Comparison of reactivity between d-propanediol and l-propanediol in intramolecular oxidation-reduction catalyzed by dioldehydrase requiring cobamide coenzyme

Yamané, Tsuneo; Kato, Tadakatsu; Shimizu, Sakayu; Fukui, Saburô

doi:10.1016/0003-9861(66)90198-6

Cited by 11 publications

(11 citation statements)

References 12 publications

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“…The S enantiomer is preferred in the binding by diol dehydratase 15. 16 The His143, Glu170, and Glu221 residues were replaced by alanine or glutamine in mutants. QM calculations were performed with the B3LYP method, which consists of the Slater and Hartree–Fock exchanges, the exchange functional of Becke,17 the correlation functional of Lee, Yang, and Parr (LYP),18 and the correlation functional of Vosko, Wilk, and Nusair 19.…”

Section: Methodsmentioning

confidence: 99%

Effect of β‐O‐Glucosylation on L‐Ser and L‐Thr Diamides: A Bias toward α‐Helical Conformations

Corzana¹,

Busto²,

Engelsen³

et al. 2006

Chemistry A European J

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Beta-D-O-glucosylation produces a remarkable effect on the peptide backbone of the model peptides derived from serine and threonine. Consequently, this type of glycosylation is responsible for the experimentally observed shift from extended conformations (model peptides) towards the folded conformations (model glycopeptides). The conclusion has been solidly assessed by a combined NMR/MD protocol. Interestingly, the MD (molecular dynamics) results for the glycopeptides point towards the existence of water-bridging molecules between the sugar and peptide moieties, which could explain the stabilization of the folded conformers in aqueous solution.

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Section: Methodsmentioning

confidence: 99%

Effect of β‐O‐Glucosylation on L‐Ser and L‐Thr Diamides: A Bias toward α‐Helical Conformations

Corzana¹,

Busto²,

Engelsen³

et al. 2006

Chemistry A European J

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“…Figure 8 illustrates the reaction with (S)-1,2-propanediol. When each enantiomer of 1,2-propanediol is run independently, the rate with the R-isomer is 1.7-1.8 times higher than that with the S-isomer [27,110,111]. But, when racemic 1,2-propanediol is used as substrate, the S-isomer reacts at a faster rate than the R-isomer [112].…”

Section: Proposed Mechanismmentioning

confidence: 98%

“…If Hish143, Asph335, and K + are assumed to constitute the only site for dehydration, the oxygen atom derived from C-1 in the S-and R-isomers would be retained in the product and lost into the solvent, respectively. Hence, the pseudo symmetry of the substrate binding site of diol dehydratase accounts for the unusual stereospecificity [27,[110][111][112], stereochemical course [25,27,28], and substrate specificity [10,113].…”

Section: Review Articlementioning

confidence: 99%

Radical catalysis of B 12 enzymes: structure, mechanism, inactivation, and reactivation of diol and glycerol dehydratases

Toraya

2000

Cellular and Molecular Life Sciences (CMLS)

153

148

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Enzymatic radical catalysis is defined as a mechanism of catalysis by which enzymes catalyze chemically difficult reactions by utilizing the high reactivity of free radicals. Adenosylcobalamin (coenzyme B12) serves as a cofactor for enzymatic radical reactions. The recent structural analysis of adenosylcobalamin-dependent diol dehydratase revealed that the substrate 1,2-propanediol and an essential potassium ion are located inside a (beta/alpha)8 barrel. Two hydroxyl groups of the substrate coordinate directly to the potassium ion which binds to the negatively charged inner part of the cavity. Cobalamin bound in the base-on mode covers the cavity to isolate the active site from solvent. Based on the three-dimensional structure and theoretical calculations, a new mechanism for diol dehydratase is proposed in which the potassium ion plays a direct role in the catalysis. The mechanisms for generation of a catalytic radical by homolysis of the coenzyme Co-C bond and for protection of radical intermediates from undesired side reactions during catalysis are discussed based on the structure. The reactivating factors for diol and glycerol dehydratases have been identified. These factors are a new type of molecular chaperone which participate in reactivation of the inactivated holoenzymes by mediating ATP-dependent exchange of the modified coenzyme for free intact coenzyme.

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“…Because C(5Ј), the radical center of the adenosyl radical in the distal conformation, comes on this symmetrical plane, it can abstract the specific hydrogen atoms of the enantiomeric substrates; that is, the pro-R and pro-S hydrogens of the (R)-and (S)-isomers, respectively. The substrate-derived 1,2-diol-1-yl radicals and 5Ј-deoxyadenosine are thus formed (4). The OH group of the substrate radicals then migrates from C(2) to C(1) by a suprafacial shift, resulting in their rearrangement to the product-derived 1,1-diol-2-yl radicals (6) through cyclic transition states (5).…”

Section: Dehydration Of 11-gem-diol Intermediates-it Has Been Reportmentioning

confidence: 99%

“…When each enantiomer of 1,2-propanediol is run independently, the rate with the (R)-isomer is 1.7-1.8 times higher than that with the (S)-isomer (3)(4)(5). However, when racemic 1,2-propanediol is used as substrate, the (S)-isomer reacts at a faster rate than the (R)-isomer (6).…”

mentioning

confidence: 97%

Structural Rationalization for the Lack of Stereospecificity in Coenzyme B12-dependent Diol Dehydratase

Shibata

Nakanishi

Fukuoka

et al. 2003

Journal of Biological Chemistry

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Adenosylcobalamin-dependent diol dehydratase of (1). This causes 60°clockwise and 70°counterclockwise rotations of the C(1)-C(2) bond of the (R)-and (S)-isomers, respectively, if viewed from K؉ . A modeling study of 1,1-gem-diol intermediates indicated that new radical center C(2) becomes close to the methyl group of 5-deoxyadenosine. Thus, the hydrogen back-abstraction (recombination) from 5-deoxyadenosine by the product radical is structurally feasible. It was also predictable that the substitution of the migrating hydroxyl group by a hydrogen atom from 5-deoxyadenosine takes place with the inversion of the configuration at C(2) of the substrate. Stereospecific dehydration of the 1,1-gem-diol intermediates can also be rationalized by assuming that Asp-␣335 and Glu-␣170 function as base catalysts in the dehydration of the (R)-and (S)-isomers, respectively. The structure-based mechanism and stereochemical courses of the reaction are proposed.

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Comparison of reactivity between d-propanediol and l-propanediol in intramolecular oxidation-reduction catalyzed by dioldehydrase requiring cobamide coenzyme

Cited by 11 publications

References 12 publications

Effect of β‐O‐Glucosylation on L‐Ser and L‐Thr Diamides: A Bias toward α‐Helical Conformations

Effect of β‐O‐Glucosylation on L‐Ser and L‐Thr Diamides: A Bias toward α‐Helical Conformations

Radical catalysis of B 12 enzymes: structure, mechanism, inactivation, and reactivation of diol and glycerol dehydratases

Structural Rationalization for the Lack of Stereospecificity in Coenzyme B12-dependent Diol Dehydratase

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