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Dali A, Sebastiani F, Gabler T, Frattini G, Moreno DM, Estrin DA, Becucci M, Hofbauer S, Smulevich G. Proximal ligand tunes active site structure and reactivity in bacterial L. monocytogenes coproheme ferrochelatase. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124120. [PMID: 38479228 DOI: 10.1016/j.saa.2024.124120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/21/2024] [Accepted: 03/03/2024] [Indexed: 04/02/2024]
Abstract
Ferrochelatases catalyze the insertion of ferrous iron into the porphyrin during the heme b biosynthesis pathway, which is fundamental for both prokaryotes and eukaryotes. Interestingly, in the active site of ferrochelatases, the proximal ligand coordinating the porphyrin iron of the product is not conserved, and its catalytic role is still unclear. Here we compare the L. monocytogenes bacterial coproporphyrin ferrochelatase native enzyme together with selected variants, where the proximal Tyr residue was replaced by a His (i.e. the most common ligand in heme proteins), a Met or a Phe (as in human and actinobacterial ferrochelatases, respectively), in their Fe(III), Fe(II) and Fe(II)-CO adduct forms. The study of the active site structure and the activity of the proteins in solution has been performed by UV-vis electronic absorption and resonance Raman spectroscopies, biochemical characterization, and classical MD simulations. All the mutations alter the H-bond interactions between the iron porphyrin propionate groups and the protein, and induce effects on the activity, depending on the polarity of the proximal ligand. The overall results confirm that the weak or non-existing coordination of the porphyrin iron by the proximal residue is essential for the binding of the substrate and the release of the final product.
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Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Thomas Gabler
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Gianfranco Frattini
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Diego M Moreno
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes, 2160 Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, Buenos Aires, Argentina
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy.
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy; INSTM Research Unit of Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy.
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2
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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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3
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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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4
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Dali A, Gabler T, Sebastiani F, Destinger A, Furtmüller PG, Pfanzagl V, Becucci M, Smulevich G, Hofbauer S. Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation. Protein Sci 2023; 32:e4534. [PMID: 36479958 PMCID: PMC9794026 DOI: 10.1002/pro.4534] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
Coproporphyrin ferrochelatases (CpfCs) are enzymes catalyzing the penultimate step in the coproporphyrin-dependent (CPD) heme biosynthesis pathway, which is mainly utilized by monoderm bacteria. Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades, nevertheless many mechanistic questions remain unanswered to date. Especially CpfCs, which are found in the CPD pathway, are currently in the spotlight of research. This pathway was identified in 2015 and revealed that the correct substrate for these ferrochelatases is coproporphyrin III (cpIII) instead of protoporphyrin IX, as believed prior the discovery of the CPD pathway. The chemistry of cpIII, which has four propionates, differs significantly from protoporphyrin IX, which features two propionate and two vinyl groups. These findings let us to thoroughly describe the physiological cpIII-ferrochelatase complex in solution and in the crystal phase. Here, we present the first crystallographic structure of the CpfC from the representative monoderm pathogen Listeria monocytogenes bound to its physiological substrate, cpIII, together with the in-solution data obtained by resonance Raman and UV-vis spectroscopy, for wild-type ferrochelatase and variants, analyzing propionate interactions. The results allow us to evaluate the porphyrin distortion and provide an in-depth characterization of the catalytically-relevant binding mode of cpIII prior to iron insertion. Our findings are discussed in the light of the observed structural restraints and necessities for this porphyrin-enzyme complex to catalyze the iron insertion process. Knowledge about this initial situation is essential for understanding the preconditions for iron insertion in CpfCs and builds the basis for future studies.
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Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Thomas Gabler
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Alina Destinger
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Paul Georg Furtmüller
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Vera Pfanzagl
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff” – DICUSUniversità di FirenzeSesto Fiorentino (FI)Italy,INSTM Research Unit of FirenzeSesto Fiorentino (Fi)Italy
| | - Stefan Hofbauer
- Department of ChemistryInstitute of Biochemistry, University of Natural Resources and Life SciencesViennaAustria
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5
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Hunter GA, Ferreira GC. Metal ion coordination sites in ferrochelatase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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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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7
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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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8
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Mitochondrial contact site and cristae organizing system (MICOS) machinery supports heme biosynthesis by enabling optimal performance of ferrochelatase. Redox Biol 2021; 46:102125. [PMID: 34517185 PMCID: PMC8441213 DOI: 10.1016/j.redox.2021.102125] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 02/04/2023] Open
Abstract
Heme is an essential cofactor required for a plethora of cellular processes in eukaryotes. In metazoans the heme biosynthetic pathway is typically partitioned between the cytosol and mitochondria, with the first and final steps taking place in the mitochondrion. The pathway has been extensively studied and its biosynthetic enzymes structurally characterized to varying extents. Nevertheless, understanding of the regulation of heme synthesis and factors that influence this process in metazoans remains incomplete. Therefore, we investigated the molecular organization as well as the physical and genetic interactions of the terminal pathway enzyme, ferrochelatase (Hem15), in the yeast Saccharomyces cerevisiae. Biochemical and genetic analyses revealed dynamic association of Hem15 with Mic60, a core component of the mitochondrial contact site and cristae organizing system (MICOS). Loss of MICOS negatively impacts Hem15 activity, affects the size of the Hem15 high-mass complex, and results in accumulation of reactive and potentially toxic tetrapyrrole precursors that may cause oxidative damage. Restoring intermembrane connectivity in MICOS-deficient cells mitigates these cytotoxic effects. These data provide new insights into how heme biosynthetic machinery is organized and regulated, linking mitochondrial architecture-organizing factors to heme homeostasis.
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Adams NBP, Bisson C, Brindley AA, Farmer DA, Davison PA, Reid JD, Hunter CN. The active site of magnesium chelatase. NATURE PLANTS 2020; 6:1491-1502. [PMID: 33257858 DOI: 10.1038/s41477-020-00806-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/14/2020] [Indexed: 06/12/2023]
Abstract
The insertion of magnesium into protoporphyrin initiates the biosynthesis of chlorophyll, the pigment that underpins photosynthesis. This reaction, catalysed by the magnesium chelatase complex, couples ATP hydrolysis by a ChlID motor complex to chelation within the ChlH subunit. We probed the structure and catalytic function of ChlH using a combination of X-ray crystallography, computational modelling, mutagenesis and enzymology. Two linked domains of ChlH in an initially open conformation of ChlH bind protoporphyrin IX, and the rearrangement of several loops envelops this substrate, forming an active site cavity. This induced fit brings an essential glutamate (E660), proposed to be the key catalytic residue for magnesium insertion, into proximity with the porphyrin. A buried solvent channel adjacent to E660 connects the exterior bulk solvent to the active site, forming a possible conduit for the delivery of magnesium or abstraction of protons.
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Affiliation(s)
- Nathan B P Adams
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.
| | - Claudine Bisson
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
- Centre for Ultrastructural Imaging, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Amanda A Brindley
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - David A Farmer
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - James D Reid
- Department of Chemistry, The University of Sheffield, Sheffield, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.
