MetaCyc Pathway: superpathway of heme biosynthesis from uroporphyrinogen-III
Traceable author statement to experimental support

Pathway diagram: superpathway of heme biosynthesis from uroporphyrinogen-III

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: BiosynthesisCofactors, Prosthetic Groups, Electron Carriers BiosynthesisPorphyrin Compounds BiosynthesisHeme Biosynthesis

Some taxa known to possess this pathway include : Escherichia coli K-12 substr. MG1655

Expected Taxonomic Range: Bacteria

Heme (protoheme, heme b) is an iron-containing prosthetic group found in many essential proteins including cytochromes and heme-containing globins. It is a porphyrin member of the cyclic tetrapyrroles. It is biosynthesized as protoheme, but different derivatives of protoheme can be formed that differ in modifications to the porphyrin ring, including how it is bound to the protein, such as heme o, heme a, heme c, and heme d.

This superpathway shows the two routes of synthesis found in the facultative anaerobe Escherichia coli. Under aerobic conditions, the transition from coproporphyrinogen III to protoporphyrinogen IX is catalyzed by the oxygen -dependent coproporphyrinogen III oxidase (EC However, when oxygen is not available, the organism is still able to catalyze this transition, using the readical-SAM enzyme coproporphyrinogen III dehydrogenase (EC, which can catalyze the transition without the need for molecular oxygen. This enzyme, which contains an iron-sulfur cluster, is able to break SAM into L-methionine and a 5'-deoxyadenosineyl radical. This radical can attack coproporphyrinogen III and bring about the conversion to protoporphyrinogen IX.

This enzyme is found in many bacteria, but does not appear to be present in archaea or eukarya (the only reference for the enzyme in a eukaryote is in the organism Tetrahymena thermophila, but this finding is based on sequence analysis alone, and has not been verified biochemically).

Important branch points within this pathway lead to biosynthesis of other important compounds such as vitamin B12 (cobalamin) (see adenosylcobalamin biosynthesis II (aerobic)), oxidized coenzyme F430 (see factor 430 biosynthesis), siroheme (see siroheme biosynthesis), heme D biosynthesis, and bacteriochlorophyll (see chlorophyllide a biosynthesis I (aerobic, light-dependent)).

Subpathways: heme biosynthesis II (anaerobic)

Variants: heme biosynthesis I (aerobic), heme biosynthesis III (from siroheme), heme d1 biosynthesis, superpathay of heme biosynthesis from glutamate, superpathway of heme biosynthesis from glycine

Unification Links: EcoCyc:PWY0-1415

Created 11-Dec-1995 by Riley M, Marine Biological Laboratory
Revised 12-Jun-2009 by Caspi R, SRI International


Caughey75: Caughey WS, Smythe GA, O'Keeffe DH, Maskasky JE, Smith MI (1975). "Heme A of cytochrome c oxicase. Structure and properties: comparisons with hemes B, C, and S and derivatives." J Biol Chem 250(19);7602-22. PMID: 170266

Frankenberg03: Frankenberg N, Moser J, Jahn D (2003). "Bacterial heme biosynthesis and its biotechnological application." Appl Microbiol Biotechnol 63(2);115-27. PMID: 13680202

Panek02: Panek H, O'Brian MR (2002). "A whole genome view of prokaryotic haem biosynthesis." Microbiology 148(Pt 8);2273-82. PMID: 12177321

Warburg51: Warburg O, Gewitz HS (1951). "Cytohamin aus Herzmuskel." Hoppe-Seyler´s Zeitschrift für physiologische Chemie 288(1);1-4.

