Serum Ribonucleases.,Gutierrez CS, Silkenath B, Kojasoy V, Pich JA, Lim DC, Raines RT RNA. 2025 Aug 20:rna.080404.125. doi: 10.1261/rna.080404.125. PMID:40835455 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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