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Articles de revues sur le sujet « Coproheme Decarboxylase »

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Auteur : Grafiati
Publié le 10 mars 2023

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1

Zhang, Ying, Junkai Wang, Chang Yuan, Wei Liu, Hongwei Tan, Xichen Li et Guangju Chen. « Ruffling drives coproheme decarboxylation by facilitating PCET : a theoretical investigation of ChdC ». Physical Chemistry Chemical Physics 22, no 28 (2020) : 16117–24. http://dx.doi.org/10.1039/d0cp02690e.

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Coproheme decarboxylase (ChdC) is an essential enzyme in the coproporphyrin-dependent heme synthesis pathway, which catalyzes oxidative decarboxylation of coproheme at the positions p2 and p4 to generate heme b under the action of hydrogen peroxide.
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Liu, Wei, Yunjie Pang, Yutian Song, Xichen Li, Hongwei Tan et Guangju Chen. « Reorienting Mechanism of Harderoheme in Coproheme Decarboxylase—A Computational Study ». International Journal of Molecular Sciences 23, no 5 (25 février 2022) : 2564. http://dx.doi.org/10.3390/ijms23052564.

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Coproheme decarboxylase (ChdC) is an important enzyme in the coproporphyrin-dependent pathway (CPD) of Gram-positive bacteria that decarboxylates coproheme on two propionates at position 2 and position 4 sequentially to generate heme b by using H2O2 as an oxidant. This work focused on the ChdC from Geobacillus stearothermophilus (GsChdC) to elucidate the mechanism of its sequential two-step decarboxylation of coproheme. The models of GsChdC in a complex with substrate and reaction intermediate were built to investigate the reorienting mechanism of harderoheme. Targeted molecular dynamics simulations on these models validated that harderoheme is able to rotate in the active site of GsChdC with a 19.06-kcal·mol−1 energy barrier after the first step of decarboxylation to bring the propionate at position 4 in proximity of Tyr145 to continue the second decarboxylation step. The harderoheme rotation mechanism is confirmed to be much easier than the release–rebinding mechanism. In the active site of GsChdC, Trp157 and Trp198 comprise a “gate” construction to regulate the clockwise rotation of the harderoheme. Lys149 plays a critical role in the rotation mechanism, which not only keeps the Trp157–Trp198 “gate” from being closed but also guides the propionate at position 4 through the gap between Trp157 and Trp198 through a salt bridge interaction.
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Sebastiani, Federico, Chiara Baroni, Gaurav Patil, Andrea Dali, Maurizio Becucci, Stefan Hofbauer et Giulietta Smulevich. « The Role of the Hydrogen Bond Network in Maintaining Heme Pocket Stability and Protein Function Specificity of C. diphtheriae Coproheme Decarboxylase ». Biomolecules 13, no 2 (25 janvier 2023) : 235. http://dx.doi.org/10.3390/biom13020235.

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Monoderm bacteria accumulate heme b via the coproporphyrin-dependent biosynthesis pathway. In the final step, in the presence of two molecules of H2O2, the propionate groups of coproheme at positions 2 and 4 are decarboxylated to form vinyl groups by coproheme decarboxylase (ChdC), in a stepwise process. Decarboxylation of propionate 2 produces an intermediate that rotates by 90° inside the protein pocket, bringing propionate 4 near the catalytic tyrosine, to allow the second decarboxylation step. The active site of ChdCs is stabilized by an extensive H-bond network involving water molecules, specific amino acid residues, and the propionate groups of the porphyrin. To evaluate the role of these H-bonds in the pocket stability and enzyme functionality, we characterized, via resonance Raman and electronic absorption spectroscopies, single and double mutants of the actinobacterial pathogen Corynebacterium diphtheriae ChdC complexed with coproheme and heme b. The selective elimination of the H-bond interactions between propionates 2, 4, 6, and 7 and the polar residues of the pocket allowed us to establish the role of each H-bond in the catalytic reaction and to follow the changes in the interactions from the substrate to the product.
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Milazzo, Lisa, Thomas Gabler, Vera Pfanzagl, Hanna Michlits, Paul G. Furtmüller, Christian Obinger, Stefan Hofbauer et Giulietta Smulevich. « The hydrogen bonding network of coproheme in coproheme decarboxylase from Listeria monocytogenes : Effect on structure and catalysis ». Journal of Inorganic Biochemistry 195 (juin 2019) : 61–70. http://dx.doi.org/10.1016/j.jinorgbio.2019.03.009.