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10
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Yadav P, Kumar M, Bansal R, Kaur P, Ethayathulla AS. Structure model of ferrochelatase from Salmonella Typhi elucidating metalation mechanism. Int J Biol Macromol 2019; 127:585-593. [PMID: 30660563 DOI: 10.1016/j.ijbiomac.2019.01.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 11/16/2022]
Abstract
A homology model of ferrochelatase (HemH), the heme biosynthesis terminal step enzyme from Salmonella Typhi was generated to understand the mechanism of metal insertion into protoporphyrin IX for heme biosynthesis. The overall fold of membrane associated ferrochelatase (StFc) from S. Typhi is similar to human and Yeast ferrochelatase than Bacillus subtilis, and Bacillus anthracis. An insertion of 16 amino acid residues in helical switch having hydrophobic patch proposed to interact with membrane lipids and in opening and closing of heme binding cleft. The sequence analysis and the docking study revealed that the protoporphyrin binding site in StFc has a crucial replacement of Tyr/Met to Leu13 unique in comparison to other known structures, where Tyr13 observed in B. subtilis/B. anthracis while Met76 in human/yeast play important role in holding protoporphyrin in optimal orientation for metalation. A sitting-a-top (SAT) complex mechanism for metalation is proposed with His194 and Glu264 lie at the bottom and Leu13 on the top of the porphyrin ring. In addition, an entry and exit mechanism is also proposed for protoporphyrin binding into cavity by opening and closing of helical switch using molecular dynamics simulation studies of Apo and heme complexed model structure of S. Typhi HemH.
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Affiliation(s)
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rohit Bansal
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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11
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Ferrochelatase π-helix: Implications from examining the role of the conserved π-helix glutamates in porphyrin metalation and product release. Arch Biochem Biophys 2018; 644:37-46. [PMID: 29481781 DOI: 10.1016/j.abb.2018.02.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/17/2018] [Accepted: 02/20/2018] [Indexed: 11/23/2022]
Abstract
Protoporphyrin ferrochelatase catalyzes the insertion of Fe2+ into protoporphyrin IX to form heme. To determine whether a conserved, active site π-helix contributes to the translocation of the metal ion substrate to the ferrochelatase-bound porphyrin substrate, the invariant π-helix glutamates were replaced with amino acids with non-negatively charged side chains, and the kinetic mechanisms of the generated variants were examined. Analysis of yeast wild-type ferrochelatase-, E314Q- and E318Q-catalyzed reactions, under multi- and single-turnover conditions, demonstrated that the mutations of the π-helix glutamates hindered both protoporphyrin metalation and release of the metalated porphyrin, by slowing each step by approximately 30-50%. Protoporphyrin metalation occurred with an apparent pKa of 7.3 ± 0.1, which was assigned to binding of Fe2+ by deprotonated Glu-314 and Glu-314-assisted Fe2+ insertion into the porphyrin ring. We propose that unwinding of the π-helix concomitant with the adoption of a protein open conformation positions the deprotonated Glu-314 to bind Fe2+ from the surface of the enzyme. Transition to the closed conformation, with π-helix winding, brings Glu-314-bound Fe2+ to the active site for incorporation into protoporphyrin.
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12
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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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13
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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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Differential Regulation of the Two Ferrochelatase Paralogues in Shewanella loihica PV-4 in Response to Environmental Stresses. Appl Environ Microbiol 2016; 82:5077-88. [PMID: 27287322 DOI: 10.1128/aem.00203-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Determining the function and regulation of paralogues is important in understanding microbial functional genomics and environmental adaptation. Heme homeostasis is crucial for the survival of environmental microorganisms. Most Shewanella species encode two paralogues of ferrochelatase, the terminal enzyme in the heme biosynthesis pathway. The function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, were investigated in Shewanella loihica PV-4. The disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), the precursor to heme, and decreased intracellular heme levels. hemH1 was constitutively expressed, and the expression of hemH2 increased when hemH1 was disrupted. The transcription of hemH1 was regulated by the housekeeping sigma factor RpoD and potentially regulated by OxyR, while hemH2 appeared to be regulated by the oxidative stress-associated sigma factor RpoE2. When an oxidative stress condition was mimicked by adding H2O2 to the medium or exposing the culture to light, PPIX accumulation was suppressed in the ΔhemH1 mutant. Consistently, transcriptome analysis indicated enhanced iron uptake and suppressed heme synthesis in the ΔhemH1 mutant. These data indicate that the two paralogues are functional in the heme synthesis pathway but regulated by environmental conditions, providing insights into the understanding of bacterial response to environmental stresses and a great potential to commercially produce porphyrin compounds. IMPORTANCE Shewanella is capable of utilizing a variety of electron acceptors for anaerobic respiration because of the existence of multiple c-type cytochromes in which heme is an essential component. The cytochrome-mediated electron transfer across cellular membranes could potentially be used for biotechnological purposes, such as electricity generation in microbial fuel cells and dye decolorization. However, the mechanism underlying the regulation of biosynthesis of heme and cytochromes is poorly understood. Our study has demonstrated that two ferrochelatase genes involved in heme biosynthesis are differentially regulated in response to environmental stresses, including light and reactive oxygen species. This is an excellent example showing how bacteria have evolved to maintain cellular heme homeostasis. More interestingly, the high yields of extracellular protoporphyrin IX by the Shewanella loihica PV-4 mutants could be utilized for commercial production of this valuable chemical via bacterial fermentation.
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Hunter GA, Vankayala SL, Gillam ME, Kearns FL, Lee Woodcock H, Ferreira GC. The conserved active site histidine-glutamate pair of ferrochelatase coordinately catalyzes porphyrin metalation. J PORPHYR PHTHALOCYA 2016. [DOI: 10.1142/s1088424616500395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferrochelatase catalyzes the insertion of ferrous iron into protoporphyrin IX to generate heme. Despite recent research on the reaction mechanism of ferrochelatase, the precise roles and localization of individual active site residues in catalysis, particularly those involved in the insertion of the ferrous iron into the protoporphyrin IX substrate, remain controversial. One outstanding question is from which side of the macrocycle of the bound porphyin substrate is the ferrous iron substrate inserted. Pre-steady state kinetic experiments done under single-turnover conditions conclusively demonstrate that metal ion insertion is pH-dependent, and that the conserved active site His-Glu pair coordinately catalyzes the metal ion insertion reaction. Further, p[Formula: see text] calculations and molecular dynamic simulations indicate that the active site His is deprotonated and the protonation state of the Glu relates to the conformational state of ferrochelatase. Specifically, the conserved Glu in the open conformation of ferrochelatase is deprotonated, while it remains protonated in the closed conformation. These findings support not only the role of the His-Glu pair in catalyzing metal ion insertion, as these residues need to be deprotonated to bind the incoming metal ion, but also the importance of the relationship between the protonation state of the Glu residue and the conformation of ferrochelatase. Finally, the results of this study are consistent with our previous proposal that the unwinding of the [Formula: see text]-helix, the major structural determinant of the closed to open conformational transition in ferrochelatase, is associated with the Glu residue binding the Fe[Formula: see text] substrate from a mitochondrial Fe[Formula: see text] donor.
