Decarboxylation involving a ferryl, propionate, and a tyrosyl group in a radical relay yields heme b

Streit, Bennett R.; Celis, Arianna I.; Moraski, Garrett C.; Shisler, Krista A.; Shepard, Eric M.; Rodgers, Kenton R.; Lukat-Rodgers, Gudrun S.; DuBois, Jennifer L.

doi:10.1074/jbc.ra117.000830

Cited by 27 publications

(46 citation statements)

References 39 publications

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“…Thus, the most likely origin of the radical is a protein amino acid residue. The EPR signal of the radical is very similar to that of the tyrosyl radical in other proteins . Additionally, we could simulate the spectrum (Figure D) by using g values, linewidths and hyperfine coupling constants similar to those reported for tyrosyl radicals in other proteins (Table ).…”

Section: Resultsmentioning

confidence: 52%

Mechanism of Diol Dehydration by a Promiscuous Radical‐SAM Enzyme Homologue of the Antiviral Enzyme Viperin (RSAD2)

et al. 2020

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has made ap rovisionalp atent application based on the discoveries demonstrated in this manuscript.Keywords: antiviral agents · nucleotide analogues · radical-SAM enzyme · tyrosyl radicals · viperin Figure 6. The proposed mechanism of catalysis by TtRSAD2. The 5'-dAdo radicalabstractst he Ha tom (red) at the C4' position of ribose to generate a C4'-centred radical intermediate. As ar esult of hyperconjugation between a po rbitalonC 4' and the s C3'ÀO3' orbital, assisted by ap rotein amino acid residue( AH), the 3'-OHg roupo ft he riboseforms awater molecule. The proton to generate the water molecule is provided by tyrosine either indirectly through ap roton hoppingp athway(1) or directly (2). Spontaneously, an electron from tyrosine reduces the substrate-radical intermediate. As a result, the nucleotide analogue product and ap rotein tyrosylradical are formed. The [4 FeÀ4S] 2 + clusteri sre-reduced and then,t he tyrosyl radicali s reducedbya ne lectron from the [4 FeÀ4S] + cluster.

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Section: Resultsmentioning

confidence: 52%

Mechanism of Diol Dehydration by a Promiscuous Radical‐SAM Enzyme Homologue of the Antiviral Enzyme Viperin (RSAD2)

et al. 2020

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“…6 Successively, transient formation of • Y147 was confirmed by electron paramagnetic resonance (EPR) spectroscopy. 11 While the proposed mechanism of the first propionyl decarboxylation (p2) is generally accepted (although experimental evidence for compound I formation is missing), the second decarboxylation reaction at the p4 position is still an open question. DuBois and co-workers proposed that decarboxylation of p4 may involve residues in the vicinity of p4, namely K151, W200, W159, and Y113 (LmChdC numbering).…”

Section: Introductionmentioning

confidence: 99%

“…6 Since the catalytic tyrosine was shown to be essential for both decarboxylation reactions, a possible mechanism involving substrate reorientation has been suggested recently. 11…”

Section: Introductionmentioning

confidence: 99%

Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme b

et al. 2019

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Coproheme decarboxylase (ChdC) catalyzes the last step in the heme biosynthesis pathway of monoderm bacteria with coproheme acting both as redox cofactor and substrate. Hydrogen peroxide mediates the stepwise decarboxylation of propionates 2 and 4 of coproheme. Here we present the crystal structures of coproheme-loaded ChdC from Listeria monocytogenes (LmChdC) and the three-propionate intermediate, for which the propionate at position 2 (p2) has been converted to a vinyl group and is rotated by 90° compared to the coproheme complex structure. Single, double, and triple mutants of LmChdC, in which H-bonding interactions to propionates 2, 4, 6, and 7 were eliminated, allowed us to obtain the assignment of the coproheme propionates by resonance Raman spectroscopy and to follow the H 2 O 2 -mediated conversion of coproheme to heme b . Substitution of H 2 O 2 by chlorite allowed us to monitor compound I formation in the inactive Y147H variant which lacks the catalytically essential Y147. This residue was demonstrated to be oxidized during turnover by using the spin-trap 2-methyl-2-nitrosopropane. Based on these findings and the data derived from molecular dynamics simulations of cofactor structures in distinct poses, we propose a reaction mechanism for the stepwise decarboxylation of coproheme that includes a 90° rotation of the intermediate three-propionate redox cofactor.

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“…In wild-type LmChdC Compound I does not accumulate due to conversion into Compound I* [oxoiron(IV) Y147 ● ], which attacks p2 and initiates the radicalic decarboxylation reaction. It is important to recall that substitution of Y147 by alanine completely inactivates all the ChdCs studied so far [7,8].…”

Section: Discussionmentioning

confidence: 99%

“…oxoiron(IV) porphyryl radical]. Formation of the tyrosyl radical is essential for decarboxylation of both p2 and p4 [8]. A lysine residue, which is H-bonded to p4 was also shown to be important (but not essential) for the catalytic reaction [9] (Fig.…”

Section: Introductionmentioning

confidence: 99%

The hydrogen bonding network of coproheme in coproheme decarboxylase from Listeria monocytogenes: Effect on structure and catalysis

Milazzo

Gabler

Pfanzagl

et al. 2019

Journal of Inorganic Biochemistry

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Coproheme decarboxylase (ChdC) catalyzes the oxidative decarboxylation of coproheme to heme b , i.e. the last step in the recently described coproporphyrin-dependent pathway. Coproheme decarboxylation from Listeria monocytogenes is a robust enzymatic reaction of low catalytic efficiency. Coproheme acts as both substrate and redox cofactor activated by H 2 O 2 . It fully depends on the catalytic Y147 close to the propionyl group at position 2. In the present study we have investigated the effect of disruption of the comprehensive and conserved hydrogen bonding network between the four propionates and heme cavity residues on (i) the conformational stability of the heme cavity, (ii) the electronic configuration of the ferric redox cofactor/substrate, (iii) the binding of carbon monoxide and, (iv) the decarboxylation reaction mediated by addition of H 2 O 2 . Nine single, double and triple mutants of ChdC from Listeria monocytogenes were produced in E. coli . The respective coproheme- and heme b -complexed proteins were studied by UV–Vis, resonance Raman, circular dichroism spectroscopy, and mass spectrometry. Interactions of propionates 2 and 4 with residues in the hydrophobic cavity are crucial for maintenance of the heme cavity architecture, for the mobile distal glutamine to interact with carbon monoxide, and to keep the heme cavity in a closed conformation during turnover. By contrast, the impact of substitution of residues interacting with solvent exposed propionates 6 and 7 was negligible. Except for Y147A and K151A all mutant ChdCs exhibited a wild-type-like catalytic activity. The findings are discussed with respect to the structure-function relationships of ChdCs.

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Decarboxylation involving a ferryl, propionate, and a tyrosyl group in a radical relay yields heme b

Cited by 27 publications

References 39 publications

Mechanism of Diol Dehydration by a Promiscuous Radical‐SAM Enzyme Homologue of the Antiviral Enzyme Viperin (RSAD2)

Mechanism of Diol Dehydration by a Promiscuous Radical‐SAM Enzyme Homologue of the Antiviral Enzyme Viperin (RSAD2)

Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme b

The hydrogen bonding network of coproheme in coproheme decarboxylase from Listeria monocytogenes: Effect on structure and catalysis

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