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Gabler T, Dali A, Bellei M, Sebastiani F, Becucci M, Battistuzzi G, Furtmüller PG, Smulevich G, Hofbauer S. Revisiting catalytic His and Glu residues in coproporphyrin ferrochelatase - unexpected activities of active site variants. FEBS J 2024. [PMID: 38390750 DOI: 10.1111/febs.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/17/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The identification of the coproporphyrin-dependent heme biosynthetic pathway, which is used almost exclusively by monoderm bacteria in 2015 by Dailey et al. triggered studies aimed at investigating the enzymes involved in this pathway that were originally assigned to the protoporphyrin-dependent heme biosynthetic pathway. Here, we revisit the active site of coproporphyrin ferrochelatase by a biophysical and biochemical investigation using the physiological substrate coproporphyrin III, which in contrast to the previously used substrate protoporphyrin IX has four propionate substituents and no vinyl groups. In particular, we have compared the reactivity of wild-type coproporphyrin ferrochelatase from the firmicute Listeria monocytogenes with those of variants, namely, His182Ala (H182A) and Glu263Gln (E263Q), involving two key active site residues. Interestingly, both variants are active only toward the physiological substrate coproporphyrin III but inactive toward protoporphyrin IX. In addition, E263 exchange impairs the final oxidation step from ferrous coproheme to ferric coproheme. The characteristics of the active site in the context of the residues involved and the substrate binding properties are discussed here using structural and functional means, providing a further contribution to the deciphering of this enigmatic reaction mechanism.
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Affiliation(s)
- Thomas Gabler
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Andrea Dali
- Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Sesto Fiorentino, Italy
| | - Marzia Bellei
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Federico Sebastiani
- Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Sesto Fiorentino, Italy
| | - Maurizio Becucci
- Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Sesto Fiorentino, Italy
| | - Gianantonio Battistuzzi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paul Georg Furtmüller
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Giulietta Smulevich
- Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Sesto Fiorentino, Italy
- INSTM Research Unit of Firenze, Sesto Fiorentino, Italy
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
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2
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Gabler T, Dali A, Sebastiani F, Furtmüller PG, Becucci M, Hofbauer S, Smulevich G. Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species. Protein Sci 2023; 32:e4788. [PMID: 37743577 PMCID: PMC10578119 DOI: 10.1002/pro.4788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/07/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Understanding the reaction mechanism of enzymes at the molecular level is generally a difficult task, since many parameters affect the turnover. Often, due to high reactivity and formation of transient species or intermediates, detailed information on enzymatic catalysis is obtained by means of model substrates. Whenever possible, it is essential to confirm a reaction mechanism based on substrate analogues or model systems by using the physiological substrates. Here we disclose the ferrous iron incorporation mechanism, in solution, and in crystallo, by the coproporphyrin III-coproporphyrin ferrochelatase complex from the firmicute, pathogen, and antibiotic resistant, Listeria monocytogenes. Coproporphyrin ferrochelatase plays an important physiological role as the metalation represents the penultimate reaction step in the prokaryotic coproporphyrin-dependent heme biosynthetic pathway, yielding coproheme (ferric coproporphyrin III). By following the metal titration with resonance Raman spectroscopy and x-ray crystallography, we prove that upon metalation the saddling distortion becomes predominant both in the crystal and in solution. This is a consequence of the readjustment of hydrogen bond interactions of the propionates with the protein scaffold during the enzymatic catalysis. Once the propionates have established the interactions typical of the coproheme complex, the distortion slowly decreases, to reach the almost planar final product.
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Affiliation(s)
- Thomas Gabler
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Andrea Dali
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Paul Georg Furtmüller
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
| | - Stefan Hofbauer
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”—DICUSUniversità di FirenzeSesto FiorentinoItaly
- INSTM Research Unit of FirenzeSesto FiorentinoItaly
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3
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Abstract
Heme (protoheme IX) is an essential cofactor for a large variety of proteins whose functions vary from one electron reactions to binding gases. While not ubiquitous, heme is found in the great majority of known life forms. Unlike most cofactors that are acquired from dietary sources, the vast majority of organisms that utilize heme possess a complete pathway to synthesize the compound. Indeed, dietary heme is most frequently utilized as an iron source and not as a source of heme. In Nature there are now known to exist three pathways to synthesize heme. These are the siroheme dependent (SHD) pathway which is the most ancient, but least common of the three; the coproporphyrin dependent (CPD) pathway which with one known exception is found only in gram positive bacteria; and the protoporphyrin dependent (PPD) pathway which is found in gram negative bacteria and all eukaryotes. All three pathways share a core set of enzymes to convert the first committed intermediate, 5-aminolevulinate (ALA) into uroporphyrinogen III. In the current review all three pathways are reviewed as well as the two known pathways to synthesize ALA. In addition, interesting features of some heme biosynthesis enzymes are discussed as are the regulation and disorders of heme biosynthesis.
