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Binding of non‐natural 3′‐nucleotides to ribonuclease A
Author(s) -
Jenkins Cara L.,
Thiyagarajan Nethaji,
Sweeney Rozamond Y.,
Guy Michael P.,
Kelemen Bradley R.,
Acharya K. Ravi,
Raines Ronald T.
Publication year - 2005
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2004.04511.x
Subject(s) - furanose , rnase p , nucleotide , nucleobase , uracil , stereochemistry , chemistry , ribonuclease , residue (chemistry) , nucleoside , deoxyuridine , uridine , ribose , ribonuclease t1 , dna , enzyme , biochemistry , rna , ring (chemistry) , organic chemistry , gene
2′‐Fluoro‐2′‐deoxyuridine 3′‐phosphate (dU F MP) and arabinouridine 3′‐phosphate (araUMP) have non‐natural furanose rings. dU F MP and araUMP were prepared by chemical synthesis and found to have three‐ to sevenfold higher affinity than uridine 3′‐phosphate (3′‐UMP) or 2′‐deoxyuridine 3′‐phosphate (dUMP) for ribonuclease A (RNase A). These differences probably arise (in part) from the phosphoryl groups of 3′‐UMP, dU F MP, and araUMP (p K a = 5.9) being more anionic than that of dUMP (p K a = 6.3). The three‐dimensional structures of the crystalline complexes of RNase A with dUMP, dU F MP and araUMP were determined at < 1.7 Å resolution by X‐ray diffraction analysis. In these three structures, the uracil nucleobases and phosphoryl groups bind to the enzyme in a nearly identical position. Unlike 3′‐UMP and dU F MP, dUMP and araUMP bind with their furanose rings in the preferred pucker. In the RNase A·araUMP complex, the 2′‐hydroxyl group is exposed to the solvent. All four 3′‐nucleotides bind more tightly to wild‐type RNase A than to its T45G variant, which lacks the residue that interacts most closely with the uracil nucleobase. These findings illuminate in atomic detail the interaction of RNase A and 3′‐nucleotides, and indicate that non‐natural furanose rings can serve as the basis for more potent inhibitors of catalysis by RNase A.