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Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 Å resolution

¹ Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
² Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Mikazuki, Sayo, Hyogo 679-5198, Japan

Reprint requests to: Dr. Rikimaru Hayashi, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan; e-mail: hayashi{at}kais.kyoto-u.ac.jp; fax: 81-75-753-6128.

The replacement of Phe120 with other hydrophobic residues causes a decrease in the activity and thermal stability in ribonuclease A (RNase A). To explain this, the crystal structures of wild-type RNase A and three mutants—F120A, F120G, and F120W—were analyzed up to a 1.4 Å resolution. Although the overall backbone structures of all mutant samples were nearly the same as that of wild-type RNase A, except for the C-terminal region of F120G with a high B-factor, two local conformational changes were observed at His119 in the mutants. First, His119 of the wild-type and F120W RNase A adopted an A position, whereas those of F120A and F120G adopted a B position, but the static crystallographic position did not reflect either the efficiency of transphosphorylation or the hydrolysis reaction. Second, His119 imidazole rings of all mutant enzymes were deviated from that of wild-type RNase A, and those of F120W and F120G appeared to be "inside out" compared with that of wild-type RNase A. Only 1 Å change in the distance between N₂ of His12 and N₁ of His119 causes a drastic decrease in k_cat, indicating that the active site requires the strict positioning of the catalytic residues. A good correlation between the change in total accessible surface area of the pockets on the surface of the mutant enzymes and enthalpy change in their thermal denaturation also indicates that the effects caused by the replacements are not localized but extend to remote regions of the protein molecule.

Keywords: Crystal structure; ribonuclease A; active site; His119; thermal stability; accessible surface area

Abbreviations: ASA, accessible surface area • CpA, cytidilyl-3`,5`-adenosine • C>p, cytidine-2`,3`-cyclic monophosphate • RMSD, root-mean-square deviation • UpA, uridilyl-3`,5`-adenosine • U>p, uridine-2`,3`-cyclic monophosphate.

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