A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase

Shibata, Naoki; Masuda, Jun; Tobimatsu, Takamasa; Toraya, Tetsuo; Suto, Kyoko; Morimoto, Yukio; Yasuoka, Noritake

doi:10.1016/s0969-2126(99)80126-9

Cited by 239 publications

(359 citation statements)

References 40 publications

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“…These enzymatic reactions are subject to suicide inactivation by the substrate glycerol (54). More recently, the crystal structure of K. oxytoca diol dehydratase-cyanocobalamin complex was solved (55).…”

Section: Discussionmentioning

confidence: 99%

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum

Raynaud

Sarçabal

Meynial-Salles

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

207

160

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The genes encoding the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum VPI1718 were characterized from a molecular and a biochemical point of view. This operon is composed of three genes, dhaB1, dhaB2, and dhaT. When grown in a vitamin B12-free mineral medium with glycerol as carbon source, Escherichia coli expressing dhaB1, dhaB2, and dhaT produces 1,3-PD and high glycerol dehydratase and 1,3-PD dehydrogenase activities. dhaB1 and dhaB2 encode, respectively, a new type of glycerol dehydratase and its activator protein. The deduced proteins DhaB1 and DhaB2, with calculated molecular masses of 88,074 and 34,149 Da, respectively, showed no homology with the known glycerol dehydratases that are all B12 dependent but significant similarity with the pyruvate formate lyases and pyruvate formate lyases activating enzymes and their homologues. The 1,158-bp dhaT gene codes for a 1,3-PD dehydrogenase with a calculated molecular mass of 41,558 Da, revealing a high level of identity with other DhaT proteins from natural 1,3-PD producers. The expression of the 1,3-PD operon in C. butyricum is regulated at the transcriptional level, and this regulation seems to involve a two-component signal transduction system DhaAS͞DhaA, which may have a similar function to DhaR, a transcriptional regulator found in other natural 1,3-PD producers. The discovery of a glycerol dehydratase, coenzyme B12 independent, should significantly influence the development of an economical vitamin B12-free biological process for the production of 1,3-PD from renewable resources.

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Section: Discussionmentioning

confidence: 99%

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum

Raynaud

Sarçabal

Meynial-Salles

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

207

160

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“…A possible functional advantage of the presence of a purinyl base in complete corrinoid cofactors in their H-bonding base-on constitution may therefore not be dismissed. Indeed, diol-dehydratase and cobamidedependent ribonucleotide reductase are two enzymes that depend upon adenosylcobamides and which have been discovered lately to carry their corrinoid cofactors in the base-on form (1,48,63).…”

Section: Discussionmentioning

confidence: 99%

“…The relevance of the base-off-His-on mode of binding of corrinoids in cobamide-dependent enzymes (46,72) was supported further by two additional crystal structures, of methylmalonyl coenzyme A mutase (52) and glutamate mutase (58), which both depend upon an adenosylcobamide as a cofactor, such as coenzyme B 12 (5Ј-deoxy-5Ј-adenosylcobalamin). In contrast, the crystal structure of a diol dehydratase showed the bound coenzyme B 12 in its "classic" base-on constitution (63). Accordingly, questions concerning the effect of the nucleotide base on the binding the B 12 cofactors by their apoproteins (35,53,69) and on the mechanisms of B 12 -dependent enzymatic reactions have received more attention (15,43).…”

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confidence: 99%

Native Corrinoids fromClostridium cochleariumAre Adeninylcobamides: Spectroscopic Analysis and Identification of Pseudovitamin B₁₂and Factor A

et al. 2000

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The corrinoids from the obligate anaerobe Clostridium cochlearium were extracted as a mixture of Co ␤ -cyano derivatives. From 50 g of frozen cells, approximately 2 mg (1.5 mol) of B 12 derivatives was obtained as a crystalline sample. Analysis of the corrinoid sample of C. cochlearium by a combination of high-pressure liquid chromatography and UV-Vis absorbance spectroscopy revealed the presence of three cyano corrinoids in a ratio of about 3:1:1. The spectroscopic data acquired for the sample indicated the main components to be pseudovitamin B 12 (Co ␤ -cyano-7؆-adeninylcobamide) (60%) and factor A (Co ␤ -cyano-7؆-[2-methyl]adeninylcobamide) (20%). Authentic pseudovitamin B 12 was prepared by guided biosynthesis from cobinamide and adenine. Both pseudovitamin B 12 and its homologue, factor A, were subjected to complete spectroscopic analysis by UV-Vis, circular dichroism, mass spectrometry, and by one-and two-dimensional 1 H, 13 C-, and 15 N nuclear magnetic resonance (NMR) spectroscopy. The third component was indicated by the mass spectra to be an isomer of factor A and is likely (according to NMR) to be 7؆-[N 6 -methyl]-adeninylcobamide, a previously unknown corrinoid. C. cochlearium thus biosynthesizes as its native "complete" B 12 cofactors the 7؆-adeninylcobamides and two homologous corrinoids, in which the nucleotide base is a methylated adenine.