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Affiliation(s)
- Gregory A. Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | | | - Mallory E. Gillam
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Fiona L. Kearns
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - Gloria C. Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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Wang Y, Shen Y. Is it possible for Fe2+ to approach protoporphyrin IX from the side of Tyr-13 in Bacillus subtilis ferrochelatase? An answer from QM/MM study. J Mol Model 2012; 19:963-71. [DOI: 10.1007/s00894-012-1627-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 10/03/2012] [Indexed: 11/28/2022]
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17
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Asuru AP, An M, Busenlehner LS. Dissection of Porphyrin-Induced Conformational Dynamics in the Heme Biosynthesis Enzyme Ferrochelatase. Biochemistry 2012; 51:7116-27. [DOI: 10.1021/bi300704c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Awuri P. Asuru
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Mier An
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Laura S. Busenlehner
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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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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19
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Hunter GA, Al-Karadaghi S, Ferreira GC. FERROCHELATASE: THE CONVERGENCE OF THE PORPHYRIN BIOSYNTHESIS AND IRON TRANSPORT PATHWAYS. J PORPHYR PHTHALOCYA 2012; 15:350-356. [PMID: 21852895 DOI: 10.1142/s108842461100332x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferrochelatase (also known as PPIX ferrochelatase; Enzyme Commission number 4.9.9.1.1) catalyzes the insertion of ferrous iron into PPIX to form heme. This reaction unites the biochemically synchronized pathways of porphyrin synthesis and iron transport in nearly all living organisms. The ferrochelatases are an evolutionarily diverse family of enzymes with no more than six active site residues known to be perfectly conserved. The availability of over thirty different crystal structures, including many with bound metal ions or porphyrins, has added tremendously to our understanding of ferrochelatase structure and function. It is generally believed that ferrous iron is directly channeled to ferrochelatase in vivo, but the identity of the suspected chaperone remains uncertain despite much recent progress in this area. Identification of a conserved metal ion binding site at the base of the active site cleft may be an important clue as to how ferrochelatases acquire iron, and catalyze desolvation during transport to the catalytic site to complete heme synthesis.
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Affiliation(s)
- Gregory A Hunter
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida, 33620
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20
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Franco R, Al-Karadaghi S, Ferreira GC. Resonance Raman Spectroscopic Examination of Ferrochelatase-induced Porphyrin Distortion. J PORPHYR PHTHALOCYA 2012; 15:357-363. [PMID: 21776189 DOI: 10.1142/s1088424611003380] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferrochelatase, the terminal enzyme of the heme biosynthetic pathway, catalyzes the insertion of ferrous iron into protoporphyrin IX to give heme. Resonance Raman spectroscopy has been instrumental in defining the distortion (mode and extent) of the porphyrin substrate, which is a critical step in the catalytic mechanism of ferrochelatase. Saddling is the predominant porphyrin out-of-plane deformation induced upon binding to ferrochelatase. Our analysis demonstrated that the intensity of the γ(15) line, which is assigned to an out-of-plane porphyrin vibration, in resonance Raman spectra obtained for wild-type- and variant ferrochelatase-bound porphyrin, correlates with the saddling deformation undergone by the porphyrin substrate. Further analysis of the three dimensional X-ray structures of bacterial, human and yeast ferrochelatases and the type and extent of distortion of the protein-bound porphyrin substrate and inhibitors using normal structure decomposition, support the view that ferrochelatase catalysis involves binding of a distorted porphyrin substrate and releasing of a flatter, metalated porphyrin.
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Affiliation(s)
- Ricardo Franco
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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21
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McIntyre NR, Franco R, Shelnutt JA, Ferreira GC. Nickel(II) chelatase variants directly evolved from murine ferrochelatase: porphyrin distortion and kinetic mechanism. Biochemistry 2011; 50:1535-44. [PMID: 21222436 DOI: 10.1021/bi101170p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heme biosynthetic pathway culminates with the ferrochelatase-catalyzed ferrous iron chelation into protoporphyrin IX to form protoheme. The catalytic mechanism of ferrochelatase has been proposed to involve the stabilization of a nonplanar porphyrin to present the pyrrole nitrogens to the metal ion substrate. Previously, we hypothesized that the ferrochelatase-induced nonplanar distortions of the porphyrin substrate impose selectivity for the divalent metal ion incorporated into the porphyrin ring and facilitate the release of the metalated porphyrin through its reduced affinity for the enzyme. Using resonance Raman spectroscopy, the structural properties of porphyrins bound to the active site of directly evolved Ni(2+)-chelatase variants are now examined with regard to the mode and extent of porphyrin deformation and related to the catalytic properties of the enzymes. The Ni(2+)-chelatase variants (S143T, F323L, and S143T/F323L), which were directly evolved to exhibit an enhanced Ni(2+)-chelatase activity over that of the parent wild-type ferrochelatase, induced a weaker saddling deformation of the porphyrin substrate. Steady-state kinetic parameters of the evolved variants for Ni(2+)- and Fe(2+)-chelatase activities increased compared to those of wild-type ferrochelatase. In particular, the reduced porphyrin saddling deformation correlated with increased catalytic efficiency toward the metal ion substrate (Ni(2+) or Fe(2+)). The results lead us to propose that the decrease in the induced protoporphyrin IX saddling mode is associated with a less stringent metal ion preference by ferrochelatase and a slower porphyrin chelation step.
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Affiliation(s)
- Neil R McIntyre
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida 33612, United States
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22
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Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization. Proc Natl Acad Sci U S A 2010; 108:97-102. [PMID: 21173279 DOI: 10.1073/pnas.1014298108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class II chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (Fe(2+) or Co(2+)) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). The structures of two related class II enzymes, CbiX(S) from Archaeoglobus fulgidus and CbiK from Salmonella enterica, that are responsible for the insertion of cobalt along the cobalamin biosynthesis pathway are presented in complex with their metallated product. A further structure of a CbiK from Desulfovibrio vulgaris Hildenborough reveals how cobalt is bound at the active site. The crystal structures show that the binding of sirohydrochlorin is distinctly different to porphyrin binding in the protoporphyrin ferrochelatases and provide a molecular overview of the mechanism of chelation. The structures also give insights into the evolution of chelatase form and function. Finally, the structure of a periplasmic form of Desulfovibrio vulgaris Hildenborough CbiK reveals a novel tetrameric arrangement of its subunits that are stabilized by the presence of a heme b cofactor. Whereas retaining colbaltochelatase activity, this protein has acquired a central cavity with the potential to chaperone or transport metals across the periplasmic space, thereby evolving a new use for an ancient protein subunit.