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5

Milazzo, Lisa, Stefan Hofbauer, Barry D. Howes, Thomas Gabler, Paul G. Furtmüller, Christian Obinger et Giulietta Smulevich. « Insights into the Active Site of Coproheme Decarboxylase from Listeria monocytogenes ». Biochemistry 57, no 13 (14 mars 2018) : 2044–57. http://dx.doi.org/10.1021/acs.biochem.8b00186.

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Streit, Bennett R., Arianna I. Celis, Krista Shisler, Kenton R. Rodgers, Gudrun S. Lukat-Rodgers et Jennifer L. DuBois. « Reactions of Ferrous Coproheme Decarboxylase (HemQ) with O2 and H2O2 Yield Ferric Heme b ». Biochemistry 56, no 1 (16 décembre 2016) : 189–201. http://dx.doi.org/10.1021/acs.biochem.6b00958.

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Sebastiani, Federico, Riccardo Risorti, Chiara Niccoli, Hanna Michlits, Maurizio Becucci, Stefan Hofbauer et Giulietta Smulevich. « An active site at work – the role of key residues in C. diphteriae coproheme decarboxylase ». Journal of Inorganic Biochemistry 229 (avril 2022) : 111718. http://dx.doi.org/10.1016/j.jinorgbio.2022.111718.

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8

Celis, Arianna I., George H. Gauss, Bennett R. Streit, Krista Shisler, Garrett C. Moraski, Kenton R. Rodgers, Gudrun S. Lukat-Rodgers, John W. Peters et Jennifer L. DuBois. « Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ) ». Journal of the American Chemical Society 139, no 5 (27 janvier 2017) : 1900–1911. http://dx.doi.org/10.1021/jacs.6b11324.

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9

Tian, Ge, Gangping Hao, Xiaohua Chen et Yongjun Liu. « Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET : Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC ». Inorganic Chemistry 60, no 17 (12 août 2021) : 13539–49. http://dx.doi.org/10.1021/acs.inorgchem.1c01864.

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10

Pfanzagl, Vera, Laurenz Holcik, Daniel Maresch, Giulia Gorgone, Hanna Michlits, Paul G. Furtmüller et Stefan Hofbauer. « Coproheme decarboxylases - Phylogenetic prediction versus biochemical experiments ». Archives of Biochemistry and Biophysics 640 (février 2018) : 27–36. http://dx.doi.org/10.1016/j.abb.2018.01.005.

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11

Dailey, Harry A., Svetlana Gerdes, Tamara A. Dailey, Joseph S. Burch et John D. Phillips. « Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin ». Proceedings of the National Academy of Sciences 112, no 7 (2 février 2015) : 2210–15. http://dx.doi.org/10.1073/pnas.1416285112.

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It has been generally accepted that biosynthesis of protoheme (heme) uses a common set of core metabolic intermediates that includes protoporphyrin. Herein, we show that the Actinobacteria and Firmicutes (high-GC and low-GC Gram-positive bacteria) are unable to synthesize protoporphyrin. Instead, they oxidize coproporphyrinogen to coproporphyrin, insert ferrous iron to make Fe-coproporphyrin (coproheme), and then decarboxylate coproheme to generate protoheme. This pathway is specified by three genes namedhemY,hemH, andhemQ. The analysis of 982 representative prokaryotic genomes is consistent with this pathway being the most ancient heme synthesis pathway in the Eubacteria. Our results identifying a previously unknown branch of tetrapyrrole synthesis support a significant shift from current models for the evolution of bacterial heme and chlorophyll synthesis. Because some organisms that possess this coproporphyrin-dependent branch are major causes of human disease, HemQ is a novel pharmacological target of significant therapeutic relevance, particularly given high rates of antimicrobial resistance among these pathogens.
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Michlits, Hanna, Bettina Lier, Vera Pfanzagl, Kristina Djinović-Carugo, Paul G. Furtmüller, Chris Oostenbrink, Christian Obinger et Stefan Hofbauer. « Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation ». ACS Catalysis 10, no 10 (9 avril 2020) : 5405–18. http://dx.doi.org/10.1021/acscatal.0c00411.

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13

Hobbs, Charlie, Harry A. Dailey et Mark Shepherd. « The HemQ coprohaem decarboxylase generates reactive oxygen species : implications for the evolution of classical haem biosynthesis ». Biochemical Journal 473, no 21 (27 octobre 2016) : 3997–4009. http://dx.doi.org/10.1042/bcj20160696.

