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1.
Front Microbiol ; 15: 1378989, 2024.
Article in English | MEDLINE | ID: mdl-38544863

ABSTRACT

Nature utilizes three distinct pathways to synthesize the essential enzyme cofactor heme. The coproporphyrin III-dependent pathway, predominantly present in Bacillaceae, employs an oxygen-dependent coproporphyrinogen III oxidase (CgoX) that converts coproporphyrinogen III into coproporphyrin III. In this study, we report the bioinformatic-based identification of a gene called ytpQ, encoding a putative oxygen-independent counterpart, which we propose to term CgoN, from Priestia (Bacillus) megaterium. The recombinantly produced, purified, and monomeric YtpQ (CgoN) protein is shown to catalyze the oxygen-independent conversion of coproporphyrinogen III into coproporphyrin III. Minimal non-enzymatic conversion of coproporphyrinogen III was observed under the anaerobic test conditions employed in this study. FAD was identified as a cofactor, and menadione served as an artificial acceptor for the six abstracted electrons, with a KM value of 3.95 µmol/L and a kcat of 0.63 per min for the substrate. The resulting coproporphyrin III, in turn, acts as an effective substrate for the subsequent enzyme of the pathway, the coproporphyrin III ferrochelatase (CpfC). Under aerobic conditions, oxygen directly serves as an electron acceptor, but is replaced by the more efficient action of menadione. An AlphaFold2 model of the enzyme suggests that YtpQ adopts a compact triangular shape consisting of three domains. The N-terminal domain appears to be flexible with respect to the rest of the structure, potentially creating a ligand binding site that opens and closes during the catalytic cycle. A catalytic mechanism similar to the oxygen-independent protoporphyrinogen IX oxidase PgoH1 (HemG), based on the flavin-dependent abstraction of six electrons from coproporphyrinogen III and their potential quinone-dependent transfer to a membrane-localized electron transport chain, is proposed.

2.
Elife ; 62017 05 29.
Article in English | MEDLINE | ID: mdl-28553927

ABSTRACT

Heme is required for survival of all cells, and in most eukaryotes, is produced through a series of eight enzymatic reactions. Although heme production is critical for many cellular processes, how it is coupled to cellular differentiation is unknown. Here, using zebrafish, murine, and human models, we show that erythropoietin (EPO) signaling, together with the GATA1 transcriptional target, AKAP10, regulates heme biosynthesis during erythropoiesis at the outer mitochondrial membrane. This integrated pathway culminates with the direct phosphorylation of the crucial heme biosynthetic enzyme, ferrochelatase (FECH) by protein kinase A (PKA). Biochemical, pharmacological, and genetic inhibition of this signaling pathway result in a block in hemoglobin production and concomitant intracellular accumulation of protoporphyrin intermediates. Broadly, our results implicate aberrant PKA signaling in the pathogenesis of hematologic diseases. We propose a unifying model in which the erythroid transcriptional program works in concert with post-translational mechanisms to regulate heme metabolism during normal development.


Subject(s)
A Kinase Anchor Proteins/metabolism , Erythropoietin/metabolism , GATA1 Transcription Factor/metabolism , Heme/biosynthesis , Signal Transduction , Animals , Cyclic AMP-Dependent Protein Kinases/metabolism , Humans , Mice , Mitochondrial Membranes/metabolism , Zebrafish
3.
Microbiol Mol Biol Rev ; 81(1)2017 03.
Article in English | MEDLINE | ID: mdl-28123057

ABSTRACT

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


Subject(s)
Archaea/metabolism , Bacteria/metabolism , Heme/analogs & derivatives , Iron/chemistry , Tetrapyrroles/biosynthesis , Aminolevulinic Acid/metabolism , Coproporphyrinogen Oxidase/metabolism , Coproporphyrins/metabolism , Heme/biosynthesis , Protoporphyrins/biosynthesis , Protoporphyrins/metabolism , Uroporphyrinogen Decarboxylase/metabolism
4.
Proc Natl Acad Sci U S A ; 112(7): 2210-5, 2015 Feb 17.
Article in English | MEDLINE | ID: mdl-25646457

