Transformation of Uroporphyrinogen III into Protohaem

  • Johanna E. Cornah
  • Alison G. Smith
Part of the Molecular Biology Intelligence Unit book series (MBIU)


Haem is an essential cofactor for virtually all organisms. It is made from the common tetrapyrrole progenitor, uroporphyrinogen III, by four sequential enzymes: uroporphyrinogen III decarboxylase, coproporphyrinogen III oxidase, protoporphyrinogen IX oxidase, and ferrochelatase. Each of the enzymes catalyses a remarkable reaction, with the first three required to carry out the same reaction at multiple sites on the substrate molecule. Now that the crystal structures are available for each of the proteins, the mechanisms of these essential enzymes are beginning to be elucidated. Despite the universality of haem synthesis however, there are differences between organisms. Firsdy in many bacteria there are anaerobic forms of the two oxidases, which appear to have completely different origins from the aerobic forms found in eukaryotes. Secondly, in certain bacteria some or all of these enzymes are missing completely; either they are pathogenic and can take up haem from their host, or there are alternative, as yet uncharacterized, enzymes. Finally, within the eukaryotes, the subcellular distribution of the enzymes differs depending on the organism, which has ramifications for the regulation of the biosynthetic pathway.


Haem Biosynthesis Terminal Enzyme Protoporphyrinogen Oxidase Uroporphyrinogen Decarboxylase COOH COOH COOH 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Panek H, O’Brian MR. A whole genome view of prokaryotic haem biosynthesis. Microbiology 2002; 148:2273–2282.PubMedGoogle Scholar
  2. 2.
    Rao AU, Carta LK, Lesuisse E et al. Lack of heme synthesis in a free-living eukaryote. Proc Natl Acad Sci USA 2005; 102:4270–4275.CrossRefPubMedGoogle Scholar
  3. 3.
    Labbe-Bois R. The ferrochelatase from Saccharomyces cerevisiae. Sequence, disruption, and expression of its structural gene HEM15. J Biol Chem 1990; 265:7278–7283.PubMedGoogle Scholar
  4. 4.
    Chow KS, Singh DP, Amanda RW et al. Two different genes encode ferrochelatase in Arabidopsis: Mapping, expression and subcellular targeting of the precursor proteins. Plant J 1998; 15:531–541.CrossRefPubMedGoogle Scholar
  5. 5.
    Santana MA, Tan FC, Smith AG. Molecular characterisation of coproporphyrinogen oxidase from Glycine max and Arabidopsis thaliana. Plant Physiol Biochem 2002; 40:289–298.CrossRefGoogle Scholar
  6. 6.
    Shoolingin-Jordan PM. The biosynthesis of coproporphyrinogen III. In: Kadish KM, Smith KM, Guilard R, eds. The Porphyrin Handbook. Vol 12. The Iron and Cobalt Pigments: Biosynthesis, Structure and Degradation. New York: Elsevier, 2003:33–74.Google Scholar
  7. 7.
    Whitby FG, Phillips JD, Kushner JP et al. Crystal structure of human uroporphyrinogen decarboxylase. EMBO J 1998; 17:2463–2471.CrossRefPubMedGoogle Scholar
  8. 8.
    Martins BM, Grimm B, Mock HP et al. Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum—Implications for the catalytic mechanism. J Biol Chem 2001; 276:44108–44116.CrossRefPubMedGoogle Scholar
  9. 9.
    Felix F, Brouillet N. Purification and properties of uroporphyrinogen decarboxylase from Saccharomyces cerevisiae. Yeast uroporphyrinogen decarboxylase. Eur J Biochem 1990; 188:393–403.CrossRefPubMedGoogle Scholar
  10. 10.
    Luo J, Lim CK. Order of uroporphyrinogen III decarboxylation on incubation of porphobilinogen and uroporphyrinogen III with erythrocyte uroporphyrinogen decarboxylase. Biochem J 1993; 289:529–532.PubMedGoogle Scholar
  11. 11.