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23
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Hansson MD, Karlberg T, Söderberg CAG, Rajan S, Warren MJ, Al-Karadaghi S, Rigby SEJ, Hansson M. Bacterial ferrochelatase turns human: Tyr13 determines the apparent metal specificity of Bacillus subtilis ferrochelatase. J Biol Inorg Chem 2010; 16:235-42. [DOI: 10.1007/s00775-010-0720-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 10/09/2010] [Indexed: 10/18/2022]
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24
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Layer G, Reichelt J, Jahn D, Heinz DW. Structure and function of enzymes in heme biosynthesis. Protein Sci 2010; 19:1137-61. [PMID: 20506125 DOI: 10.1002/pro.405] [Citation(s) in RCA: 213] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. Heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. Further, enzymes such as catalases, peroxidases, or cytochromes P450 rely on heme as essential cofactors. Heme is synthesized in most organisms via a highly conserved biosynthetic route. In humans, defects in heme biosynthesis lead to severe metabolic disorders called porphyrias. The elucidation of the 3D structures for all heme biosynthetic enzymes over the last decade provided new insights into their function and elucidated the structural basis of many known diseases. In terms of structure and function several rather unique proteins were revealed such as the V-shaped glutamyl-tRNA reductase, the dipyrromethane cofactor containing porphobilinogen deaminase, or the "Radical SAM enzyme" coproporphyrinogen III dehydrogenase. This review summarizes the current understanding of the structure-function relationship for all heme biosynthetic enzymes and their potential interactions in the cell.
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Affiliation(s)
- Gunhild Layer
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig D-38106, Germany
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25
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Davidson RE, Chesters CJ, Reid JD. Metal ion selectivity and substrate inhibition in the metal ion chelation catalyzed by human ferrochelatase. J Biol Chem 2009; 284:33795-9. [PMID: 19767646 DOI: 10.1074/jbc.m109.030205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protoporphyrin IX ferrochelatase (EC 4.99.1.1) catalyzes the terminal step in the heme biosynthetic pathway, the insertion of ferrous iron into protoporphyrin IX. Ferrochelatase shows specificity, in vitro, for multiple metal ion substrates and exhibits substrate inhibition in the case of zinc, copper, cobalt, and nickel. Zinc is the most biologically significant of these; when iron is depleted, zinc porphyrins are formed physiologically. Examining the k(cat)/K(m)(app) ratios for zinc and iron reveals that, in vitro, zinc is the preferred substrate at all concentrations of porphyrin. This is not the observed biological specificity, where zinc porphyrins are abnormal; these data argue for the existence of a specific iron delivery mechanism in vivo. We demonstrate that zinc acts as an uncompetitive substrate inhibitor, suggesting that ferrochelatase acts via an ordered pathway. Steady-state characterization demonstrates that the apparent k(cat) depends on zinc and shows substrate inhibition. Although porphyrin substrate is not inhibitory, zinc inhibition is enhanced by increasing porphyrin concentration. This indicates that zinc inhibits by binding to an enzyme-product complex (EZnD(IX)) and is likely to be the second substrate in an ordered mechanism. Our analysis shows that substrate inhibition by zinc is not a mechanism that can promote specificity for iron over zinc, but is instead one that will reduce the production of all metalloporphyrins in the presence of high concentrations of zinc.
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Affiliation(s)
- Ruth E Davidson
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
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26
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Hunter GA, Sampson MP, Ferreira GC. Metal ion substrate inhibition of ferrochelatase. J Biol Chem 2008; 283:23685-91. [PMID: 18593702 DOI: 10.1074/jbc.m803372200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ferrochelatase catalyzes the insertion of ferrous iron into protoporphyrin IX to form heme. Robust kinetic analyses of the reaction mechanism are complicated by the instability of ferrous iron in aqueous solution, particularly at alkaline pH values. At pH 7.00 the half-life for spontaneous oxidation of ferrous ion is approximately 2 min in the absence of metal complexing additives, which is sufficient for direct comparisons of alternative metal ion substrates with iron. These analyses reveal that purified recombinant ferrochelatase from both murine and yeast sources inserts not only ferrous iron but also divalent cobalt, zinc, nickel, and copper into protoporphyrin IX to form the corresponding metalloporphyrins but with considerable mechanistic variability. Ferrous iron is the preferred metal ion substrate in terms of apparent k(cat) and is also the only metal ion substrate not subject to severe substrate inhibition. Substrate inhibition occurs in the order Cu(2+) > Zn(2+) > Co(2+) > Ni(2+) and can be alleviated by the addition of metal complexing agents such as beta-mercaptoethanol or imidazole to the reaction buffer. These data indicate the presence of two catalytically significant metal ion binding sites that may coordinately regulate a selective processivity for the various potential metal ion substrates.
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Affiliation(s)
- Gregory A Hunter
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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Schagerlöf U, Elmlund H, Gakh O, Nordlund G, Hebert H, Lindahl M, Isaya G, Al-Karadaghi S. Structural basis of the iron storage function of frataxin from single-particle reconstruction of the iron-loaded oligomer. Biochemistry 2008; 47:4948-54. [PMID: 18393441 PMCID: PMC3932613 DOI: 10.1021/bi800052m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The mitochondrial protein frataxin plays a central role in mitochondrial iron homeostasis, and frataxin deficiency is responsible for Friedreich ataxia, a neurodegenerative and cardiac disease that affects 1 in 40000 children. Here we present a single-particle reconstruction from cryoelectron microscopic images of iron-loaded 24-subunit oligomeric frataxin particles at 13 and 17 A resolution. Computer-aided classification of particle images showed heterogeneity in particle size, which was hypothesized to result from gradual accumulation of iron within the core structure. Thus, two reconstructions were created from two classes of particles with iron cores of different sizes. The reconstructions show the iron core of frataxin for the first time. Compared to the previous reconstruction of iron-free particles from negatively stained images, the higher resolution of the present reconstruction allowed a more reliable analysis of the overall three-dimensional structure of the 24-meric assembly. This was done after docking the X-ray structure of the frataxin trimer into the EM reconstruction. The structure revealed a close proximity of the suggested ferroxidation sites of different monomers to the site proposed to serve in iron nucleation and mineralization. The model also assigns a new role to the N-terminal helix of frataxin in controlling the channel at the 4-fold axis of the 24-subunit oligomer. The reconstructions show that, together with some common features, frataxin has several unique features which distinguish it from ferritin. These include the overall organization of the oligomers, the way they are stabilized, and the mechanisms of iron core nucleation.
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Affiliation(s)
- Ulrika Schagerlöf
- Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Hans Elmlund
- Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet and School of Technology and Health, Royal Institute of Technology, SE-14157 Huddinge, Sweden
| | - Oleksandr Gakh
- Departments of Pediatric and Adolescent Medicine and of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905
| | - Gustav Nordlund
- Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet and School of Technology and Health, Royal Institute of Technology, SE-14157 Huddinge, Sweden
| | - Martin Lindahl
- Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet and School of Technology and Health, Royal Institute of Technology, SE-14157 Huddinge, Sweden
| | - Grazia Isaya
- Departments of Pediatric and Adolescent Medicine and of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905
| | - Salam Al-Karadaghi
- Departments of Pediatric and Adolescent Medicine and of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905
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Karlberg T, Hansson MD, Yengo RK, Johansson R, Thorvaldsen HO, Ferreira GC, Hansson M, Al-Karadaghi S. Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues. J Mol Biol 2008; 378:1074-83. [PMID: 18423489 DOI: 10.1016/j.jmb.2008.03.040] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 03/14/2008] [Accepted: 03/19/2008] [Indexed: 11/19/2022]
Abstract
The specific insertion of a divalent metal ion into tetrapyrrole macrocycles is catalyzed by a group of enzymes called chelatases. Distortion of the tetrapyrrole has been proposed to be an important component of the mechanism of metallation. We present the structures of two different inhibitor complexes: (1) N-methylmesoporphyrin (N-MeMP) with the His183Ala variant of Bacillus subtilis ferrochelatase; (2) the wild-type form of the same enzyme with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride (dSDP). Analysis of the structures showed that only one N-MeMP isomer out of the eight possible was bound to the protein and it was different from the isomer that was earlier found to bind to the wild-type enzyme. A comparison of the distortion of this porphyrin with other porphyrin complexes of ferrochelatase and a catalytic antibody with ferrochelatase activity using normal-coordinate structural decomposition reveals that certain types of distortion are predominant in all these complexes. On the other hand, dSDP, which binds closer to the protein surface compared to N-MeMP, does not undergo any distortion upon binding to the protein, underscoring that the position of the porphyrin within the active site pocket is crucial for generating the distortion required for metal insertion. In addition, in contrast to the wild-type enzyme, Cu(2+)-soaking of the His183Ala variant complex did not show any traces of porphyrin metallation. Collectively, these results provide new insights into the role of the active site residues of ferrochelatase in controlling stereospecificity, distortion and metallation.