ABSTRACT

It has been generally accepted that biosynthesis of protoheme (heme) uses a common set of core metabolic intermediates that includes protoporphyrin. Herein, we show that the Actinobacteria and Firmicutes (high-GC and low-GC Gram-positive bacteria) are unable to synthesize protoporphyrin. Instead, they oxidize coproporphyrinogen to coproporphyrin, insert ferrous iron to make Fe-coproporphyrin (coproheme), and then decarboxylate coproheme to generate protoheme. This pathway is specified by three genes named hemY, hemH, and hemQ. The analysis of 982 representative prokaryotic genomes is consistent with this pathway being the most ancient heme synthesis pathway in the Eubacteria. Our results identifying a previously unknown branch of tetrapyrrole synthesis support a significant shift from current models for the evolution of bacterial heme and chlorophyll synthesis. Because some organisms that possess this coproporphyrin-dependent branch are major causes of human disease, HemQ is a novel pharmacological target of significant therapeutic relevance, particularly given high rates of antimicrobial resistance among these pathogens.


Subject(s)
Actinobacteria/metabolism , Coproporphyrins/physiology , Gram-Positive Bacteria/metabolism , Heme/biosynthesis , Protoporphyrins/metabolism , Actinobacteria/genetics , Chromatography, High Pressure Liquid , Genome, Bacterial , Gram-Positive Bacteria/genetics
5.
J Clin Invest ; 124(10): 4294-304, 2014 Oct.
Article in English | MEDLINE | ID: mdl-25157825

ABSTRACT

The transport and intracellular trafficking of heme biosynthesis intermediates are crucial for hemoglobin production, which is a critical process in developing red cells. Here, we profiled gene expression in terminally differentiating murine fetal liver-derived erythroid cells to identify regulators of heme metabolism. We determined that TMEM14C, an inner mitochondrial membrane protein that is enriched in vertebrate hematopoietic tissues, is essential for erythropoiesis and heme synthesis in vivo and in cultured erythroid cells. In mice, TMEM14C deficiency resulted in porphyrin accumulation in the fetal liver, erythroid maturation arrest, and embryonic lethality due to profound anemia. Protoporphyrin IX synthesis in TMEM14C-deficient erythroid cells was blocked, leading to an accumulation of porphyrin precursors. The heme synthesis defect in TMEM14C-deficient cells was ameliorated with a protoporphyrin IX analog, indicating that TMEM14C primarily functions in the terminal steps of the heme synthesis pathway. Together, our data demonstrate that TMEM14C facilitates the import of protoporphyrinogen IX into the mitochondrial matrix for heme synthesis and subsequent hemoglobin production. Furthermore, the identification of TMEM14C as a protoporphyrinogen IX importer provides a genetic tool for further exploring erythropoiesis and congenital anemias.


Subject(s)
Erythropoiesis/genetics , Heme/metabolism , Mitochondria/metabolism , Mitochondrial Membrane Transport Proteins/metabolism , Anemia/metabolism , Animals , Cell Line , Erythroid Cells/metabolism , Gene Expression Regulation , Hemoglobins/metabolism , Liver/embryology , Membrane Proteins/genetics , Membrane Proteins/metabolism , Mice , Mitochondrial Membrane Transport Proteins/genetics , Mitochondrial Membranes/metabolism , Porphyrins/metabolism , Protoporphyrins/metabolism , RNA, Small Interfering/metabolism
6.
Nature ; 491(7425): 608-12, 2012 Nov 22.
Article in English | MEDLINE | ID: mdl-23135403

ABSTRACT

Defects in the availability of haem substrates or the catalytic activity of the terminal enzyme in haem biosynthesis, ferrochelatase (Fech), impair haem synthesis and thus cause human congenital anaemias. The interdependent functions of regulators of mitochondrial homeostasis and enzymes responsible for haem synthesis are largely unknown. To investigate this we used zebrafish genetic screens and cloned mitochondrial ATPase inhibitory factor 1 (atpif1) from a zebrafish mutant with profound anaemia, pinotage (pnt (tq209)). Here we describe a direct mechanism establishing that Atpif1 regulates the catalytic efficiency of vertebrate Fech to synthesize haem. The loss of Atpif1 impairs haemoglobin synthesis in zebrafish, mouse and human haematopoietic models as a consequence of diminished Fech activity and elevated mitochondrial pH. To understand the relationship between mitochondrial pH, redox potential, [2Fe-2S] clusters and Fech activity, we used genetic complementation studies of Fech constructs with or without [2Fe-2S] clusters in pnt, as well as pharmacological agents modulating mitochondrial pH and redox potential. The presence of [2Fe-2S] cluster renders vertebrate Fech vulnerable to perturbations in Atpif1-regulated mitochondrial pH and redox potential. Therefore, Atpif1 deficiency reduces the efficiency of vertebrate Fech to synthesize haem, resulting in anaemia. The identification of mitochondrial Atpif1 as a regulator of haem synthesis advances our understanding of the mechanisms regulating mitochondrial haem homeostasis and red blood cell development. An ATPIF1 deficiency may contribute to important human diseases, such as congenital sideroblastic anaemias and mitochondriopathies.


