Crystal Structure of Precorrin-8x Methyl Mutase

Shipman, Lance W.; Ding, Li; Roessner, Charles A.; Scott, A. Ian; Sacchettini, James C.

doi:10.1016/s0969-2126(01)00618-9

Cited by 36 publications

(28 citation statements)

References 31 publications

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“…Several possible pericyclic enzymatic reactions include the [3,3]-sigmatropy (the Claisen rearrangement) in chorismate mutase (CM) 27 , the [1,5]-hydrogen shift in isochorismate pyruvate lyase 28, 29 , and the [1,5]-sigmatropic shift of the methyl group in precorrin-8x methyl mutase (CobH) 30 . The reaction mechanisms of CM and CobH have been elucidated on the basis of X-ray crystallographic studies 27, 30 .…”

Section: Discussionmentioning

confidence: 99%

“…The reaction mechanisms of CM and CobH have been elucidated on the basis of X-ray crystallographic studies 27, 30 . The most distinguishing feature of a concerted pericyclic reaction is that it does not require catalytic groups to promote the reaction.…”

Section: Discussionmentioning

confidence: 99%

“…In agreement with this feature, there were no functional groups such as an acid or a base in the active site of CM. However, the [1,5]-sigmatropy in CobH is enhanced by protonation of the nitrogen atom in the diene moiety 30 . We therefore expect that similar protonation at the Nα-imino nitrogen in the possible precursor of intermediate 4 could facilitate the [1,5]-hydrogen shift.…”

Section: Discussionmentioning

confidence: 99%

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X-Ray snapshots of a pyridoxal enzyme: a catalytic mechanism involving concerted [1,5]-hydrogen sigmatropy in methionine γ-lyase

Sato

Shiba

Karaki

et al. 2017

Sci Rep

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Pyridoxal 5′-phosphate (PLP)-enzymes are essentially involved in amino acid and amine metabolism of a wide variety of organisms. Despite their extensive biochemical studies, there are little evidence and structural data to comprehensively elaborate the catalytic mechanism. We obtained X-ray snapshots of l-methionine γ-lyase from Entamoeba histolytica (EhMGL), a PLP-enzyme catalyzing the γ-elimination reaction of methionine. Here, we suggest a catalytic mechanism of EhMGL by using the X-ray snapshots covering all stages of this multistep catalysis reaction. Initial formation of a Michaelis complex is followed by the migration of double bond from the C4′=Nα–Cα moiety in an intermediate PLP-methionine imine to C4′–Nα=Cα in pyridoxamine 5′-phosphate (PMP)-α,β-dehydromethionine imine without intervention of a putative quinonoid intermediate. The enzyme can facilitate the subsequent γ-elimination of methanethiol by the possible general acid-base catalysis of Tyr108 for the E1cB mechanism, enabling to form the ene-imine C4′–Nα=Cα–Cβ=Cγ structure with the s-cis conformation, which is prerequisite for the non-enzymatic symmetry-allowed suprafacial [1,5]-hydrogen shift to complete the catalytic cycle by releasing α-ketobutyrate. The mechanism based on the X-ray snapshots is consistent with the reactivity of MGL toward methionine analogues. The generality of such a mechanism involving non-enzymatic concerted reaction in other PLP enzymes is discussed.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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X-Ray snapshots of a pyridoxal enzyme: a catalytic mechanism involving concerted [1,5]-hydrogen sigmatropy in methionine γ-lyase

Sato

Shiba

Karaki

et al. 2017

Sci Rep

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“…It suggests that dimerization is necessary for having biological function in CbiC/CobH family. Two identical cavities formed by two CbiC/CobH molecules in a dimer are also essential for their substrates binding (Shipman et al, 2001).…”

Section: Structure Overviewmentioning

confidence: 99%

“…2A and C). Recently, the complex structure of Pseudomonas denitrificans CobH (CobH_PSEDE) binding with hydrogenobyrinic acid (HBA), which is the product of the reaction catalyzed by CobH, has been solved (Shipman et al, 2001). This structure shows that the cavities supply the binding surface for the substrates.…”

Section: Comparison With Other Cbic/cobhmentioning

confidence: 99%

The crystal structure of putative precorrin isomerase CbiC in cobalamin biosynthesis

Xue

Wei

et al. 2006

Journal of Structural Biology

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Synthetic Biology in Metabolic Engineering: From Complex Biochemical Pathways to Compartmentalized Metabolic Processes - a Vitamin Connection

Deery

Frank

Lawrence

et al. 2014

Encyclopedia of Molecular Cell Biology and Molecular Medicine

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Crystal Structure of Precorrin-8x Methyl Mutase

Abstract: Analysis of the structure with bound product suggests that the [1,5]-sigmatropic shift proceeds by protonation of the ring C nitrogen, leading to subsequent methyl migration.

Cited by 36 publications

References 31 publications

X-Ray snapshots of a pyridoxal enzyme: a catalytic mechanism involving concerted [1,5]-hydrogen sigmatropy in methionine γ-lyase

X-Ray snapshots of a pyridoxal enzyme: a catalytic mechanism involving concerted [1,5]-hydrogen sigmatropy in methionine γ-lyase

The crystal structure of putative precorrin isomerase CbiC in cobalamin biosynthesis

Synthetic Biology in Metabolic Engineering: From Complex Biochemical Pathways to Compartmentalized Metabolic Processes - a Vitamin Connection

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