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Affiliation(s)
- Tobias Karlberg
- Department of Molecular Biophysics, Centre for Molecular Protein Science, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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Medlock AE, Dailey TA, Ross TA, Dailey HA, Lanzilotta WN. A pi-helix switch selective for porphyrin deprotonation and product release in human ferrochelatase. J Mol Biol 2007; 373:1006-16. [PMID: 17884090 PMCID: PMC2083577 DOI: 10.1016/j.jmb.2007.08.040] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 08/14/2007] [Accepted: 08/16/2007] [Indexed: 11/17/2022]
Abstract
Ferrochelatase (protoheme ferrolyase, EC 4.99.1.1) is the terminal enzyme in heme biosynthesis and catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme IX (heme). Due to the many critical roles of heme, synthesis of heme is required by the vast majority of organisms. Despite significant investigation of both the microbial and eukaryotic enzyme, details of metal chelation remain unidentified. Here we present the first structure of the wild-type human enzyme, a lead-inhibited intermediate of the wild-type enzyme with bound metallated porphyrin macrocycle, the product bound form of the enzyme, and a higher resolution model for the substrate-bound form of the E343K variant. These data paint a picture of an enzyme that undergoes significant changes in secondary structure during the catalytic cycle. The role that these structural alterations play in overall catalysis and potential protein-protein interactions with other proteins, as well as the possible molecular basis for these changes, is discussed. The atomic details and structural rearrangements presented herein significantly advance our understanding of the substrate binding mode of ferrochelatase and reveal new conformational changes in a structurally conserved pi-helix that is predicted to have a central role in product release.
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Affiliation(s)
- Amy E Medlock
- Biomedical and Health Sciences Institute, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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30
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Dailey HA, Wu CK, Horanyi P, Medlock AE, Najahi-Missaoui W, Burden AE, Dailey TA, Rose J. Altered orientation of active site residues in variants of human ferrochelatase. Evidence for a hydrogen bond network involved in catalysis. Biochemistry 2007; 46:7973-9. [PMID: 17567154 PMCID: PMC2424199 DOI: 10.1021/bi700151f] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ferrochelatase catalyzes the terminal step in heme biosynthesis, the insertion of ferrous iron into protoporphyrin to form protoheme IX. The crystal structures of human ferrochelatase both with and without the protoporphyrin substrate bound have been determined previously. The substrate-free enzyme has an open active site pocket, while in the substrate-bound enzyme, the active site pocket is closed around the porphyrin macrocycle and a number of active site residues have reoriented side chains. To understand how and why these structural changes occur, we have substituted three amino acid residues (H263, H341, and F337) whose side chains occupy different spatial positions in the substrate-free versus substrate-bound ferrochelatases. The catalytic and structural properties of ferrochelatases containing the amino acid substitutions H263C, H341C, and F337A were examined. It was found that in the H263C and H341C variants, but not the F337A variant enzymes, the side chains of N75, M76, R164, H263, F337, H341, and E343 are oriented in a fashion similar to what is found in ferrochelatase with the bound porphyrin substrate. However, all of the variant forms possess open active site pockets which are found in the structure of porphyrin-free ferrochelatase. Thus, while the interior walls of the active site pocket are remodeled in these variants, the exterior lips remain unaltered in position. One possible explanation for this collective reorganization of active site side chains is the presence of a hydrogen bond network among H263, H341, and E343. This network is disrupted in the variants by alteration of H263C or H341C. In the substrate-bound enzyme, the formation of a hydrogen bond between H263 and a pyrrole nitrogen results in disruption of the network. The possible role of this network in catalysis is discussed.
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Affiliation(s)
- Harry A Dailey
- Biomedical and Health Sciences Institute, Department of Microbiology, Paul D. Coverdell Center, University of Georgia, Athens, Georgia 30602, USA.
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Hoggins M, Dailey H, Hunter C, Reid J. Direct measurement of metal ion chelation in the active site of human ferrochelatase. Biochemistry 2007; 46:8121-7. [PMID: 17566985 PMCID: PMC2396339 DOI: 10.1021/bi602418e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The final step in heme biosynthesis, insertion of ferrous iron into protoporphyrin IX, is catalyzed by protoporphyrin IX ferrochelatase (EC 4.99.1.1). We demonstrate that pre-steady state human ferrochelatase (R115L) exhibits a stoichiometric burst of product formation and substrate consumption, consistent with a rate-determining step following metal ion chelation. Detailed analysis shows that chelation requires at least two steps, rapid binding followed by a slower (k approximately 1 s-1) irreversible step, provisionally assigned to metal ion chelation. Comparison with steady state data reveals that the rate-determining step in the overall reaction, conversion of free porphyrin to free metalloporphyrin, occurs after chelation and is most probably product release. We have measured rate constants for significant steps on the enzyme and demonstrate that metal ion chelation, with a rate constant of 0.96 s-1, is approximately 10 times faster than the rate-determining step in the steady state (kcat = 0.1 s-1). The effect of an additional E343D mutation is apparent at multiple stages in the reaction cycle with a 7-fold decrease in kcat and a 3-fold decrease in kchel. This conservative mutation primarily affects events occurring after metal ion chelation. Further evaluation of structure-function data on site-directed mutants will therefore require both steady state and pre-steady state approaches.
