1DET
RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP
Summary for 1DET
| Entry DOI | 10.2210/pdb1det/pdb |
| Descriptor | RIBONUCLEASE T1, SODIUM ION, GUANOSINE-2'-MONOPHOSPHATE, ... (4 entities in total) |
| Functional Keywords | hydrolase, endoribonuclease, nuclease, endonuclease, hydrolase (endoribonuclease) |
| Biological source | Aspergillus oryzae |
| Total number of polymer chains | 1 |
| Total formula weight | 11560.88 |
| Authors | Ishikawa, K.,Suzuki, E.,Tanokura, M.,Takahashi, K. (deposition date: 1996-02-20, release date: 1996-07-11, Last modification date: 2024-06-05) |
| Primary citation | Ishikawa, K.,Suzuki, E.,Tanokura, M.,Takahashi, K. Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP. Biochemistry, 35:8329-8334, 1996 Cited by PubMed Abstract: The carboxymethylation of RNase T1 at the gamma-carboxyl group of Glu58 leads to a complete loss of the enzymatic activity while it retains substrate-binding ability. Accompanying the carboxymethylation, RNase T1 undergoes a remarkable thermal stabilization of 9 degrees C in the melting temperature (Tm). In order to clarify the inactivation and stabilization mechanisms of RNase T1 by carboxymethylation, the crystal structure of carboxymethylated RNase T1 (CM-RNase T1) complexed with 2'-GMP was determined at 1.8 A resolution. The structure, including 79 water molecules and two Na+, was refined to an R factor of 0.194 with 10 354 reflections > 1 sigma (F). The carboxyl group of CM-Glu58, which locates in the active site, occupies almost the same position as the phosphate group of 2'-GMP in the crystal structure of intact RNase T1.2'-GMP complex. Therefore, the phosphate group of 2'-GMP cannot locate in the active site but protrudes toward the solvent. This forces 2'-GMP to adopt an anti form, which contrasts with the syn form in the crystal of the intact RNase T1.2'-GMP complex. The inaccessibility of the phosphate group to the active site can account for the lack of the enzymatic activity in CM-RNase T1. One of the carboxyl oxygen atoms of CM-Glu58 forms two hydrogen bonds with the side-chains of Tyr38 and His40. These hydrogen bonds are considered to mainly contribute to the higher thermal stability of CM-RNase T1. Another carboxyl oxygen atoms of CM-Glu58 is situated nearby His40 and Arg77. This may provide additional electrostatic stabilization. PubMed: 8679590DOI: 10.1021/bi960493d PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.8 Å) |
Structure validation
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