    Phillips JD, Whitby FG, Kushner JP et al. Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase. EMBO J 2003; 22:6225–6233.CrossRefPubMedGoogle Scholar
  12. 12.
    Hansson M, Hederstedt L. Cloning and characterization of the Bacillus subtilis hemEHY gene cluster, which encodes protoheme IX biosynthetic enzymes. J Bacteriol 1992; 174:8081–8093.PubMedGoogle Scholar
  13. 13.
    Ishida T, Yu L, Akutsu H et al. A primitive pathway of porphyrin biosynthesis and enzymology in Desulfovibrio vulgaris. Proc Natl Acad Sci USA 1998; 95:4853–4858.CrossRefPubMedGoogle Scholar
  14. 14.
    Akhtar M. Coproporphyrinogen III and protoporphyrinogen IX oxidases. In: Kadish KM, Smith KM, Guilard R, eds. The Porphyrin Handbook. Vol 12. The Iron and Cobalt Pigments: Biosynthesis, Structrue and Degradation. New York: Elsevier, 2003:75–92.Google Scholar
  15. 15.
    Layer G, Verfurth K, Mahlitz E et al. Oxygen-independent coproporphyrinogen-III oxidase HemN from Escherichia coli. J Biol Chem 2002; 277:34136–34142.CrossRefPubMedGoogle Scholar
  16. 16.
    Layer G, Moser J, Heinz DW et al. Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes. EMBO J 2003; 22:6214–6224.CrossRefPubMedGoogle Scholar
  17. 17.
    Lee DS, Flachsova E, Bodnarova M et al. Structural basis of hereditary coproporphyria. Proc Natl Acad Sci USA 2005; 102:14232–14237.CrossRefPubMedGoogle Scholar
  18. 18.
    Kohno H, Furukawa T, Tokunaga R et al. Mouse coproporphyrinogen oxidase is a copper-containing enzyme: Expression in Escherichia coli and site-directed mutagenesis. Biochim Biophys Acta 1996; 1292:156–162.PubMedGoogle Scholar
  19. 19.
    Breckau D, Mahlitz E, Sauerwald A et al. Oxygen-dependent coproporphyrinogen III oxidase (HemF) from Escherichia coli is stimulated by manganese. J Biol Chem 2003; 278:46625–46631.CrossRefPubMedGoogle Scholar
  20. 20.
    Phillips JD, Whitby FG, Warby CA et al. Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae. J Biol Chem 2004; 279:38960–38968.CrossRefPubMedGoogle Scholar
  21. 21.
    Lash TD. The enigma of coproporphyrinogen oxidase: How does this unusual enzyme carry out oxidative decarboxylations to afford vinyl groups? Bioorg Med Chem Lett 2005; 15:4506–4509.CrossRefPubMedGoogle Scholar
  22. 22.
    Lash TD, Kaprak TA, Shen L et al. Metabolism of analogues of coproporphyrinogen-III with modified side chains: Implications for binding at the active site of coproporphyrinogen oxidase. Bioorg Med Chem Lett 2002; 12:451–456.CrossRefPubMedGoogle Scholar
  23. 23.
    Jones MA, He J, Lash TD. Kinetic studies of novel di-and tri-propionate substrates for the chicken red blood cell enzyme coproporphyrinogen oxidase. J Biochem (Tokyo) 2002; 131:201–205.Google Scholar
  24. 24.
    Narita S, Taketani S, Inokuchi H. Oxidation of protoporphyrinogen IX in Escherichia coli is mediated by the aerobic coproporphyrinogen III oxidase. Mol Gen Genet 1999; 261:1012–1020.CrossRefPubMedGoogle Scholar
  25. 25.
    Dailey TA, Dailey HA. Identification of an FAD superfamily containing protoporphyrinogen oxidases, monoamine oxidases, and phytoene desaturase. Expression and characterization of phytoene desaturase of Myxococcus xanthus. J Biol Chem 1998; 273:13658–13662.CrossRefPubMedGoogle Scholar
  26. 26.