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Affiliation(s)
- Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Department of Microbiology, University of Georgia, Athens, GA 30602-1111, USA
| | - Amy E Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, USA
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4
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Obi CD, Bhuiyan T, Dailey HA, Medlock AE. Ferrochelatase: Mapping the Intersection of Iron and Porphyrin Metabolism in the Mitochondria. Front Cell Dev Biol 2022; 10:894591. [PMID: 35646904 PMCID: PMC9133952 DOI: 10.3389/fcell.2022.894591] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/14/2022] [Indexed: 12/29/2022] Open
Abstract
Porphyrin and iron are ubiquitous and essential for sustaining life in virtually all living organisms. Unlike iron, which exists in many forms, porphyrin macrocycles are mostly functional as metal complexes. The iron-containing porphyrin, heme, serves as a prosthetic group in a wide array of metabolic pathways; including respiratory cytochromes, hemoglobin, cytochrome P450s, catalases, and other hemoproteins. Despite playing crucial roles in many biological processes, heme, iron, and porphyrin intermediates are potentially cytotoxic. Thus, the intersection of porphyrin and iron metabolism at heme synthesis, and intracellular trafficking of heme and its porphyrin precursors are tightly regulated processes. In this review, we discuss recent advances in understanding the physiological dynamics of eukaryotic ferrochelatase, a mitochondrially localized metalloenzyme. Ferrochelatase catalyzes the terminal step of heme biosynthesis, the insertion of ferrous iron into protoporphyrin IX to produce heme. In most eukaryotes, except plants, ferrochelatase is localized to the mitochondrial matrix, where substrates are delivered and heme is synthesized for trafficking to multiple cellular locales. Herein, we delve into the structural and functional features of ferrochelatase, as well as its metabolic regulation in the mitochondria. We discuss the regulation of ferrochelatase via post-translational modifications, transportation of substrates and product across the mitochondrial membrane, protein-protein interactions, inhibition by small-molecule inhibitors, and ferrochelatase in protozoal parasites. Overall, this review presents insight on mitochondrial heme homeostasis from the perspective of ferrochelatase.
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Affiliation(s)
- Chibuike David Obi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Tawhid Bhuiyan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Harry A. Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Amy E. Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, United States
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5
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Insight into the function of active site residues in the catalytic mechanism of human ferrochelatase. Biochem J 2021; 478:3239-3252. [PMID: 34402499 DOI: 10.1042/bcj20210460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Ferrochelatase catalyzes the insertion of ferrous iron into a porphyrin macrocycle to produce the essential cofactor, heme. In humans this enzyme not only catalyzes the terminal step, but also serves a regulatory step in the heme synthesis pathway. Over a dozen crystal structures of human ferrochelatase have been solved and many variants have been characterized kinetically. In addition, hydrogen deuterium exchange, resonance Raman, molecular dynamics, and high level quantum mechanic studies have added to our understanding of the catalytic cycle of the enzyme. However, an understanding of how the metal ion is delivered and the specific role that active site residues play in catalysis remain open questions. Data are consistent with metal binding and insertion occurring from the side opposite from where pyrrole proton abstraction takes place. To better understand iron delivery and binding as well as the role of conserved residues in the active site, we have constructed and characterized a series of enzyme variants. Crystallographic studies as well as rescue and kinetic analysis of variants were performed. Data from these studies are consistent with the M76 residue playing a role in active site metal binding and formation of a weak iron protein ligand being necessary for product release. Additionally, structural data support a role for E343 in proton abstraction and product release in coordination with a peptide loop composed of Q302, S303 and K304 that act a metal sensor.
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6
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Fujishiro T, Ogawa S. The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis. Chem Sci 2021; 12:2172-2180. [PMID: 34163982 PMCID: PMC8179277 DOI: 10.1039/d0sc05439a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The class II chelatase CfbA catalyzes Ni2+ insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatase in vitro. Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni2+ and Co2+ remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures of Methanocaldococcus jannaschii wild-type CfbA with various ligands, including SHC, Ni2+, Ni-SHC, and Co2+ were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni2+-SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co2+ than Ni2+. Meanwhile, an in vitro activity assay confirmed the different reaction rates for Ni2+ and Co2+ by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni2+ insertion catalytic mechanism was proposed: Ni2+ insertion to SHC is promoted by the support of an acetate side chain of SHC.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Shimo-Okubo 255 Sakura Saitama 338-8570 Japan +81-48-858-9293
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Shimo-Okubo 255 Sakura Saitama 338-8570 Japan +81-48-858-9293
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7
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Layer G. Heme biosynthesis in prokaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118861. [PMID: 32976912 DOI: 10.1016/j.bbamcr.2020.118861] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
The cyclic tetrapyrrole heme is used as a prosthetic group in a broad variety of different proteins in almost all organisms. Often, it is essential for vital biochemical processes such as aerobic and anaerobic respiration as well as photosynthesis. In Nature, heme is made from the common tetrapyrrole precursor 5-aminolevulinic acid, and for a long time it was assumed that heme is biosynthesized by a single, common pathway in all organisms. However, although this is indeed the case in eukaryotes, heme biosynthesis is more diverse in the prokaryotic world, where two additional pathways exist. The final elucidation of the two 'alternative' heme biosynthesis routes operating in some bacteria and archaea was achieved within the last decade. This review summarizes the three different heme biosynthesis pathways with a special emphasis on the two 'new' prokaryotic routes.