Subject(s)
Erythroblasts/metabolism , Erythropoiesis , Heme/biosynthesis , Mitochondria/metabolism , Mitochondrial Proteins/metabolism , Proteins/metabolism , Anemia, Sideroblastic/genetics , Anemia, Sideroblastic/metabolism , Anemia, Sideroblastic/pathology , Animals , Disease Models, Animal , Erythroblasts/cytology , Ferrochelatase/metabolism , Genetic Complementation Test , Humans , Hydrogen-Ion Concentration , Mice , Mitochondria/pathology , Mitochondrial Proteins/deficiency , Mitochondrial Proteins/genetics , Oxidation-Reduction , Proteins/genetics , Zebrafish/metabolism , ATPase Inhibitory Protein
7.
Biochemistry ; 51(27): 5422-33, 2012 Jul 10.
Article in English | MEDLINE | ID: mdl-22712763

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.


Subject(s)
Ferrochelatase/chemistry , Ferrochelatase/metabolism , Solvents/metabolism , Biocatalysis , Catalytic Domain , Humans , Hydrogen Bonding , Kinetics , Models, Molecular , Protein Multimerization , Protein Structure, Quaternary
8.
mBio ; 2(6): e00248-11, 2011.
Article in English | MEDLINE | ID: mdl-22068980

ABSTRACT

UNLABELLED: The protein YfeX from Escherichia coli has been proposed to be essential for the process of iron removal from heme by carrying out a dechelation of heme without cleavage of the porphyrin macrocycle. Since this proposed reaction is unique and would represent the first instance of the biological dechelation of heme, we undertook to characterize YfeX. Our data reveal that YfeX effectively decolorizes the dyes alizarin red and Cibacron blue F3GA and has peroxidase activity with pyrogallal but not guiacol. YfeX oxidizes protoporphyrinogen to protoporphyrin in vitro. However, we were unable to detect any dechelation of heme to free porphyrin with purified YfeX or in cellular extracts of E. coli overexpressing YfeX. Additionally, Vibrio fischeri, an organism that can utilize heme as an iron source when grown under iron limitation, is able to grow with heme as the sole source of iron when its YfeX homolog is absent. Plasmid-driven expression of YfeX in V. fischeri grown with heme did not result in accumulation of protoporphyrin. We propose that YfeX is a typical dye-decolorizing peroxidase (or DyP) and not a dechelatase. The protoporphyrin reported to accumulate when YfeX is overexpressed in E. coli likely arises from the intracellular oxidation of endogenously synthesized protoporphyrinogen and not from dechelation of exogenously supplied heme. Bioinformatic analysis of bacterial YfeX homologs does not identify any connection with iron acquisition but does suggest links to anaerobic-growth-related respiratory pathways. Additionally, some genes encoding homologs of YfeX have tight association with genes encoding a bacterial cytoplasmic encapsulating protein. IMPORTANCE: Acquisition of iron from the host during infection is a limiting factor for growth and survival of pathogens. Host heme is the major source of iron in infections, and pathogenic bacteria have evolved complex mechanisms to acquire heme and abstract the iron from heme. Recently Létoffé et al. (Proc. Natl. Acad. Sci. U.S.A. 106:11719-11724, 2009) reported that the protein YfeX from E. coli is able to dechelate heme to remove iron and leave an intact tetrapyrrole. This is totally unlike any other described biological system for iron removal from heme and, thus, would represent a dramatically new feature with potentially profound implications for our understanding of bacterial pathogenesis. Given that this reaction has no precedent in biological systems, we characterized YfeX and a related protein. Our data clearly demonstrate that YfeX is not a dechelatase as reported but is a peroxidase that oxidizes endogenous porphyrinogens to porphyrins.