    Lermontova I, Kruse E, Mock HP et al. Cloning and characterization of a plastidal and a mitochondrial isoform of tobacco protoporphyrinogen IX oxidase. Proc Nad Acad Sci USA 1997; 94:8895–8900.CrossRefGoogle Scholar
  27. 27.
    Che FS, Watanabe N, Iwano M et al. Molecular characterization and subcellular localization of protoporphyrinogen oxidase in spinach chloroplasts. Plant Physiol 2000; 124:59–70.CrossRefPubMedGoogle Scholar
  28. 28.
    Arnould S, Takahashi M, Camadro JM. Acylation stabilizes a protease-resistant conformation of protoporphyrinogen oxidase, the molecular target of diphenyl ether-type herbicides. Proc Natl Acad Sci USA 1999; 96:14825–14830.CrossRefPubMedGoogle Scholar
  29. 29.
    Koch M, Breithaupt C, Kiefersauer R et al. Crystal structure of protoporphyrinogen IX oxidase: A key enzyme in haem and chlorophyll biosynthesis. EMBO J 2004; 23:1720–1728.CrossRefPubMedGoogle Scholar
  30. 30.
    Matringe M, Camadro JM, Labbe P et al. Protoporphyrinogen oxidase as a molecular target for diphenyl ether herbicides. Biochem J 1989; 260:231–235.PubMedGoogle Scholar
  31. 31.
    Smith AG, Marsh O, Elder GH. Investigation of the subcellular location of the tetrapyrrole-biosynthesis enzyme coproporphyrinogen oxidase in higher-plants. Biochem J 1993; 292:503–508.PubMedGoogle Scholar
  32. 32.
    Lee HJ, Duke MV, Duke SO. Cellular Localization of protoporphyrinogen-oxidizing activities of etiolated barley (Hordeum vulgare L.) leaves (relationship to mechanism of action of protoporphyrinogen oxidase-inhibiting herbicides). Plant Physiol 1993; 102:881–889.PubMedGoogle Scholar
  33. 33.
    Fingar VH, Wieman TJ, McMahon KS et al. Photodynamic therapy using a protoporphyrinogen oxidase inhibitor. Cancer Res 1997; 57:4551–4556.PubMedGoogle Scholar
  34. 34.
    Dailey HA. Terminal steps of haem biosynthesis. Biochem Soc Trans 2002; 30:590–595.CrossRefPubMedGoogle Scholar
  35. 35.
    Sasarman A, Letowski J, Czaika G et al. Nucleotide sequence of the hemG gene involved in the protoporphyrinogen oxidase activity of Escherichia coli K12. Can J Microbiol 1993; 39:1155–1161.PubMedCrossRefGoogle Scholar
  36. 36.
    Dailey TA, Dailey HA, Meissner P et al. Cloning, sequence, and expression of mouse protoporphyrinogen oxidase. Arch Biochem Biophys 1995; 324:379–384.CrossRefPubMedGoogle Scholar
  37. 37.
    Narita S, Taketani S, Inokuchi H. Oxidation of protoporphyrinogen IX in Escherichia coli is mediated by the aerobic coproporphyrinogen oxidase. Mol Gen Genet 1999; 261:1012–1020.CrossRefPubMedGoogle Scholar
  38. 38.
    Dailey HA, Dailey TA, Wu CK et al. Ferrochelatase at the millennium: Structures, mechanisms and [2Fe-2S] clusters. Cell Mol Life Sci 2000; (57):1909–1926.Google Scholar
  39. 39.
    Dailey H, Dailey T. Ferrochelatase. In: Kadish KM, Smith KM, Guilard R, eds. The Porphyrin Handbook. Vol 12. The Iron and Cobalt Pigments: Biosynthesis, Structure and Degradation. New York: Elsevier, 2003:93–121.Google Scholar
  40. 40.