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Affiliation(s)
- Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Institut für Pharmazeutische Wissenschaften, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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8
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Mamardashvili GM, Zhdanova DY, Mamardashvili NZ, Koifman OI, Dehaen W. Catalytic and inhibiting effect of amino acids on the porphyrin metallation reactions. J PORPHYR PHTHALOCYA 2017. [DOI: 10.1142/s1088424617500663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the present work, using the interaction of tetra-(4-sulfophenyl)porphyrin with copper(II) chloride as an example, it has been shown how different amino acid additives (glycine, valine, leucine and tryptophan) catalyze or inhibit the formation of Cu-porphyrin as a function of the chemical environment (borate buffer (pH7.4), DMSO) and the concentration of the additive. It has been demonstrated that the type of amino acid affects the complexation reaction rate. Possible mechanisms of metalloporphyrin formation and the ways of their acceleration are discussed.
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Affiliation(s)
- Galina M. Mamardashvili
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Academicheskay st. 1, Ivanovo, 153045, Russia
| | - Daria Yu. Zhdanova
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Academicheskay st. 1, Ivanovo, 153045, Russia
| | - Nugzar Zh. Mamardashvili
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Academicheskay st. 1, Ivanovo, 153045, Russia
| | - Oskar I. Koifman
- Research Institute of Macroheterocycles, Ivanovo State University of Chemistry and Technology, Sheremetevskiy Av. 7, Ivanovo 153000, Russia
| | - Wim Dehaen
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven, B-3001, Belgium
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9
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The coproporphyrin ferrochelatase of Staphylococcus aureus: mechanistic insights into a regulatory iron-binding site. Biochem J 2017; 474:3513-3522. [PMID: 28864672 PMCID: PMC5633918 DOI: 10.1042/bcj20170362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 11/21/2022]
Abstract
The majority of characterised ferrochelatase enzymes catalyse the final step of classical haem synthesis, inserting ferrous iron into protoporphyrin IX. However, for the recently discovered coproporphyrin-dependent pathway, ferrochelatase catalyses the penultimate reaction where ferrous iron is inserted into coproporphyrin III. Ferrochelatase enzymes from the bacterial phyla Firmicutes and Actinobacteria have previously been shown to insert iron into coproporphyrin, and those from Bacillus subtilis and Staphylococcus aureus are known to be inhibited by elevated iron concentrations. The work herein reports a Km (coproporphyrin III) for S. aureus ferrochelatase of 1.5 µM and it is shown that elevating the iron concentration increases the Km for coproporphyrin III, providing a potential explanation for the observed iron-mediated substrate inhibition. Together, structural modelling, site-directed mutagenesis, and kinetic analyses confirm residue Glu271 as being essential for the binding of iron to the inhibitory regulatory site on S. aureus ferrochelatase, providing a molecular explanation for the observed substrate inhibition patterns. This work therefore has implications for how haem biosynthesis in S. aureus is regulated by iron availability.
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10
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Wu J, Wen S, Zhou Y, Chao H, Shen Y. Human Ferrochelatase: Insights for the Mechanism of Ferrous Iron Approaching Protoporphyrin IX by QM/MM and QTCP Free Energy Studies. J Chem Inf Model 2016; 56:2421-2433. [PMID: 27801584 DOI: 10.1021/acs.jcim.6b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferrochelatase catalyzes the insertion of ferrous iron into protoporphyrin IX, the terminal step in heme biosynthesis. Some disputes in its mechanism remain unsolved, especially for human ferrochelatase. In this paper, high-level quantum mechanical/molecular mechanics (QM/MM) and free-energy studies were performed to address these controversial issues including the iron-binding site, the optimal reaction path, the substrate porphyrin distortion, and the presence of the sitting-atop (SAT) complex. Our results reveal that the ferrous iron is probably at the binding site coordinating with Met76, and His263 plays the role of proton acceptor. The rate-determining step is either the first proton removed by His263 or the proton transition within the porphyrin with an energy barrier of 14.99 or 14.87 kcal/mol by the quantum mechanical thermodynamic cycle perturbation (QTCP) calculations, respectively. The fast deprotonation step with the conservative residues rather than porphyrin deformation found in solution provides the driving force for biochelation. The SAT complex is not a necessity for the catalysis though it induces a modest distortion on the porphyrin ring.
