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Volumn 132, Issue 34, 2010, Pages 11993-12005

ONIOM study on a missing piece in our understanding of heme chemistry: Bacterial tryptophan 2,3-dioxygenase with dual oxidants

Author keywords

[No Author keywords available]

Indexed keywords

C-C BONDS; DIOXETANES; DIOXYGEN ACTIVATION; DIOXYGENASES; L-TRYPTOPHAN; MECHANISTIC PATHWAYS; NON-HEME OXYGENASES; OXIDATIVE CLEAVAGES; PYRROLE RING; RADICAL ADDITION; REACTION MECHANISM; REGIOSPECIFIC; RING OPENING; RING-CLOSURE; SUPEROXIDES; X RAY CRYSTAL STRUCTURES; XANTHOMONAS CAMPESTRIS;

EID: 77956092331     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja103530v     Document Type: Article
Times cited : (73)

References (161)
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    • 3 2 was found in our ONIOM(B3LYP:Amber) calculations. Moreover, these two studies adopted a few different computational settings, and the key ones are listed as follows: (1) This work used chain A and most of the chain B; EY used most of chain A with a few residues of chain B. (2) In this work, additional TS structures and epoxidation TS structures were accurately determined by the recent TS optimization method and verified by frequency calculations;
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    • xcTDO is a tetramer protein, in which the active site is formed from the dimer. The shortest distances between the active site in chain A and residues in chain C: Glu224,11.8 Å; Val227, 12.9 Å; Thr231, 12.8 Å; Phe276, 11.9 Å; Arg279, 9.3 Å; Thr280, 11.3 Å; and Val282, 11.4 Å. To estimate the error of excluding these residues in chain C, we superimposed the X-ray crystal tetramer structure and the ONIOM-optimized reactant. We then took coordinates of these residues in chain C, added hydrogen atoms, and represented them as the point charges. Additional B3LYP calculations show negligible error of these electrostatic interactions (data in parentheses in column 12 of Table S3; maximum error of 0.2 kcal/mol). ONIOM-calculated free energies are put in Table S3. More reliable QM/MM free energy calculations will be performed and reported in due course
    • xcTDO is a tetramer protein, in which the active site is formed from the dimer. The shortest distances between the active site in chain A and residues in chain C: Glu224,11.8 Å; Val227, 12.9 Å; Thr231, 12.8 Å; Phe276, 11.9 Å; Arg279, 9.3 Å; Thr280, 11.3 Å; and Val282, 11.4 Å. To estimate the error of excluding these residues in chain C, we superimposed the X-ray crystal tetramer structure and the ONIOM-optimized reactant. We then took coordinates of these residues in chain C, added hydrogen atoms, and represented them as the point charges. Additional B3LYP calculations show negligible error of these electrostatic interactions (data in parentheses in column 12 of Table S3; maximum error of 0.2 kcal/mol). ONIOM-calculated free energies are put in Table S3. More reliable QM/MM free energy calculations will be performed and reported in due course.
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    • The optimized protein and its active site are similar to the X-ray crystal structure (Figure S1). The calculated RMSD is about 0.50 Å.
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    • css 1′′ is further decreased to 1.2-1.3 kcal/mol by the ONIOM-EE//ONIOM-ME method, irrespective of using larger basis set BS2 or B3LYP* functional.
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    • 5 4 in the quintet state is -1.7 and 2.2 kcal/mol, respectively. Compared to the triplet state, the higher-energy quintet state should be unimportant in the reactions.
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    • In the gas-phase calculation, only the ring-closure transition state, but not the Criegee-type rearrangement transition state, was located for the simple radical hydroperoxy intermediate (Figure S11).
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    • 3 IV in Figure S17) in the protein. Moreover, the recent experiment using N -methyl-Trp as the substrate showed that proton or hydrogen transfer from the indole is not necessary (16)
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    • -1)
    • -1).


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.