    Al-Karadaghi S, Hansson M, Nikonov S et al. Crystal structure of ferrochelatase: The terminal enzyme in heme biosynthesis. Structure 1997; 5:1501–1510.CrossRefPubMedGoogle Scholar
  41. 41.
    Wu CK, Dailey HA, Rose JP et al. The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis. Nat Struct Biol 2001; 8:156–160.CrossRefPubMedGoogle Scholar
  42. 42.
    Grzybowska E, Gora M, Plochocka D et al. Saccharomyces cerevisiae ferrochelatase forms a homodimer. Arch Biochem Biophys 2002; 398:170–178.CrossRefPubMedGoogle Scholar
  43. 43.
    Matringe M, Camadro JM, Joyard J et al. Localization of ferrochelatase activity within mature pea chloroplasts. J Biol Chem 1994; 269:15010–15015.PubMedGoogle Scholar
  44. 44.
    Roper JM, Smith AG. Molecular localisation of ferrochelatase in higher plant chloroplasts. Eur J Biochem 1997; 246:32–37.CrossRefPubMedGoogle Scholar
  45. 45.
    Cornah JE, Roper JM, Singh DP et al. Measurement of ferrochelatase activity using a novel assay suggests that plastids are the major site of haem biosynthesis in both photosynthetic and nonphotosynthetic cells of pea (Pisum sativum L.). Biochem J 2002; 362:423–432.CrossRefPubMedGoogle Scholar
  46. 46.
    Karlberg T, Lecerof D, Gora M et al. Metal binding to Saccharomyces cerevisiae ferrochelatase. Biochemistry 2002; 41:13499–13506.CrossRefPubMedGoogle Scholar
  47. 47.
    Lecerof D, Fodje MN, Alvarez Leon R et al. Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites. J Biol Inorg Chem 2003; 8:452–458.PubMedGoogle Scholar
  48. 48.
    Suzuki T, Masuda T, Singh DP et al. Two types of ferrochelatase in photosynthetic and nonphotosynthetic tissues of cucumber—Their difference in phylogeny, gene expression, and localization. J Biol Chem 2002; 277:4731–4737.CrossRefPubMedGoogle Scholar
  49. 49.
    Singh DP, Cornah JE, Hadingham S et al. Expression analysis of the two ferrochelatase genes in Arabidopsis in different tissues and under stress conditions reveals their different roles in haem biosynthesis. Plant Mol Biol 2002; 50:773–788.CrossRefPubMedGoogle Scholar
  50. 50.
    Jansson S. A guide to the LHC genes and their relatives in Arabidopsis. Trends Plant Sci 1999; 4:236–240.CrossRefPubMedGoogle Scholar
  51. 51.
    Jansson S, Andersson J, Kim SJ et al. An Arabidopsis thaliana protein homologous to cyanobacterial high-light-inducible proteins. Plant Mol Biol 2000; 42:345–351.CrossRefPubMedGoogle Scholar
  52. 52.
    Cornah JE, Terry MJ, Smith AG. Green or red: What stops the traffic in the tetrapyrrole pathway? Trends Plant Sci 2003; 8:224–230.CrossRefPubMedGoogle Scholar
  53. 53.
    Walker CJ, Willows RD. Mechanism and regulation of Mg-chelatase. Biochem J 1997; 327:321–333.PubMedGoogle Scholar
  54. 54.
    Schubert HL, Raux E, Wilson KS et al. Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis. Biochemistry 1999; 38:10660–10669.CrossRefPubMedGoogle Scholar
  55. 55.
    Nakahigashi K, Nishimura K, Miyamoto K et al. Photosensitivity of a protoporphyrin-accumulating, light-sensitive mutant (visA) of Escherichia coli K-12. Proc Natl Acad Sci USA 1991; 88:10520–10524.CrossRefPubMedGoogle Scholar
  56. 56.