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“…The structure reveals that AdoCbl is bound by a Rossmann domain and that PLP, which is tethered to the B 12 -binding domain by means of its imine linkage, is bound in the putative active site, at the top of a triosephosphate isomerase (TIM) barrel domain. Thus, 5,6-LAM joins a group of three other AdoCbl-dependent radical enzymes (GM, MCM, and diol dehydratase) (19)(20)(21) and one AdoMet-dependent radical enzyme (biotin synthase) (22) in using the TIM barrel fold to sequester substrates that form free-radical intermediates. Our structure is distinctive among all PLP-dependent enzymes in that Abbreviations: AdoCbl, adenosylcobalamin or coenzyme B12; Ado, adenosyl group; Ado • , 5Ј-deoxyadenosyl radical; AdoH, 5Ј-deoxyadenosine; AdoMet, S-adenosylmethionine; Cbl, cobalamin; DMB, dimethylbenzimidazole; GM, glutamate mutase; 5,6-LAM, lysine 5,6-aminomutase; 2,3-LAM, lysine 2,3-aminomutase; MCM, methylmalonyl-coenzyme A mutase; PLP, pyridoxal 5Ј-phosphate; TIM, triosephosphate isomerase.…”

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confidence: 99%

A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase

Berkovitch

Behshad

Tang

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

105

109

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Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5 -phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of DL-lysine and of L-␤-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5 -phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, Ϸ25 Å from the active site. In this mode of pyridoxal-5 -phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5 -phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.A denosylcobalamin (AdoCbl; coenzyme B 12 ) is nature's biochemical radical reservoir, capable of catalyzing challenging chemical reactions by way of H atom abstraction and the generation of free-radical intermediates (1-3). AdoCbldependent isomerases catalyze 1,2 shifts between an H atom and a functional group such as -OH, -NH 3 ϩ , -(CO)S-coenzyme A, or other carbon-based groups. The catalytic power of AdoCbl lies in the homolytic cleavage of its weak (Ϸ30 kcal͞mol) organometallic C-Co bond, formed between an octahedral Co(III) center with five N coordinations and a 5Ј-deoxyadenosyl (Ado) axial ligand. C-Co bond homolysis results in the transient formation of cob(II)alamin and 5Ј-deoxyadenosyl radical (Ado • ). Ado • abstracts an H atom from the substrate, forming a substrate radical and 5Ј-deoxyadenosine (AdoH). To close the catalytic cycle, substrate reabstracts the H atom from AdoH, and recombination of cob(II)alamin and Ado • accompanies product formation. Amazingly, the enzymatic rate of C-Co bond homolysis is enhanced by a factor of Ϸ10 12 over nonenzymatic homolysis (4, 5). AdoCbl-dependent isomerases are often present in catabolic pathways and can serve to rearrange the substrate's carbon skeleton and͞or functional groups for further degradation. One such pathway that operates in several bacterial species is the fermentation of lysine to yield acetate. Interestingly, the lysine fermentation pathway contains two analogous enzymes: lysine 5,6-aminomutase (5,6-LAM), which is AdoCbl-dependent (6, 7), and lysine 2,3-aminomutase (2,3-LAM), which is an S-adenosylmethionine (AdoMet or SAM)-dependent ironsulfur enzyme (8-10). Both enzymes require pyridoxal 5Ј-phosphate (PLP) (8, 11) in addition to AdoCbl or AdoMet, and both catalyze a 1,2 amino group shift with concomitant H atom migration (Fig. 1A). In 5,6-LAM, AdoCbl is the source of the transient Ado • , whereas, in 2,3-L...

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A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase

Cited by 239 publications

References 40 publications

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum

Native Corrinoids fromClostridium cochleariumAre Adeninylcobamides: Spectroscopic Analysis and Identification of Pseudovitamin B₁₂and Factor A

A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase

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A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase

Cited by 239 publications

References 40 publications

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum

Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum

Native Corrinoids fromClostridium cochleariumAre Adeninylcobamides: Spectroscopic Analysis and Identification of Pseudovitamin B12and Factor A

A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase

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About

Native Corrinoids fromClostridium cochleariumAre Adeninylcobamides: Spectroscopic Analysis and Identification of Pseudovitamin B₁₂and Factor A