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Affiliation(s)
- M. Hoggins
- Department of Molecular biology and Biotechnology, University of Sheffield, Sheffield, UK S10 2TN
| | - H.A. Dailey
- Biomedical and Health Sciences Institute, Paul D. Coverdell Center, University of Georgia, Athens, GA 30602−7394
| | - C.N. Hunter
- Department of Molecular biology and Biotechnology, University of Sheffield, Sheffield, UK S10 2TN
| | - J.D. Reid
- Department of Chemistry, University of Sheffield, Sheffield, UK S3 7HF
- To whom correspondence should be addressed: J.D.R., Department of Chemistry, University of Sheffield, Sheffield, U.K., S3 7HF. Telephone +44 114 222 29558 . Fax +44 114 222 9346. Email
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Bencze KZ, Kondapalli KC, Cook JD, McMahon S, Millán-Pacheco C, Pastor N, Stemmler TL. The structure and function of frataxin. Crit Rev Biochem Mol Biol 2006; 41:269-91. [PMID: 16911956 PMCID: PMC2859089 DOI: 10.1080/10409230600846058] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Frataxin, a highly conserved protein found in prokaryotes and eukaryotes, is required for efficient regulation of cellular iron homeostasis. Humans with a frataxin deficiency have the cardio- and neurodegenerative disorder Friedreich's ataxia, commonly resulting from a GAA trinucleotide repeat expansion in the frataxin gene. While frataxin's specific function remains a point of controversy, the general consensus is that the protein assists in controlling cellular iron homeostasis by directly binding iron. This review focuses on the structural and biochemical aspects of iron binding by the frataxin orthologs and outlines molecular attributes that may help explain the protein's role in different cellular pathways.
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Affiliation(s)
- Krisztina Z Bencze
- Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan 48201, USA
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Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MNG. Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus. ACTA ACUST UNITED AC 2006; 7:37-50. [PMID: 16835730 DOI: 10.1007/s10969-006-9008-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Accepted: 04/20/2006] [Indexed: 10/24/2022]
Abstract
The Archaeoglobus fulgidus gene af0721 encodes CbiX(S), a small cobaltochelatase associated with the anaerobic biosynthesis of vitamin B12 (cobalamin). The protein was shown to have activity both in vivo and in vitro, catalyzing the insertion of Co2+ into sirohydrochlorin. The structure of CbiX(S) was determined in two different crystal forms and was shown to consist of a central mixed beta-sheet flanked by four alpha-helices, one of which originates in the C-terminus of a neighboring molecule. CbiX(S) is about half the size of other Class II tetrapyrrole chelatases. The overall topography of CbiX(S) exhibits substantial resemblance to both the N- and C-terminal regions of several members of the Class II metal chelatases involved in tetrapyrrole biosynthesis. Two histidines (His10 and His74), are in similar positions as the catalytic histidine residues in the anaerobic cobaltochelatase CbiK (His145 and His207). In light of the hypothesis that suggests the larger chelatases evolved via gene duplication and fusion from a CbiX(S)-like enzyme, the structure of AF0721 may represent that of an "ancestral" precursor of class II metal chelatases.
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Affiliation(s)
- Jiang Yin
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada, T6G 2H7
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Shepherd M, Dailey T, Dailey H. A new class of [2Fe-2S]-cluster-containing protoporphyrin (IX) ferrochelatases. Biochem J 2006; 397:47-52. [PMID: 16548850 PMCID: PMC1479749 DOI: 10.1042/bj20051967] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Protoporphyrin (IX) ferrochelatase catalyses the insertion of ferrous iron into protoporphyrin IX to form haem. These ferrochelatases exist as monomers and dimers, both with and without [2Fe-2S] clusters. The motifs for [2Fe-2S] cluster co-ordination are varied, but in all cases previously reported, three of the four cysteine ligands are present in the 30 C-terminal residues and the fourth ligand is internal. In the present study, we demonstrate that a group of micro-organisms exist which possess protoporphyrin (IX) ferrochelatases containing [2Fe-2S] clusters that are co-ordinated by a group of four cysteine residues contained in an internal amino acid segment of approx. 20 residues in length. This suggests that these ferrochelatases have evolved along a different lineage than other bacterial protoporphyrin (IX) ferrochelatases. For example, Myxococcus xanthus protoporphyrin (IX) ferrochelatase ligates a [2Fe-2S] cluster via cysteine residues present in an internal segment. Site-directed mutagenesis of this ferrochelatase demonstrates that changing one cysteine ligand into serine results in loss of the cluster, but unlike eukaryotic protoporphyrin (IX) ferrochelatases, this enzyme retains its activity. These data support a role for the [2Fe-2S] cluster in iron affinity, and strongly suggest convergent evolution of this feature in prokaryotes.
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Affiliation(s)
- Mark Shepherd
- Biomedical and Health Sciences Institute, Paul D. Coverdell Center, University of Georgia, Athens, GA 30602, U.S.A
| | - Tamara A. Dailey
- Biomedical and Health Sciences Institute, Paul D. Coverdell Center, University of Georgia, Athens, GA 30602, U.S.A
| | - Harry A. Dailey
- Biomedical and Health Sciences Institute, Paul D. Coverdell Center, University of Georgia, Athens, GA 30602, U.S.A
- To whom correspondence should be addressed (email )
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Al-Karadaghi S, Franco R, Hansson M, Shelnutt JA, Isaya G, Ferreira GC. Chelatases: distort to select? Trends Biochem Sci 2006; 31:135-42. [PMID: 16469498 PMCID: PMC2997100 DOI: 10.1016/j.tibs.2006.01.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 12/06/2005] [Accepted: 01/24/2006] [Indexed: 02/07/2023]
Abstract
Chelatases catalyze the insertion of a specific metal ion into porphyrins, a key step in the synthesis of metalated tetrapyrroles that are essential for many cellular processes. Despite apparent common structural features among chelatases, no general reaction mechanism accounting for metal ion specificity has been established. We propose that chelatase-induced distortion of the porphyrin substrate not only enhances the reaction rate by decreasing the activation energy of the reaction but also modulates which divalent metal ion is incorporated into the porphyrin ring. We evaluate the recently recognized interaction between ferrochelatase and frataxin as a way to regulate iron delivery to ferrochelatase, and thus iron and heme metabolism. We postulate that the ferrochelatase-frataxin interaction controls the type of metal ion that is delivered to ferrochelatase.
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Affiliation(s)
- Salam Al-Karadaghi
- Department of Molecular Biophysics, Lund University, Box 124, SE-22100 Lund, Sweden
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36
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Al-Karadaghi S, Franco R, Hansson M, Shelnutt JA, Isaya G, Ferreira GC. Chelatases: distort to select? Trends Biochem Sci 2006. [PMID: 16469498 DOI: 10.1016/j.tibs.2006.01.001.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chelatases catalyze the insertion of a specific metal ion into porphyrins, a key step in the synthesis of metalated tetrapyrroles that are essential for many cellular processes. Despite apparent common structural features among chelatases, no general reaction mechanism accounting for metal ion specificity has been established. We propose that chelatase-induced distortion of the porphyrin substrate not only enhances the reaction rate by decreasing the activation energy of the reaction but also modulates which divalent metal ion is incorporated into the porphyrin ring. We evaluate the recently recognized interaction between ferrochelatase and frataxin as a way to regulate iron delivery to ferrochelatase, and thus iron and heme metabolism. We postulate that the ferrochelatase-frataxin interaction controls the type of metal ion that is delivered to ferrochelatase.