Subject(s)
Cation Transport Proteins/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/enzymology , Heme/metabolism , Oxidoreductases/metabolism , Porphyrinogens/metabolism , Aliivibrio fischeri/enzymology , Aliivibrio fischeri/genetics , Anthraquinones/metabolism , Escherichia coli/genetics , Peroxidase/metabolism , Pyrogallol/metabolism , Triazines/metabolism
9.
J Biol Chem ; 285(34): 25978-86, 2010 Aug 20.
Article in English | MEDLINE | ID: mdl-20543190

ABSTRACT

Here we identify a previously undescribed protein, HemQ, that is required for heme synthesis in Gram-positive bacteria. We have characterized HemQ from Bacillus subtilis and a number of Actinobacteria. HemQ is a multimeric heme-binding protein. Spectroscopic studies indicate that this heme is high spin ferric iron and is ligated by a conserved histidine with the sixth coordination site available for binding a small molecule. The presence of HemQ along with the terminal two pathway enzymes, protoporphyrinogen oxidase (HemY) and ferrochelatase, is required to synthesize heme in vivo and in vitro. Although the exact role played by HemQ remains to be characterized, to be fully functional in vitro it requires the presence of a bound heme. HemQ possesses minimal peroxidase activity, but as a catalase it has a turnover of over 10(4) min(-1). We propose that this activity may be required to eliminate hydrogen peroxide that is generated by each turnover of HemY. Given the essential nature of heme synthesis and the restricted distribution of HemQ, this protein is a potential antimicrobial target for pathogens such as Mycobacterium tuberculosis.


Subject(s)
Biosynthetic Pathways , Gram-Positive Bacteria/metabolism , Heme/biosynthesis , Actinobacteria/metabolism , Bacillus subtilis/metabolism , Catalase/metabolism , Hydrogen Peroxide/metabolism , Peroxidase/metabolism
10.
J Mol Biol ; 393(2): 308-19, 2009 Oct 23.
Article in English | MEDLINE | ID: mdl-19703464

ABSTRACT

Ferrochelatase (protoheme ferrolyase, E.C. 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). Within the past two years, X-ray crystallographic data obtained with human ferrochelatase have clearly shown that significant structural changes occur during catalysis that are predicted to facilitate metal insertion and product release. One unanswered question about ferrochelatase involves defining the mechanism whereby some metals, such as divalent Fe, Co, Ni, and Zn, can be used by the enzyme in vitro to produce the corresponding metalloporphyrins, while other metals, such as divalent Mn, Hg, Cd, or Pb, are inhibitors of the enzyme. Through the use of high-resolution X-ray crystallography along with characterization of metal species via their anomalous diffraction, the identity and position of Hg, Cd, Ni, or Mn in the center of enzyme-bound porphyrin macrocycle were determined. When Pb, Hg, Cd, or Ni was present in the macrocycle, the conserved pi helix was in the extended, partially unwound "product release" state. Interestingly, in the structure of ferrochelatase with Mn-porphyrin bound, the pi helix is not extended or unwound and is in the "substrate-bound" conformation. These findings show that at least in the cases of Mn, Pb, Cd, and Hg, metal "inhibition" of ferrochelatase is not due to the inability of the enzyme to insert the metal into the macrocycle or by binding to a second metal binding site as has been previously proposed. Rather, inhibition occurs after metal insertion and results from poor or diminished product release. Possible explanations for the lack of product release are proposed herein.


Subject(s)
Ferrochelatase/chemistry , Ferrochelatase/metabolism , Metals/metabolism , Cadmium/chemistry , Cadmium/metabolism , Cobalt/chemistry , Cobalt/metabolism , Crystallography, X-Ray , Ferrochelatase/genetics , Heme/chemistry , Heme/metabolism , Humans , Iron/chemistry , Iron/metabolism , Lead/chemistry , Lead/metabolism , Mercury/chemistry , Mercury/metabolism , Metals/chemistry , Nickel/chemistry , Nickel/metabolism , Protein Structure, Secondary , Protoporphyrins/chemistry , Protoporphyrins/metabolism , Substrate Specificity , Zinc/chemistry , Zinc/metabolism
11.
Biochemistry ; 48(29): 6705-11, 2009 Jul 28.
Article in English | MEDLINE | ID: mdl-19583219