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Affiliation(s)
- Jingheng Wu
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| | - Sixiang Wen
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| | - Yiwei Zhou
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| | - Hui Chao
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
| | - Yong Shen
- School of Chemistry, Sun Yat-sen University , 510275 Guangzhou, P R China
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11
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Bali S, Rollauer S, Roversi P, Raux-Deery E, Lea SM, Warren MJ, Ferguson SJ. Identification and characterization of the 'missing' terminal enzyme for siroheme biosynthesis in α-proteobacteria. Mol Microbiol 2014; 92:153-63. [PMID: 24673795 PMCID: PMC4063343 DOI: 10.1111/mmi.12542] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2014] [Indexed: 11/27/2022]
Abstract
It has recently been shown that the biosynthetic route for both the d1 -haem cofactor of dissimilatory cd1 nitrite reductases and haem, via the novel alternative-haem-synthesis pathway, involves siroheme as an intermediate, which was previously thought to occur only as a cofactor in assimilatory sulphite/nitrite reductases. In many denitrifiers (which require d1 -haem), the pathway to make siroheme remained to be identified. Here we identify and characterize a sirohydrochlorin-ferrochelatase from Paracoccus pantotrophus that catalyses the last step of siroheme synthesis. It is encoded by a gene annotated as cbiX that was previously assumed to be encoding a cobaltochelatase, acting on sirohydrochlorin. Expressing this chelatase from a plasmid restored the wild-type phenotype of an Escherichia coli mutant-strain lacking sirohydrochlorin-ferrochelatase activity, showing that this chelatase can act in the in vivo siroheme synthesis. A ΔcbiX mutant in P. denitrificans was unable to respire anaerobically on nitrate, proving the role of siroheme as a precursor to another cofactor. We report the 1.9 Å crystal structure of this ferrochelatase. In vivo analysis of single amino acid variants of this chelatase suggests that two histidines, His127 and His187, are essential for siroheme synthesis. This CbiX can generally be identified in α-proteobacteria as the terminal enzyme of siroheme biosynthesis.
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Affiliation(s)
- Shilpa Bali
- Department of Biochemistry, University of OxfordSouth Parks Road, Oxford, OX1 3QU, UK
| | - Sarah Rollauer
- Sir William Dunn School of Pathology, University of OxfordSouth Parks Road, Oxford, OX1 3RE, UK
| | - Pietro Roversi
- Department of Biochemistry, University of OxfordSouth Parks Road, Oxford, OX1 3QU, UK
- Sir William Dunn School of Pathology, University of OxfordSouth Parks Road, Oxford, OX1 3RE, UK
| | | | - Susan M Lea
- Sir William Dunn School of Pathology, University of OxfordSouth Parks Road, Oxford, OX1 3RE, UK
| | - Martin J Warren
- School of Biosciences, University of KentCanterbury, Kent, CT2 7NJ, UK
| | - Stuart J Ferguson
- Department of Biochemistry, University of OxfordSouth Parks Road, Oxford, OX1 3QU, UK
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12
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Medlock AE, Najahi-Missaoui W, Ross TA, Dailey TA, Burch J, O'Brien JR, Lanzilotta WN, Dailey HA. Identification and characterization of solvent-filled channels in human ferrochelatase. Biochemistry 2012; 51:5422-33. [PMID: 22712763 DOI: 10.1021/bi300598g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferrochelatase catalyzes the formation of protoheme from two potentially cytotoxic products, iron and protoporphyrin IX. While much is known from structural and kinetic studies on human ferrochelatase of the dynamic nature of the enzyme during catalysis and the binding of protoporphyrin IX and heme, little is known about how metal is delivered to the active site and how chelation occurs. Analysis of all ferrochelatase structures available to date reveals the existence of several solvent-filled channels that originate at the protein surface and continue to the active site. These channels have been proposed to provide a route for substrate entry, water entry, and proton exit during the catalytic cycle. To begin to understand the functions of these channels, we investigated in vitro and in vivo a number of variants that line these solvent-filled channels. Data presented herein support the role of one of these channels, which originates at the surface residue H240, in the delivery of iron to the active site. Structural studies of the arginyl variant of the conserved residue F337, which resides at the back of the active site pocket, suggest that it not only regulates the opening and closing of active site channels but also plays a role in regulating the enzyme mechanism. These data provide insight into the movement of the substrate and water into and out of the active site and how this movement is coordinated with the reaction mechanism.
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Affiliation(s)
- Amy E Medlock
- Biomedical and Health Sciences Institute, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, 30602, United States.
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