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Affiliation(s)
- Salam Al-Karadaghi
- Department of Molecular Biophysics, Lund University, Box 124, SE-22100 Lund, Sweden
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37
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Hansson MD, Lindstam M, Hansson M. Crosstalk between metal ions in Bacillus subtilis ferrochelatase. J Biol Inorg Chem 2006; 11:325-33. [PMID: 16453119 DOI: 10.1007/s00775-006-0080-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Accepted: 01/09/2006] [Indexed: 10/25/2022]
Abstract
Ferrochelatase (EC 4.99.1.1), the terminal enzyme in the heme biosynthetic pathway, catalyzes the insertion of Fe2+ into protoporphyrin IX, generating heme. In vitro assays have shown that all characterized ferrochelatases can also incorporate Zn2+ into protoporphyrin IX. Previously Zn2+ has been observed at an inner metal binding site close to the porphyrin binding site. Mg2+, which stimulates Zn2+ insertion by Bacillus subtilis ferrochelatase, has been observed at an outer metal binding site. Exchange of Glu272 to a serine eliminated the stimulative effect of Mg2+. We found that Zn2+ quenched the fluorescence of B. subtilis ferrochelatase and this quenching was used to estimate the metal affinity. Trp230 was identified as the intrinsic fluorophore responsible for the observed quenching pattern. The affinity for Zn2+ could be increased by incubating the ferrochelatase with the transition state analogue N-methyl mesoporphyrin IX, which reflected a close collaborative arrangement between the two substrates in the active site. We also showed that the affinity for Zn2+ was lowered in the presence of Mg2+ and that bound Zn2+ was released upon binding of Mg2+. In the ferrochelatase with a Glu272Ser modification, the interaction between Zn2+ and Mg2+ was abolished. It could thereby be demonstrated that the presence of a metal at one metal binding site affected the metal affinity of another, providing the enzyme with a site that regulates the enzymatic activity.
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Affiliation(s)
- Mattias D Hansson
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
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38
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Shipovskov S, Karlberg T, Fodje M, Hansson MD, Ferreira GC, Hansson M, Reimann CT, Al-Karadaghi S. Metallation of the Transition-state Inhibitor N-methyl Mesoporphyrin by Ferrochelatase: Implications for the Catalytic Reaction Mechanism. J Mol Biol 2005; 352:1081-90. [PMID: 16140324 DOI: 10.1016/j.jmb.2005.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 07/27/2005] [Accepted: 08/03/2005] [Indexed: 11/20/2022]
Abstract
Insertion of metals into various tetrapyrroles is catalysed by a group of enzymes called chelatases, e.g. nickel, cobalt, magnesium and ferro-chelatase. It has been proposed that catalytic metallation includes distorting the porphyrin substrate by the enzyme towards a transition state-like geometry in which at least one of the pyrrole rings will be available for metal chelation. Here, we present a study of metal insertion into the transition-state inhibitor of protoporphyrin IX ferrochelatase, N-methyl mesoporphyrin (N-MeMP), by time-resolved crystallography and mass spectrometry with and without the presence of ferrochelatase. The results show that metallation of N-MeMP has a very limited effect on the conformation of the residues that participate in porphyrin and metal binding. These findings support theoretical data, which indicate that product release is controlled largely by the strain created by metal insertion into the distorted porphyrin. The results suggest that, similar to non-catalytic metallation of N-MeMP, the ferrochelatase-assisted metallation depends on the ligand exchange rate for the respective metal. Moreover, ferrochelatase catalyses insertion of Cu(II) and Zn(II) into N-MeMP with a rate that is about 20 times faster than non-enzymatic metallation in solution, suggesting that the catalytic strategy of ferrochelatase includes a stage of acceleration of the rate of ligand exchange for the metal substrate. The greater efficiency of N-MeMP metallation by Cu(II), as compared to Zn(II), contrasts with the K(m) values for Zn(II) (17 microM) and Cu(II) (170 microM) obtained for metallation of protoporphyrin IX. We suggest that this difference in metal specificity depends on the type of distortion imposed by the enzyme on protoporphyrin IX, which is different from the intrinsic non-planar distortion of N-MeMP. A mechanism of control of metal specificity by porphyrin distortion may be general for different chelatases, and may have common features with the mechanism of metal specificity in crown ethers.
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Affiliation(s)
- Stepan Shipovskov
- Department of Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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39
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Franco R, Bai G, Prosinecki V, Abrunhosa F, Ferreira G, Bastos M. Porphyrin-substrate binding to murine ferrochelatase: effect on the thermal stability of the enzyme. Biochem J 2005; 386:599-605. [PMID: 15496139 PMCID: PMC1134880 DOI: 10.1042/bj20040921] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Revised: 10/07/2004] [Accepted: 10/21/2004] [Indexed: 11/17/2022]
Abstract
Ferrochelatase (EC 4.99.1.1), the terminal enzyme of the haem biosynthetic pathway, catalyses the chelation of Fe(II) into the protoporphyrin IX ring. The energetics of the binding between murine ferrochelatase and mesoporphyrin were determined using isothermal titration calorimetry, which revealed a stoichiometry of one molecule of mesoporphyrin bound per protein monomer. The binding is strongly exothermic, with a large intrinsic enthalpy (DeltaH=-97.1 kJ x mol(-1)), and is associated with the uptake of two protons from the buffer. This proton transfer suggests that hydrogen bonding between ferrochelatase and mesoporphyrin is a key factor in the thermodynamics of the binding reaction. Differential scanning calorimetry thermograms indicated a co-operative two-state denaturation process with a single transition temperature of 56 degrees C for wild-type murine ferrochelatase. An increase in the thermal stability of ferrochelatase is dependent upon mesoporphyrin binding. Similarly, murine ferrochelatase variants, in which the active site Glu-289 was replaced by either glutamine or alanine and, when purified, contained specifically-bound protoporphyrin, exhibited enhanced protein stability when compared with wild-type ferrochelatase. However, in contrast with the wild-type enzyme, the thermal denaturation of ferrochelatase variants was best described as a non-co-operative denaturation process.
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Affiliation(s)
- Ricardo Franco
- *Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Guangyue Bai
- †CIQ(UP), Departamento de Química, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, 4169-007 Porto, Portugal
| | - Vesna Prosinecki
- *Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Filipa Abrunhosa
- †CIQ(UP), Departamento de Química, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, 4169-007 Porto, Portugal
| | - Gloria C. Ferreira
- ‡Department of Biochemistry and Molecular Biology, College of Medicine, University of South Florida, Tampa, FL 33612, U.S.A
- §H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL 33612, U.S.A
| | - Margarida Bastos
- †CIQ(UP), Departamento de Química, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, 4169-007 Porto, Portugal
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40
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Leung YK, Wong KF, Lee HK, Ho JW. Cloning and characterization of chironomidae ferrochelatase: copper activation of the purified ferrochelatase. Mol Cell Biochem 2004; 262:225-31. [PMID: 15532727 DOI: 10.1023/b:mcbi.0000038238.27488.9f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
All organisms utilize ferrochelatase (EC 4.99.1.1) to catalyze the insertion of ferrous iron into protoposphyrin IX in the terminal step of the heme biosynthetic pathway. Different metal-binding affinity for the enzyme leads to changes in enzyme activity. In this work, we have cloned and over-expressed the enzyme from chironomidae in E. coli. The enzyme was purified and characterized. The recombinant enzyme showed higher enzymatic activity (four-fold increase) in the presence of copper ions and unaffected by calcium ions. Other divalent metal ions including magnesium, manganese, lead, reduced the enzyme activity by >60%. Over 90% of the enzyme activity was inhibited by Zn2+. The sequence alignment of amino acid residues reveals 83% homology with other ferrochelatases. The results of electron proton resonance (EPR) analysis showed that Fe2+ ion was present in the cluster of the recombinant enzyme complex. The recombinant enzyme also contained the [2Fe-2S] center with two-fold higher enzymatic activity than human ferrochelatase.