ABSTRACT

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) catalyzes the six-electron oxidation of protoporphyrinogen IX to the fully conjugated protoporphyrin IX. Eukaryotes and Gram-positive bacteria possess an oxygen-dependent, FAD-containing enzyme for this step, while the majority of Gram-negative bacteria lack this oxygen-dependent PPO. In Escherichia coli, PPO activity is known to be linked to respiration and the quinone pool. In E. coli SASX38, the knockout of hemG causes a loss of measurable PPO activity. HemG is a small soluble protein typical of long chain flavodoxins. Herein, purified recombinant HemG was shown to be capable of a menadione-dependent conversion of protoporphyrinogen IX to protoporphyrin IX. Electrochemical analysis of HemG revealed similarities to other flavodoxins. Interestingly, HemG, a member of a class of the long chain flavodoxin family that is unique to the gamma-proteobacteria, possesses a 22-residue sequence that, when transferred into E. coli flavodoxin A, produces a chimera that will complement an E. coli hemG mutant, indicating that this region confers PPO activity to the flavodoxin. These findings reveal a previously unidentified class of PPO enzymes that do not utilize oxygen as an electron acceptor, thereby allowing gamma-proteobacteria to synthesize heme in both aerobic and anaerobic environments.


Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Genes, Bacterial , Protoporphyrinogen Oxidase/metabolism , Vitamin K 3/metabolism , Amino Acid Sequence , Catalysis , Electron Spin Resonance Spectroscopy , Escherichia coli/genetics , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Molecular Sequence Data , Plasmids , Protoporphyrinogen Oxidase/chemistry , Protoporphyrinogen Oxidase/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid
12.
J Mol Biol ; 373(4): 1006-16, 2007 Nov 02.
Article in English | MEDLINE | ID: mdl-17884090

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.


Subject(s)
Ferrochelatase/chemistry , Ferrochelatase/metabolism , Protoporphyrins/metabolism , Binding Sites/genetics , Catalysis , Crystallography, X-Ray/methods , Ferrochelatase/genetics , Heme/chemistry , Heme/metabolism , Humans , Models, Biological , Models, Molecular , Mutation , Protein Structure, Secondary , Protein Structure, Tertiary , Protoporphyrins/chemistry
13.
Biochemistry ; 46(27): 7973-9, 2007 Jul 10.
Article in English | MEDLINE | ID: mdl-17567154

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.


Subject(s)
Ferrochelatase/metabolism , Binding Sites , Catalysis , Ferrochelatase/chemistry , Humans , Hydrogen Bonding , Models, Molecular
14.
Proc Natl Acad Sci U S A ; 104(6): 1789-93, 2007 Feb 06.
Article in English | MEDLINE | ID: mdl-17261801

ABSTRACT

Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme IX. Human ferrochelatase is a homodimeric, inner mitochondrial membrane-associated enzyme that possesses an essential [2Fe-2S] cluster. In this work, we report the crystal structure of human ferrochelatase with the substrate protoporphyrin IX bound as well as a higher resolution structure of the R115L variant without bound substrate. The data presented reveal that the porphyrin substrate is bound deep within an enclosed pocket. When compared with the location of N-methylmesoporphyrin in the Bacillus subtilis ferrochelatase, the porphyrin is rotated by approximately 100 degrees and is buried an additional 4.5 A deeper within the active site. The propionate groups of the substrate do not protrude into solvent and are bound in a manner similar to what has been observed in uroporphyrinogen decarboxylase. Furthermore, in the substrate-bound form, the jaws of the active site mouth are closed so that the porphyrin substrate is completely engulfed in the pocket. These data provide insights that will aid in the determination of the mechanism for ferrochelatase.


Subject(s)
Ferrochelatase/chemistry , Ferrochelatase/metabolism , Protoporphyrins/chemistry , Protoporphyrins/metabolism , Amino Acid Substitution/genetics , Binding Sites/genetics , Crystallography, X-Ray , Ferrochelatase/genetics , Humans , Protein Binding/physiology , Substrate Specificity/genetics
15.
Biochem J ; 397(1): 47-52, 2006 Jul 01.
Article in English | MEDLINE | ID: mdl-16548850

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.


