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Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucleotide reductase and the related species
Author(s) -
Shoji Mitsuo,
Isobe Hiroshi,
Takano Yu,
Kitagawa Yasutaka,
Yamanaka Shusuke,
Okumura Mitsutaka,
Yamaguchi Kizashi
Publication year - 2007
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.21469
Subject(s) - ribonucleotide reductase , chemistry , active site , ribonucleotide , stereochemistry , hydrogen bond , crystallography , electron transfer , computational chemistry , photochemistry , molecule , protein subunit , enzyme , organic chemistry , nucleotide , biochemistry , gene
Abstract The radical harvesting state of a ribonucleotide reductase R2 subunit (RNR‐R2) is theoretically investigated at the broken‐symmetry DFT level. Recently, a high‐resolution X‐ray crystallography revealed a precise location of the active site structure of RNR‐R2 (Class 1b) from C. ammoniagenes , and found a linking water near the tyrosine (Tyr) radical site. In this study, the magnetic interaction between the Tyr radical and the diiron core J TyrFe is investigated for the first time. Used theoretical model for the active site is composed of diiron core, the Tyr residue, and surrounding side‐chain groups. After the geometrical structure optimization of the core structures, the magnetic interaction between the iron centers was calculated to be J FeFe = −77.82 cm −1 , which was comparable to the experimental result of J FeFe = −84 cm −1 . The natural orbital analysis clearly showed that the magnetic interaction between the two iron centers mainly interact through the p orbital of the bridging μ‐oxo. It was also calculated that the J TyrFe interaction is negligibly weak, and the Tyr radical is almost in an isolated or a free radical state. These results suggest that the linking water may be used for (1) a confinement of the reactive Tyr radical in the hydrogen bonds or (2) a hydrogen‐transfer coupled with electron transfer at the radical formation step of the Tyr. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007