    Hu G, Yalpani N, Briggs SP et al. A porphyrin pathway impairment is responsible for the phenotype of a dominant disease lesion mimic mutant of maize. Plant Cell 1998; 10:1095–1105.CrossRefPubMedGoogle Scholar
  57. 57.
    Ferreira GC, Andrew TL, Karr SW et al. Organization of the terminal two enzymes of the heme biosynthetic pathway. Orientation of protoporphyrinogen oxidase and evidence for a membrane complex. J Biol Chem 1988; 263:3835–3839.PubMedGoogle Scholar
  58. 58.
    Smith AG, Cornah JE, Roper JM et al. Compartmentation of tetrapyrrole metabolism in higher plants. In: Bryant JA, Burrell MM, Kruger NJ, eds. Plant Carbohydrate Metabolism. Oxford: BIOS Scientific Publishers, 1999:281–294.Google Scholar
  59. 59.
    Watanabe N, Che FS, Iwano M et al. Dual targeting of spinach protoporphyrinogen oxidase II to mitochondria and chloroplasts by alternative use of two in-frame initiation codons. J Biol Chem 2001; 276:20474–20481.CrossRefPubMedGoogle Scholar
  60. 60.
    Chow KS, Singh DP, Roper JM et al. A single precursor protein for ferrochelatase-I from Arabidopsis is imported in vitro into both chloroplasts and mitochondria. J Biol Chem 1997; 272:27565–27571.CrossRefPubMedGoogle Scholar
  61. 61.
    Cleary SP, Tan FC, Nakrieko KA et al. Isolated plant mitochondria import chloroplast precursor proteins in vitro with the same efficiency as chloroplasts. J Biol Chem 2002; 277:5562–5569.CrossRefPubMedGoogle Scholar
  62. 62.
    Jacobs JM, Jacobs NJ. Porphyrin accumulation and export by isolated barley (Hordeum vulgare) plastids (effect of diphenyl ether herbicides). Plant Physiol 1993; 101:1181–1187.PubMedGoogle Scholar
  63. 63.
    Harbin BM, Dailey HA. Orientation of ferrochelatase in bovine liver mitochondria. Biochemistry 1985; 24:366–370.CrossRefPubMedGoogle Scholar
  64. 64.
    Proulx KL, Woodard SI, Dailey HA. In situ conversion of coproporphyrinogen to heme by murine mitochondria: Terminal steps of the heme biosynthetic pathway. Protein Sci 1993; 2:1092–1098.CrossRefPubMedGoogle Scholar
  65. 65.
    Olsson U, Billberg A, Sjovall S et al. In vivo and in vitro studies of Bacillus subtilis ferrochelatase mutants suggest substrate channeling in the heme biosynthesis pathway. J Bacteriol 2002; 184:4018–4024.CrossRefPubMedGoogle Scholar
  66. 66.
    Matringe M, Camadro JM, Block MA et al. Localization within chloroplasts of protoporphyrinogen oxidase, the target enzyme for diphenylether-like herbicides. J Biol Chem 1992; 267:4646–4651.PubMedGoogle Scholar
  67. 67.
    Hamza I, Chauhan S, Hassett R et al. The bacterial irr protein is required for coordination of heme biosynthesis with iron availability. J Biol Chem 1998; 273:21669–21674.CrossRefPubMedGoogle Scholar
  68. 68.
    Lange H, Kispal G, Lill R. Mechanism of iron transport to the site of heme synthesis inside yeast mitochondria. J Biol Chem 1999; 274:18989–18996.CrossRefPubMedGoogle Scholar
  69. 69.
    Yoon T, Cowan JA. Frataxin-mediated iron delivery to ferrochelatase in the final step of heme biosynthesis. J Biol Chem 2004; 279:25943–25946.CrossRefPubMedGoogle Scholar

Copyright information

© Landes Bioscience and Springer Science+Business Media 2009

Authors and Affiliations

  1. 1.Department of Plant SciencesUniversity of CambridgeCambridgeUK

Personalised recommendations