Subject(s)
Bacterial Proteins/metabolism , Evolution, Molecular , Ferrochelatase/metabolism , Iron/analysis , Protoporphyrins/metabolism , Sulfur/analysis , Amino Acid Motifs , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Caulobacter crescentus/enzymology , Cloning, Molecular , Cystine , Ferrochelatase/chemistry , Ferrochelatase/genetics , Kinetics , Membrane Proteins/chemistry , Membrane Proteins/genetics , Membrane Proteins/metabolism , Molecular Sequence Data , Mutagenesis, Site-Directed , Mycobacterium tuberculosis/enzymology
16.
Biochem J ; 386(Pt 2): 381-6, 2005 Mar 01.
Article in English | MEDLINE | ID: mdl-15482256

ABSTRACT

The initial and the terminal three enzymes of the mammalian haem biosynthetic pathway are nuclear encoded, cytoplasmically synthesized and post-translationally translocated into the mitochondrion. The first enzyme, ALAS (5-aminolaevulinate synthase), occurs as an isoenzyme encoded on different chromosomes and is synthesized either as a housekeeping protein (ALAS-1) in all non-erythroid cell types, or only in differentiating erythroid precursor cells (ALAS-2). Both ALAS proteins possess mitochondrial targeting sequences that have putative haem-binding motifs. In the present study, evidence is presented demonstrating that two haem-binding motifs in the leader sequence, as well as one present in the N-terminus of the mature ALAS-1 function in vivo in the haem-regulated translocation of ALAS-1. Coproporphyrinogen oxidase, the antepenultimate pathway enzyme, possesses a leader sequence that is approx. 120 residues long. In contrast with an earlier report suggesting that only 30 residues were required for translocation of the coproporphyrinogen oxidase, we report that the complete leader is necessary for translocation and that this process is not haem-sensitive in vivo. PPO (protoporphyrinogen oxidase) lacks a typical mitochondrial targeting leader sequence and was found to be effectively targeted by just 17 N-terminal residues. Bacillus subtilis PPO, which is very similar to human PPO at its N-terminal end, is not targeted to the mitochondrion when expressed in mammalian cells, demonstrating that the translocation is highly specific with regard to both the length and spacing of charged residues in this targeting region. Ferrochelatase, the terminal enzyme, possesses a typical N-terminal leader sequence and no evidence of a role for the C-terminus was found in mitochondrial targeting.


Subject(s)
5-Aminolevulinate Synthetase/metabolism , Heme/biosynthesis , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , 5-Aminolevulinate Synthetase/genetics , Amino Acid Motifs/genetics , Animals , Carcinoma, Hepatocellular/pathology , Cell Line, Tumor , Cloning, Molecular , Coproporphyrinogen Oxidase/genetics , Exons/genetics , Ferrochelatase/metabolism , Flavoproteins , Humans , Liver Neoplasms, Experimental/pathology , Mice , Mitochondria/enzymology , Mitochondria/genetics , Molecular Sequence Data , Oxidoreductases Acting on CH-CH Group Donors/metabolism , Peptide Fragments/genetics , Peptide Fragments/metabolism , Protoporphyrinogen Oxidase , Protoporphyrins
17.
J Struct Funct Genomics ; 5(1-2): 159-65, 2004.
Article in English | MEDLINE | ID: mdl-15263854

ABSTRACT

The human protein production group at the Southeast Collaboratory for Structural Genomics is charged with producing human proteins for both X-ray crystallography and NMR structural studies. Eukaryotic, and human proteins in particular, are notoriously difficult to express in bacterial systems. For various reasons, T7-based expression often results in protein expressed in an insoluble form. Overcoming this requires either introduction of a step to screen expression conditions or inclusion of a troublesome refolding step during purification. Our laboratory uses a trc-based expression vector that addresses many of the difficulties of the commonly used T7-based expression systems. Proteins expressed under the trc promoter, a weak promoter compared to the strong T7 promoter, are produced in a soluble form and include necessary cofactors. The details of this system will be discussed.


Subject(s)
Genomics/methods , Proteomics/methods , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Cloning, Molecular , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors , Georgia , Humans , Laboratories , Molecular Structure , Promoter Regions, Genetic , Recombinant Proteins/isolation & purification , Solubility
18.
Protein Sci ; 12(5): 1109-18, 2003 May.
Article in English | MEDLINE | ID: mdl-12717032

ABSTRACT

The crystal structure of recombinant rat augmenter of liver regeneration (ALRp) has been determined to 1.8 A. The protein is a homodimer, stabilized by extensive noncovalent interactions and a network of hydrogen bonds, and possesses a noncovalently bound FAD in a motif previously found only in the related protein ERV2p. ALRp functions in vitro as a disulfide oxidase using dithiothreitol as reductant. Reduction of the flavin by DTT occurs under aerobic conditions resulting in a spectrum characteristic of a neutral semiquinone. This semiquinone is stable and is only fully reduced by addition of dithionite. Mutation of either of two cysteine residues that are located adjacent to the FAD results in inactivation of the oxidase activity. A comparison of ALRp with ERV2p is made that reveals a number of significant structural differences, which are related to the in vivo functions of these two proteins. Possible physiological roles of ALR are examined and a hypothesis that it may serve multiple roles is proposed.


