Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucleotide reductase and the related species

Mitsuo Shoji, Hiroshi Isobe, Yu Takano, Yasutaka Kitagawa, Shusuke Yamanaka, Mitsutaka Okumura, Kizashi Yamaguchi

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

The radical harvesting state of a ribonucleotide reductase R2 subunit (RNRR2) 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 lb) 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 Tyr-Fe 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 JFe_Fe = -77.82 cm-1, which was comparable to the experimental result of JFe_Fe = -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 JTyr_Fe 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.

Original languageEnglish
Pages (from-to)3250-3265
Number of pages16
JournalInternational Journal of Quantum Chemistry
Volume107
Issue number15
DOIs
Publication statusPublished - Dec 1 2007
Externally publishedYes

Fingerprint

Ribonucleotide Reductases
tyrosine
Chemical bonds
chemical bonds
Tyrosine
Iron
Water
X ray crystallography
Crystal symmetry
Discrete Fourier transforms
Free Radicals
Hydrogen
Hydrogen bonds
interactions
iron
orbitals
tyrosine radical
Electrons
free radicals
water

Keywords

  • Magnetic interaction
  • Natural orbital analysis
  • Ribonucleotide reductate
  • Tyrosine radical

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucleotide reductase and the related species. / Shoji, Mitsuo; Isobe, Hiroshi; Takano, Yu; Kitagawa, Yasutaka; Yamanaka, Shusuke; Okumura, Mitsutaka; Yamaguchi, Kizashi.

In: International Journal of Quantum Chemistry, Vol. 107, No. 15, 01.12.2007, p. 3250-3265.

Research output: Contribution to journalArticle

Shoji, Mitsuo ; Isobe, Hiroshi ; Takano, Yu ; Kitagawa, Yasutaka ; Yamanaka, Shusuke ; Okumura, Mitsutaka ; Yamaguchi, Kizashi. / Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucleotide reductase and the related species. In: International Journal of Quantum Chemistry. 2007 ; Vol. 107, No. 15. pp. 3250-3265.
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