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Affiliation(s)
- Yuet Kin Leung
- Department of Biochemistry, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
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41
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Shi Z, Ferreira GC. Probing the Active Site Loop Motif of Murine Ferrochelatase by Random Mutagenesis. J Biol Chem 2004; 279:19977-86. [PMID: 14981080 DOI: 10.1074/jbc.m313821200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ferrochelatase catalyzes the terminal step of the heme biosynthetic pathway by inserting ferrous iron into protoporphyrin IX. A conserved loop motif was shown to form part of the active site and contact the bound porphyrin by molecular dynamics calculations and structural analysis. We applied a random mutagenesis approach and steady-state kinetic analysis to assess the role of the loop motif in murine ferrochelatase function, particularly with respect to porphyrin interaction. Functional substitutions in the 10 consecutive loop positions Gln(248)-Leu(257) were identified by genetic complementation in Escherichia coli strain Deltavis. Lys(250), Val(251), Pro(253), Val(254), and Pro(255) tolerated a variety of replacements including single substitutions and contained low informational content. Gln(248), Ser(249), Gly(252), Trp(256), and Leu(257) possessed high informational content, since permissible replacements were limited and only observed in multiply substituted mutants. Selected active loop variants exhibited k(cat) values comparable with or higher than that of wild-type murine ferrochelatase. The K(m) values for porphyrin increased, except for the single mutant V251L. Other than a moderate increase observed in the triple mutant S249A/K250Q/V251C, the K(m) values for Fe(2+) were lowered. The k(cat)/K(m) for porphyrin remained largely unchanged, with the exception of a 10-fold reduction in the triple mutant K250M/V251L/W256Y. The k(cat)/K(m) for Fe(2+) was improved. Molecular modeling of these active loop variants indicated that loop mutations resulted in alterations of the active site architecture. However, despite the plasticity of the loop primary structure, the relative spatial positioning of the loop in the active site appeared to be maintained in functional variants, supporting a role for the loop in ferrochelatase function.
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Affiliation(s)
- Zhen Shi
- Department of Biochemistry and Molecular Biology, College of Medicine and H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL 33612, USA
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42
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Park S, Gakh O, O'Neill HA, Mangravita A, Nichol H, Ferreira GC, Isaya G. Yeast frataxin sequentially chaperones and stores iron by coupling protein assembly with iron oxidation. J Biol Chem 2003; 278:31340-51. [PMID: 12732649 DOI: 10.1074/jbc.m303158200] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have investigated the mechanism of frataxin, a conserved mitochondrial protein involved in iron metabolism and neurodegenerative disease. Previous studies revealed that the yeast frataxin homologue (mYfh1p) is activated by Fe(II) in the presence of O2 and assembles stepwise into a 48-subunit multimer (alpha48) that sequesters >2000 atoms of iron in 2-4-nm cores structurally similar to ferritin iron cores. Here we show that mYfh1p assembly is driven by two sequential iron oxidation reactions: A ferroxidase reaction catalyzed by mYfh1p induces the first assembly step (alpha --> alpha3), followed by a slower autoxidation reaction that promotes the assembly of higher order oligomers yielding alpha48. Depending on the ionic environment, stepwise assembly is associated with accumulation of 50-75 Fe(II)/subunit. Initially, this Fe(II) is loosely bound to mYfh1p and can be readily mobilized by chelators or made available to the mitochondrial enzyme ferrochelatase to synthesize heme. Transfer of mYfh1p-bound Fe(II) to ferrochelatase occurs in the presence of citrate, a physiologic ferrous iron chelator, suggesting that the transfer involves an intermolecular interaction. If mYfh1p-bound Fe(II) is not transferred to a ligand, iron oxidation, and mineralization proceed to completion, Fe(III) becomes progressively less accessible, and a stable iron-protein complex is formed. Iron oxidation-driven stepwise assembly is a novel mechanism by which yeast frataxin can function as an iron chaperone or an iron store.
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Affiliation(s)
- Sungjo Park
- Department of Pediatric, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
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Cornah JE, Terry MJ, Smith AG. Green or red: what stops the traffic in the tetrapyrrole pathway? TRENDS IN PLANT SCIENCE 2003; 8:224-30. [PMID: 12758040 DOI: 10.1016/s1360-1385(03)00064-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Regulation of tetrapyrrole biosynthesis is crucial to plant metabolism. The two pivotal control points are formation of the initial precursor, 5-aminolaevulinic acid (ALA), and the metal-ion insertion step: chelation of Fe(2+) into protoporphyrin IX leads to haem and phytochromobilin, whereas insertion of Mg(2+) is the first step to chlorophyll. Recent studies with mutants and transgenic plants have demonstrated that perturbation of the branch point affects ALA formation. Moreover, one of the signals that controls the expression of genes for nuclear-encoded chloroplast proteins has been shown to be Mg-protoporphyrin-IX. Here, we discuss the regulation of branch-point flux and the relative contributions of the haem and chlorophyll branches to the regulation of ALA synthesis and thus to flow through the tetrapyrrole pathway.
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Affiliation(s)
- Johanna E Cornah
- Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, Scotland, UK EH9 3JR
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Current awareness on yeast. Yeast 2003; 20:455-62. [PMID: 12728936 DOI: 10.1002/yea.943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Lecerof D, Fodje MN, Alvarez León R, Olsson U, Hansson A, Sigfridsson E, Ryde U, Hansson M, Al-Karadaghi S. Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites. J Biol Inorg Chem 2003; 8:452-8. [PMID: 12761666 DOI: 10.1007/s00775-002-0436-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2002] [Accepted: 11/21/2002] [Indexed: 11/28/2022]
Abstract
Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyses metal insertion into protoporphyrin IX. The location of the metal binding site with respect to the bound porphyrin substrate and the mode of metal binding are of central importance for understanding the mechanism of porphyrin metallation. In this work we demonstrate that Zn(2+), which is commonly used as substrate in assays of the ferrochelatase reaction, and Cd(2+), an inhibitor of the enzyme, bind to the invariant amino acids His183 and Glu264 and water molecules, all located within the porphyrin binding cleft. On the other hand, Mg(2+), which has been shown to bind close to the surface at 7 A from His183, was largely absent from its site. Activity measurements demonstrate that Mg(2+) has a stimulatory effect on the enzyme, lowering K(M) for Zn(2+) from 55 to 24 micro M. Changing one of the Mg(2+) binding residues, Glu272, to serine abolishes the effect of Mg(2+). It is proposed that prior to metal insertion the metal may form a sitting-atop (SAT) complex with the invariant His-Glu couple and the porphyrin. Metal binding to the Mg(2+) site may stimulate metal release from the protein ligands and its insertion into the porphyrin.
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Affiliation(s)
- David Lecerof
- Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, PO Box 124, 221 00 Lund, Sweden
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