Subject(s)
Oxidoreductases/chemistry , Proteins/chemistry , Amino Acid Sequence , Animals , Crystallography, X-Ray , Cysteine , Dithiothreitol , Flavin-Adenine Dinucleotide/chemistry , Models, Molecular , Molecular Structure , Mutagenesis, Site-Directed , Oxidation-Reduction , Oxidoreductases/metabolism , Protein Conformation , Protein Structure, Quaternary , Proteins/metabolism , Rats , Sequence Alignment
19.
Arch Biochem Biophys ; 407(2): 196-201, 2002 Nov 15.
Article in English | MEDLINE | ID: mdl-12413491

ABSTRACT

The cDNA for p22HBP has been cloned from human and mouse, and the protein expressed, purified, and characterized. Both mouse and human proteins bind heme and porphyrins with micromolar K(d)s, are highly homologous, monomeric, and soluble, and have a cytoplasmic location. The proteins bind metalloporphyrins, free porphyrins, and N-methylprotoporphyrin with similar affinities, and mutations of a selected set of putative metal ligating residues did not have any significant effect on the measured K(d)s. That the presence or absence of metal in the porphyrin has no effect on the binding constants and the observation that the EPR signal for heme does not change upon binding to the protein strongly suggest that p22HBP is a generic tetrapyrrole-binding protein rather than a dedicated heme-binding protein. A role for p22HBP in cellular porphyrin metabolism is discussed.


Subject(s)
Carrier Proteins/metabolism , Hemeproteins , Pyrroles/metabolism , Amino Acid Sequence , Animals , Carrier Proteins/analysis , Carrier Proteins/genetics , Cloning, Molecular , Cytoplasm/chemistry , Heme/metabolism , Heme-Binding Proteins , Humans , Mice , Molecular Sequence Data , Porphyrins/metabolism , Protein Binding , Proteins/analysis , Proteins/genetics , Proteins/metabolism , Sequence Alignment , Tetrapyrroles , Tumor Cells, Cultured
20.
Cell Mol Biol (Noisy-le-grand) ; 48(1): 61-9, 2002 Feb.
Article in English | MEDLINE | ID: mdl-11929049

ABSTRACT

The murine protoporphyrinogen oxidase gene has been isolated, characterized and localized. The gene spans 4.2 kb, is comprised of 13 exons and 12 introns, and is located on chromosome 1 in band 1 H2. Analysis of 1.2 kb of the 5' upstream region revealed a promoter which is not GC rich and lacks any TATA boxes or initiator elements in the vicinity of the transcription start site. A variety of putative transcriptional element binding sequences were identified and gel shift assays support the presence of two GATA-1 sites near -760 bp as well as AP-1, AP-2, and Sp1 sites in the -1200 bp 5' flanking region. Luciferase reporter constructs transiently expressed in erythroid cell lines demonstrated erythroid-specific expression with the -1160 bp, but not with the -746 bp or -198 bp constructs. Expression in nonerythroid cells occurred maximally with -1160 bp, but was significant with -746 bp and absent with -198 bp. Expression of both housekeeping and erythroid-specific fusions in the transient expression systems was greatly decreased in the -5000 bp constructs suggesting the presence of repressor elements in the -1160 to -5000 bp region.


Subject(s)
Genes, Essential/genetics , Mice/genetics , Oxidoreductases Acting on CH-CH Group Donors , Oxidoreductases/genetics , 5' Flanking Region/genetics , Animals , Base Sequence , Chromosome Mapping , Cloning, Molecular , Erythrocytes/metabolism , Exons , Flavoproteins , Gene Expression , Introns , Mitochondrial Proteins , Molecular Sequence Data , Protoporphyrinogen Oxidase , Response Elements/genetics , Tumor Cells, Cultured
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