Roles of β-d-ribofuranose ring and the functional groups of the d-ribose moiety of adenosylcobalamin in the diol dehydratase reaction

Ichikawa, Mai; Toraya, Tetsuo

doi:10.1016/0167-4838(88)90115-x

Cited by 13 publications

(13 citation statements)

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“…For Aristeromycylcobalamin (AdoCbl analogue in which the ribosyl oxygen atom is replaced by ‐CH 2 ‐) is 36–44% and 38% as active as AdoCbl in diol dehydratase [27,43,44] and glycerol dehydratase [44], respectively, but it serves as a strong competitive inhibitor for ethanolamine ammonia‐lyase [44] and ribonucleotide reductase [29] and a weak competitive inhibitor for methylmalonyl‐CoA mutase [44]. 2′‐DeoxyAdoCbl is 31%, 17%, and 5–13% as active as AdoCbl for diol dehydratase [38,45], glycerol dehydratase [41], and ribonucleotide reductase [29,35], respectively, but shows only 1–2% activity for methylmalonyl‐CoA mutase [46] or no activity for glutamate mutase [45]. Two series of AdoCbl analogues are of special interest.…”

Section: Discussionmentioning

confidence: 99%

Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B₁₂‐dependent diol dehydratase and ethanolamine ammonia‐lyase

et al. 2005

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AdoCbl participates as coenzyme for the enzymes that catalyze carbon skeleton rearrangements, heteroatom eliminations, and intramolecular amino group migrations [1][2][3]. For example, diol dehydratase (EC 4.2.1.28) and ethanolamine ammonia-lyase (EC 4.3.1.7) catalyze the dehydration of 1,2-diols and the deamination of ethanolamine to the corresponding aldehydes, respectively [4][5][6]. These reactions proceed by a radical mechanism, and an essential early event in all the AdoCbl-dependent rearrangements is the generation of a catalytic radical (adenosyl radical) by homolytic cleavage of the coenzyme's Co-C bond [1,7].Recently, the X-ray structures of several AdoCbldependent enzymes have been solved in complexes with cobalamins [8][9][10][11][12][13]. Spatial isolation of the radical intermediates in the active site cavity seems to be the common strategy for the so-called 'negative catalysis' of the Re´tey's concept [14]. The interactions of the coenzyme's adenine moiety with enzymes were revealed with methylmalonyl-CoA mutase [15,16] [x-(Adenosyl)alkyl]cobalamins (homoadenosylcobalamins) are useful analogues of adenosylcobalamin to get information about the distance between Co and C5¢, which is critical for Co-C bond activation. In order to use them as probes for exploring the active sites of enzymes, the coenzymic properties of homoadenosylcobalamins for diol dehydratase and ethanolamine ammonia-lyase were investigated. The k cat and k cat ⁄ K m values for adenosylmethylcobalamin were about 0.27% and 0.15% that for the regular coenzyme with diol dehydratase, respectively. The k cat ⁄ k inact value showed that the holoenzyme with this analogue becomes inactivated on average after about 3000 catalytic turnovers, indicating that the probability of inactivation during catalysis is almost 500 times higher than that for the regular holoenzyme. The k cat value for adenosylmethylcobalamin was about 0.13% that of the regular coenzyme for ethanolamine ammonialyase, as judged from the initial velocity, but the holoenzyme with this analogue underwent inactivation after on average about 50 catalytic turnovers. This probability of inactivation is 3800 times higher than that for the regular holoenzyme. When estimated from the spectra of reacting holoenzymes, the steady state concentration of cob(II)alamin intermediate from adenosylmethylcobalamin was very low with either diol dehydratase or ethanolamine ammonia-lyase, which is consistent with its extremely low coenzymic activity. In contrast, neither adenosylethylcobalamin nor adeninylpentylcobalamin served as active coenzyme for either enzyme and did not undergo Co-C bond cleavage upon binding to apoenzymes. AbbreviationsAdoCbl, adenosylcobalamin or coenzyme B 12 ; AdoEtCbl, adenosylethylcobalamin; AdoMeCbl, adenosylmethylcobalamin or homocoenzyme B 12 ; AdePeCbl, adeninylpentylcobalamin.