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Bacteria require a haem biosynthetic pathway for the assembly of a variety of protein complexes, including cytochromes, peroxidases, globins, and catalase. Haem is synthesised via a series of tetrapyrrole intermediates, including non-metallated porphyrins, such as protoporphyrin IX, which is well known to generate reactive oxygen species in the presence of light and oxygen. Staphylococcus aureus has an ancient haem biosynthetic pathway that proceeds via the formation of coproporphyrin III, a less reactive porphyrin. Here, we demonstrate, for the first time, that HemY of S. aureus is able to generate both protoporphyrin IX and coproporphyrin III, and that the terminal enzyme of this pathway, HemQ, can stimulate the generation of protoporphyrin IX (but not coproporphyrin III). Assays with hydrogen peroxide, horseradish peroxidase, superoxide dismutase, and catalase confirm that this stimulatory effect is mediated by superoxide. Structural modelling reveals that HemQ enzymes do not possess the structural attributes that are common to peroxidases that form compound I [FeIV==O]+, which taken together with the superoxide data leaves Fenton chemistry as a likely route for the superoxide-mediated stimulation of protoporphyrinogen IX oxidase activity of HemY. This generation of toxic free radicals could explain why HemQ enzymes have not been identified in organisms that synthesise haem via the classical protoporphyrin IX pathway. This work has implications for the divergent evolution of haem biosynthesis in ancestral microorganisms, and provides new structural and mechanistic insights into a recently discovered oxidative decarboxylase reaction.
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14

Michlits, Hanna, Nina Valente, Georg Mlynek et Stefan Hofbauer. « Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes ». Frontiers in Bioengineering and Biotechnology 9 (24 janvier 2022). http://dx.doi.org/10.3389/fbioe.2021.807678.

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The oxidative decarboxylation of coproheme to form heme b by coproheme decarboxylase is a stereospecific two-step reaction. In the first step, the propionate at position two (p2) is cleaved off the pyrrole ring A to form a vinyl group at this position. Subsequently, the propionate at position four (p4) on pyrrole ring B is cleaved off and heme b is formed. In this study, we attempted to engineer coproheme decarboxylase from Corynebacterium diphtheriae to alter the stereospecificity of this reaction. By introducing a tyrosine residue in proximity to the propionate at position 4, we were able to create a new radical center in the active site. However, the artificial Tyr183• radical could not be shown to catalyze any decarboxylation.
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15

Bromberg, Raquel, Kai Cai, Yirui Guo, Daniel Plymire, Tabitha Emde, Maciej Puzio, Dominika Borek et Zbyszek Otwinowski. « The His-tag as a decoy modulating preferred orientation in cryoEM ». Frontiers in Molecular Biosciences 9 (17 octobre 2022). http://dx.doi.org/10.3389/fmolb.2022.912072.

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The His-tag is a widely used affinity tag that facilitates purification by means of affinity chromatography of recombinant proteins for functional and structural studies. We show here that His-tag presence affects how coproheme decarboxylase interacts with the air-water interface during grid preparation for cryoEM. Depending on His-tag presence or absence, we observe significant changes in patterns of preferred orientation. Our analysis of particle orientations suggests that His-tag presence can mask the hydrophobic and hydrophilic patches on a protein’s surface that mediate the interactions with the air-water interface, while the hydrophobic linker between a His-tag and the coding sequence of the protein may enhance other interactions with the air-water interface. Our observations suggest that tagging, including rational design of the linkers between an affinity tag and a protein of interest, offer a promising approach to modulating interactions with the air-water interface.
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16

Sebastiani, Federico, Chiara Niccoli, Hanna Michlits, Riccardo Risorti, Maurizio Becucci, Stefan Hofbauer et Giulietta Smulevich. « Spectroscopic evidence of the effect of hydrogen peroxide excess on the coproheme decarboxylase from actinobacterial Corynebacterium diphtheriae ». Journal of Raman Spectroscopy, 8 mars 2022. http://dx.doi.org/10.1002/jrs.6326.

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17

Dailey, Harry A., Tamara A. Dailey, Svetlana Gerdes, Dieter Jahn, Martina Jahn, Mark R. O'Brian et Martin J. Warren. « Prokaryotic Heme Biosynthesis : Multiple Pathways to a Common Essential Product ». Microbiology and Molecular Biology Reviews 81, no 1 (25 janvier 2017). http://dx.doi.org/10.1128/mmbr.00048-16.

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SUMMARY The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.
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