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J. Biochem, 1988, Vol. 103, No. 2 354-366
© 1988 Japanese Biochemical Society

research-article

Refined X-Ray Structure of the Low pH Form of Ribonuclease T1-2'-Guanylic Acid Complex at 1.9 Å Resolution1

Shigetoshi Sugio, Faculty of Pharmaceutical Sciences2, Takashi Amisaki, Faculty of Pharmaceutical Sciences3, Hirofumi Ohishi, Faculty of Pharmaceutical Sciences4 and Ken-ichi Tomita, Faculty of Pharmaceutical Sciences5

Osaka University Suita, Osaka 565

5To whom correspondence should be addressed.

The three-dimensional X-ray structure of the RNase T1 [EC 3.1.27.3 [EC] ]-2'GMP complex crystallized at low pH value (4.0) was determined, and refined to 1.9 Å resolution to give a final R value of 0.203. The refined model includes 781 protein atoms, 24 inhibitor atoms, and 43 solvent molecules. The imidazole rings of His27 and His40 interact with the carboxyl side chains of Glu82 and Glu58, respectively, whereas that of His92 is in contact with the main chain carbonyl oxygen of Ala75. In the complex, the ribose ring of the 2'GMP molecule adopts a C2'-endo puckering, and the exocyclic conformation is gauche(–)-gauche(+). The glycosyl torsion angle is in the syn range with an intramolecular hydrogen bond between N3 and 05', and the 2'-phosphate orientation is trans-gauche(-). The guanine base of the inhibitor is tightly bound to the base recognition site with five hydrogen bonds (N1- - Glu460{varepsilon}2, N2- - -Asn980, O6- - -Asn44N, and N7- -Asn43N{delta}2/Asn43N) and is sandwiched between the phenolic ring portions of Tyr42 and Tyr45 by stacking interactions. The 2'-phosphate group interacts with Arg77N{eta}2, Glu580{varepsilon}2, and Tyr380{eta} but not with any of the histidine residues. Arg77N{eta} 2 also interacts with Tyr380{eta}. There is no interaction between the ribose moiety of the inhibitor and the enzyme.

1This work was partly supported by a Grant-in-Aid for specially distinguished research, No. 59065006, from the Ministry of Education, Science and Culture of Japan and a grant for Japan-Germany Cooperative Research Projects from the Japanese Society for Promotion of Science.

2Present address: Central Research Laboratories Research Division, The Green Cross Corporation, Hirakata, Osaka 573.

3Present address: Department of Hospital Pharmacy, Tottori University School of Medicine, Yonago, Tottori 683.

4Present address: Osaka College of Pharmacy, Matsubara, Osaka 580.


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