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Section: Discussionmentioning

confidence: 99%

Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B₁₂‐dependent diol dehydratase and ethanolamine ammonia‐lyase

et al. 2005

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“…The i-D-ribofuranose ring itself, possibly its rigid structure, is essential for activity [115]. The importance of the functional groups of the ribose moiety decreases in the order i-D-ribofuranose ring 3%-OH\2%-OH\-O- [115]. Formation of Cbl II during catalysis was spectroscopically observed with active analogues, but not with inactive ones.…”

Section: Formation Of a Catalytic Radical By Homolysis Of The Co-c Bomentioning

confidence: 96%

“…Time courses of the diol dehydratase reaction with certain analogues of AdoCbl as coenzymes are not linear due to concomitant inactivation during catalysis [38,39,42,115,118]. This tendency is most marked with the imidazolyl and pyridyl trimethylene analogues with which the reaction ceases almost completely within about 2 and 8 min, respectively [39,118].…”

Section: Inactivation By Coenzyme Analoguesmentioning

confidence: 99%

“…The importance of the nitrogen atoms of the adenine moiety for manifestation of catalytic function and for activation (labilization) of the Co-C bond decreases in the order N-7 \6-NH 2 \N-3\N-1 [42,114]. The i-D-ribofuranose ring itself, possibly its rigid structure, is essential for activity [115]. The importance of the functional groups of the ribose moiety decreases in the order i-D-ribofuranose ring 3%-OH\2%-OH\-O- [115].…”

Section: Formation Of a Catalytic Radical By Homolysis Of The Co-c Bomentioning

confidence: 99%

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

Toraya

2000

Cellular and Molecular Life Sciences (CMLS)

154

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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“…The structure‐function study with diol dehydratase was the most extensive one conducted thus far with B 12 enzymes 34–37. To briefly summarize, the corrin ring including the peripheral amide side chains29 and the adenine ring of the adenosyl group28,38 are required for tight binding to the apoenzyme, and the ribosyl moiety of the adenosyl group is required for transmitting strains to the CoC bond 39. Thus, it was concluded that these components are indispensable for CoC bond activation, i.e., catalytic radical formation, by binding to the apoenzyme 35,36.…”

Section: Biochemical Studiesmentioning

confidence: 99%

Enzymatic Radical Catalysis: Coenzyme B₁₂‐Dependent Diol Dehydratase

Toraya

2002

The Chemical Record

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A peculiar function resides in a peculiar structure. Coenzyme B(12) or adenosylcobalamin, a naturally occurring organometallic compound, serves as a cofactor for enzymatic radical reactions. How do the enzymes form catalytic radicals at the active sites? How do the enzymes utilize and control the high reactivity of the radicals for catalysis? Recently, three-dimensional structures of several radical-containing or radical-forming enzymes including B(12) enzymes have been reported, enabling the analysis of the fine mechanisms of the action of these interesting enzymes. Our biochemical, mutational, and crystallographic studies as well as theoretical calculations on diol dehydratase, an adenosylcobalamin-dependent enzyme, revealed that its structure is adapted for its function-that is, activation of the Cobond;C bond toward homolysis, abstraction of a specific hydrogen atom from the substrate and its recombination to a particular product, and transition state stabilization in the hydroxyl group migration of a substrate-derived radical. The functions of K(+) and the active-site amino acid residues in enzyme catalysis are also investigated. Based on the results, the fine mechanism of the enzyme and the energetic feasibility of enzymatic radical catalysis are described here.

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Roles of β-d-ribofuranose ring and the functional groups of the d-ribose moiety of adenosylcobalamin in the diol dehydratase reaction

Cited by 13 publications

References 28 publications

Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B₁₂‐dependent diol dehydratase and ethanolamine ammonia‐lyase

Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B₁₂‐dependent diol dehydratase and ethanolamine ammonia‐lyase

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

Enzymatic Radical Catalysis: Coenzyme B₁₂‐Dependent Diol Dehydratase

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Roles of β-d-ribofuranose ring and the functional groups of the d-ribose moiety of adenosylcobalamin in the diol dehydratase reaction

Cited by 13 publications

References 28 publications

Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B12‐dependent diol dehydratase and ethanolamine ammonia‐lyase

Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B12‐dependent diol dehydratase and ethanolamine ammonia‐lyase

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

Enzymatic Radical Catalysis: Coenzyme B12‐Dependent Diol Dehydratase

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Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B₁₂‐dependent diol dehydratase and ethanolamine ammonia‐lyase

Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B₁₂‐dependent diol dehydratase and ethanolamine ammonia‐lyase

Enzymatic Radical Catalysis: Coenzyme B₁₂‐Dependent Diol Dehydratase