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Boynton09: Boynton TO, Daugherty LE, Dailey TA, Dailey HA (2009). "Identification of Escherichia coli HemG as a novel, menadione-dependent flavodoxin with protoporphyrinogen oxidase activity." Biochemistry 48(29):6705-11. PMID: 19583219

Breckau03: Breckau D, Mahlitz E, Sauerwald A, Layer G, Jahn D (2003). "Oxygen-dependent coproporphyrinogen III oxidase (HemF) from Escherichia coli is stimulated by manganese." J Biol Chem 278(47);46625-31. PMID: 12975365

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Cantoni84: Cantoni L, Dal Fiume D, Ruggieri R (1984). "Decarboxylation of uroporphyrinogen I and III in 2,3,7,8-tetrachlorodibenzo-p-dioxin induced porphyria in mice." Int J Biochem 16(5);561-5. PMID: 6724109

Cao07: Cao J, Woodhall MR, Alvarez J, Cartron ML, Andrews SC (2007). "EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in E. coli O157:H7." Mol Microbiol 65(4);857-75. PMID: 17627767

Cartron07: Cartron ML, Mitchell SA, Woodhall MR, Andrews SC, Watson KA (2007). "Preliminary X-ray diffraction analysis of YcdB from Escherichia coli: a novel haem-containing and Tat-secreted periplasmic protein with a potential role in iron transport." Acta Crystallogr Sect F Struct Biol Cryst Commun 63(Pt 1);37-41. PMID: 17183171

Collins81: Collins MD, Jones D (1981). "Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication." Microbiol Rev 45(2);316-54. PMID: 7022156

Corrigall98: Corrigall AV, Siziba KB, Maneli MH, Shephard EG, Ziman M, Dailey TA, Dailey HA, Kirsch RE, Meissner PN (1998). "Purification of and kinetic studies on a cloned protoporphyrinogen oxidase from the aerobic bacterium Bacillus subtilis." Arch Biochem Biophys 358(2);251-6. PMID: 9784236

Dailey00: Dailey HA, Dailey TA, Wu CK, Medlock AE, Wang KF, Rose JP, Wang BC (2000). "Ferrochelatase at the millennium: structures, mechanisms and [2Fe-2S] clusters." Cell Mol Life Sci 57(13-14);1909-26. PMID: 11215517

Dailey02: Dailey TA, Dailey HA (2002). "Identification of [2Fe-2S] clusters in microbial ferrochelatases." J Bacteriol 184(9);2460-4. PMID: 11948160

Dailey11: Dailey HA, Septer AN, Daugherty L, Thames D, Gerdes S, Stabb EV, Dunn AK, Dailey TA, Phillips JD (2011). "The Escherichia coli protein YfeX functions as a porphyrinogen oxidase, not a heme dechelatase." MBio 2(6);e00248-11. PMID: 22068980

Dailey86a: Dailey HA (1986). "Purification and characterization of bacterial ferrochelatase." Methods Enzymol 123;408-15. PMID: 3702737

Dailey94: Dailey HA, Sellers VM, Dailey TA (1994). "Mammalian ferrochelatase. Expression and characterization of normal and two human protoporphyric ferrochelatases." J Biol Chem 269(1);390-5. PMID: 8276824

Dailey96: Dailey TA, Dailey HA (1996). "Human protoporphyrinogen oxidase: expression, purification, and characterization of the cloned enzyme." Protein Sci 5(1);98-105. PMID: 8771201

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Frey01: Frey PA (2001). "Radical mechanisms of enzymatic catalysis." Annu Rev Biochem 70;121-48. PMID: 11395404

Frey08: Frey PA, Hegeman AD, Ruzicka FJ (2008). "The Radical SAM Superfamily." Crit Rev Biochem Mol Biol 43(1);63-88. PMID: 18307109

Frustaci93: Frustaci JM, O'Brian MR (1993). "The Escherichia coli visA gene encodes ferrochelatase, the final enzyme of the heme biosynthetic pathway." J Bacteriol 175(7);2154-6. PMID: 8458858

Fujimoto12: Fujimoto N., Kosaka T., Yamada M. (2012). "Menaquinone as Well as Ubiquinone as a Crucial Component in the Escherichia coli Respiratory Chain." Chapter 10 in Chemical Biology, edited by D Ekinci, ISBN 978-953-51-0049-2.

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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