Lysine 2,3-Aminomutase

Baraniak, Janina; Moss, Marcia L.; Frey, Perry A.

doi:10.1016/s0021-9258(18)94194-3

Cited by 91 publications

(46 citation statements)

References 10 publications

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“…A related radical formation involving reductive cleavage of SAM in anaerobic bacteria has also been established for lysine 2,3-aminomutase from Clostridium SB4. In this case, a postulated adenosyl radical intermediate is believed to function catalytically as a Bn surrogate (Baraniak et al, 1989; Moss & Frey, 1987). In addition, transient radical intermediates generated subsequent to the cleavage of SAM have been observed by EPR (Ballinger et al, 1992).…”

Section: Discussionmentioning

confidence: 99%

Molecular properties of pyruvate formate-lyase activating enzyme

Wong

Murray²,

Lewisch³

et al. 1993

Biochemistry

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Pyruvate formate-lyase is a radical-containing enzyme that catalyzes the nonoxidative cleavage of pyruvate via a postulated homolytic mechanism. The formation of this enzymic radical in vitro requires an activating system composed of PFL-activating enzyme, S-adenosylmethionine, ferrous ion, a reduced flavin, DTT, and pyruvate as an allosteric effector. The need for large quantities of PFL-activating enzyme for biochemical and biophysical studies on the mechanism of protein radical formation has prompted us to clone the act gene and overexpress the gene product in Escherichia coli. Using PCR technology, the act gene was isolated and subcloned into various expression vectors. The overexpression of the protein was as high as 30-50% of the total cellular protein. However, the majority of the protein resided in the form of insoluble inclusion bodies. A procedure was developed to denature and isolate the inclusion bodies followed by refolding under anaerobic conditions. This purification method affords 5 mg of purified protein from 1 g of cells. Biochemical characterization demonstrated that the enzyme can bind one Fe(II) per protein monomer, and the protein did not exhibit any visible chromophore as previously observed. Co(II) and Cu(II) can be reconstituted into the protein with similar stoichiometries. Kinetic studies showed that the rate of radical formation was independent of ionic strength and the Km's for SAM and inactive PFL were determined to be 2.8 and 1.2 microM, respectively. Fluorescent binding data revealed that the Kd for SAM binding to the activating enzyme alone was comparable to the Km for SAM in the PFL activation indicating that the binding site for SAM resides on AE.(ABSTRACT TRUNCATED AT 250 WORDS)

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Section: Discussionmentioning

confidence: 99%

Molecular properties of pyruvate formate-lyase activating enzyme

Wong

Murray²,

Lewisch³

et al. 1993

Biochemistry

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“…However, there is some precedent for this idea based on the recent characterization of the 2OG‐dependent dioxygenase TqaL, which produces an aziridine intermediate during the biosynthesis of 2‐aminoisobutyrate, although by a mechanism that is distinct from that we envision for DfmD [35] . The radical SAM enzyme lysine 2,3‐amino mutase is also believed to utilize an aziridine intermediate [36] . The proposed DfmD‐catalyzed rearrangement would begin by hydrogen atom transfer from one of the trimethyl groups, which is positioned 4.6 Å above the Fe II , in the homology model.…”

Section: Resultsmentioning

confidence: 99%

“…[35] The radical SAM enzyme lysine 2,3-amino mutase is also believed to utilize an aziridine intermediate. [36] The proposed DfmD-catalyzed rearrangement would begin by hydrogen atom transfer from one of the trimethyl groups, which is positioned 4.6 Å above the Fe II , in the homology model. Support for this initial reaction is provided by the strong isotope effect of deuterated N-methyl groups, which we showed prevents the rearrangement, but not the desaturation.…”

Section: Resultsmentioning

confidence: 99%

An Unusual Oxidative Rearrangement Catalyzed by a Divergent Member of the 2‐Oxoglutarate‐Dependent Dioxygenase Superfamily during Biosynthesis of Dehydrofosmidomycin

et al. 2022

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The biosynthesis of the natural product dehydrofosmidomycin involves an unusual transformation in which 2‐(trimethylamino)ethylphosphonate is rearranged, desaturated and demethylated by the enzyme DfmD, a divergent member of the 2‐oxoglutarate‐dependent dioxygenase superfamily. Although other members of this enzyme family catalyze superficially similar transformations, the combination of all three reactions in a single enzyme has not previously been observed. By characterizing the products of in vitro reactions with labeled and unlabeled substrates, we show that DfmD performs this transformation in two steps, with the first involving desaturation of the substrate to form 2‐(trimethylamino)vinylphosphonate, and the second involving rearrangement and demethylation to form methyldehydrofosmidomycin. These data reveal significant differences from the desaturation and rearrangement reactions catalyzed by other family members.

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“…Most isomerization reactions require the use of AdoCbl as a coenzyme, but 2,3-LAM uses AdoMet and a [4Fe-4S] + cluster to mediate hydrogen transfer by radical propagation. Since AdoMet is not as easily cleaved as AdoCbl, the iron-sulfur cluster is needed as an electron source to convert AdoMet into methionine and an Ado radical ( Baraniak et al, 1989 ; Ballinger et al, 1992 ). Because of the essential nature of the iron-sulfur cluster, 2,3-LAM is catalytically limited by cluster formation and reduction to the +1 state.…”

Section: Diverse Plp-dependent Proteins and Their Allosteric Mechanismsmentioning

confidence: 99%

Structural Basis for Allostery in PLP-dependent Enzymes

Tran

Brown

2022

Front. Mol. Biosci.

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Pyridoxal 5′-phosphate (PLP)-dependent enzymes are found ubiquitously in nature and are involved in a variety of biological pathways, from natural product synthesis to amino acid and glucose metabolism. The first structure of a PLP-dependent enzyme was reported over 40 years ago, and since that time, there is a steady wealth of structural and functional information revealed for a wide array of these enzymes. A functional mechanism that is gaining more appreciation due to its relevance in drug design is that of protein allostery, where binding of a protein or ligand at a distal site influences the structure, organization, and function at the active site. Here, we present a review of current structure-based mechanisms of allostery for select members of each PLP-dependent enzyme family. Knowledge of these mechanisms may have a larger potential for identifying key similarities and differences among enzyme families that can eventually be exploited for therapeutic development.

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Lysine 2,3-Aminomutase

Cited by 91 publications

References 10 publications

Molecular properties of pyruvate formate-lyase activating enzyme

Molecular properties of pyruvate formate-lyase activating enzyme

An Unusual Oxidative Rearrangement Catalyzed by a Divergent Member of the 2‐Oxoglutarate‐Dependent Dioxygenase Superfamily during Biosynthesis of Dehydrofosmidomycin

Structural Basis for Allostery in PLP-dependent Enzymes

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