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MetaCyc Enzyme: protoporphyrinogen oxidase

Gene: hemG Accession Numbers: EG11485 (MetaCyc), b3850, ECK3842

Synonyms: yihB

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of protoporphyrinogen oxidase = [HemG]4

Summary:
Protoporphyrinogen oxidase (PPO) catalyzes the six-electron oxidation of protoporphyrinogen IX to protoporphyrin IX. The enzyme belongs to the flavodoxin family of proteins, and the long chain insert loop which distinguishes it from other flavodoxins may be responsible for PPO activity [Boynton09].

Until recently ([Boynton09]), the E. coli enzyme had only been assayed in crude extracts, and the activity was associated with the membrane fraction [Jacobs78].

Under aerobic conditions, the electron acceptor for the protoporphyrinogen oxidase reaction was thought to be molecular oxygen [Jacobs76]. Under anaerobic conditions, the reaction can be coupled to nitrate or fumarate reduction within the anaerobic electron transport chain [Jacobs76, Jacobs77]. Protoporphyrinogen oxidase is inactivated by treatment with detergent, suggesting that the enzyme requires an intact electron transport system for activity [Jacobs84]. In vitro, the purified enzyme can use menadione as the electron acceptor [Boynton09].

The presence of a flavodoxin motif in the sequence indicates that the enzyme may utilize FMN as a cofactor [Nishimura95]. A probable FMN cofactor was detected by MALDI-TOF, measurement of the UV-visible spectrum, and the EPR signal during redox titrations [Boynton09].

Overexpression of hemF, the gene encoding coproporphyrinogen III oxidase, rescues the growth defect of a hemG mutant [Narita99], although HemF does not have PPO activity in vitro [Breckau03].

In later work, potential electron transport chains for both aerobic and anaerobic E. coli HemG protoporphyrinogen oxidase activity were reconstituted in vitro from purified components and tested. Ubiquinone and menaquinone functioned as electron acceptors during HemG catalysis. Fumarate reductase, nitrate reductase, cytochrome bd and cytochrome bo were shown to function as electron acceptors for HemG. In vivo experiments using E. coli respiratory chain mutant strains confirmed the in vitro results. These data showed that HemG catalysis and overall heme biosynthesis is dependent upon respiratory electron transport. A model for respiratory chain-driven protoporphyrinogen oxidase was proposed [Mobius10].

There is a disagreement in the literature regarding the oligomerization state of purified, recombinant HemG. In [Mobius10] a homohexamer was determined by high performance gel permeation chromatography, whereas in [Boynton09] a homotetramer was determined by gel filtration FPLC .

Review: [Layer10]

Locations: cytosol, membrane

Map Position: [4,032,631 -> 4,033,176]

Molecular Weight of Polypeptide: 21.226 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012577 , CGSC:642 , DIP:DIP-35890N , EchoBASE:EB1448 , EcoGene:EG11485 , EcoliWiki:b3850 , ModBase:P0ACB4 , OU-Microarray:b3850 , PortEco:hemG , Protein Model Portal:P0ACB4 , RefSeq:NP_418292 , RegulonDB:EG11485 , String:511145.b3850 , UniProt:P0ACB4

Relationship Links: InterPro:IN-FAMILY:IPR001226 , InterPro:IN-FAMILY:IPR008254 , InterPro:IN-FAMILY:IPR026816 , Pfam:IN-FAMILY:PF12724 , Prosite:IN-FAMILY:PS00201 , Prosite:IN-FAMILY:PS50902

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006779 - porphyrin-containing compound biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, Nishimura95]
GO:0006783 - heme biosynthetic process Inferred from experiment [Sasarman79]
GO:0006782 - protoporphyrinogen IX biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004729 - oxygen-dependent protoporphyrinogen oxidase activity Inferred from experiment [Sasarman93]
GO:0010181 - FMN binding Inferred from experiment Inferred by computational analysis [GOA01, Boynton09]
GO:0042802 - identical protein binding Inferred from experiment [Mobius10, Boynton09]
GO:0070819 - menaquinone-dependent protoporphyrinogen oxidase activity Inferred from experiment [Boynton09]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Zhang07]
GO:0016020 - membrane [Jacobs78]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers heme, porphyrine

Credits:
Created in EcoCyc 13-Jul-2009 by Keseler I , SRI International
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: protoporphyrinogen oxidase

Synonyms: protoporphyrinogen-IX:oxygen oxidoreductase, PPO

EC Number: 1.3.3.4

protoporphyrinogen IX + 3 oxygen <=> protoporphyrin IX + 3 hydrogen peroxide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathay of heme biosynthesis from glutamate , heme biosynthesis I (aerobic) , superpathway of heme biosynthesis from uroporphyrinogen-III

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: protoporphyrinogen dehydrogenase (protoporphyrinogen oxidase)

EC Number: 1.3.5.3

protoporphyrinogen IX + 3 a menaquinone <=> protoporphyrin IX + 3 a menaquinol

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for a menaquinone: menadione [Boynton09 ]

In Pathways: superpathway of heme biosynthesis from uroporphyrinogen-III , heme biosynthesis II (anaerobic)

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
With fumarate as the final electron acceptor, the reaction is dependent on menaquinone as the electron carrier and is independent of cytochromes [Jacobs78].

The enzymatic activity is specific for protoporphyrinogen IX [Boynton09].

Cofactors or Prosthetic Groups: FMN [Mobius10, Boynton09]

Kinetic Parameters:

Substrate
Km (μM)
Citations
protoporphyrinogen IX
7.0
[Boynton09]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 3 -> 172
[UniProt09]
UniProt: Flavodoxin-like;

History:
1/26/1998 (pkarp) Merged genes G7810/b3850 and EG11485/hemG


References

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

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Jacobs76: Jacobs NJ, Jacobs JM (1976). "Nitrate, fumarate, and oxygen as electron acceptors for a late step in microbial heme synthesis." Biochim Biophys Acta 449(1);1-9. PMID: 788792

Jacobs77: Jacobs NJ, Jacobs JM (1977). "Evidence for involvement of the electron transport system at a late step of anaerobic microbial heme synthesis." Biochim Biophys Acta 459(1);141-4. PMID: 318855

Jacobs78: Jacobs NJ, Jacobs JM (1978). "Quinones as hydrogen carriers for a late step in anaerobic heme biosynthesis in Escherichia coli." Biochim Biophys Acta 544(3);540-6. PMID: 365243

Jacobs84: Jacobs JM, Jacobs NJ (1984). "Protoporphyrinogen oxidation, an enzymatic step in heme and chlorophyll synthesis: partial characterization of the reaction in plant organelles and comparison with mammalian and bacterial systems." Arch Biochem Biophys 229(1);312-9. PMID: 6703698

Layer10: Layer G, Reichelt J, Jahn D, Heinz DW (2010). "Structure and function of enzymes in heme biosynthesis." Protein Sci 19(6);1137-61. PMID: 20506125

Mobius10: Mobius K, Arias-Cartin R, Breckau D, Hannig AL, Riedmann K, Biedendieck R, Schroder S, Becher D, Magalon A, Moser J, Jahn M, Jahn D (2010). "Heme biosynthesis is coupled to electron transport chains for energy generation." Proc Natl Acad Sci U S A 107(23);10436-41. PMID: 20484676

Narita99: Narita S, Taketani S, Inokuchi H (1999). "Oxidation of protoporphyrinogen IX in Escherichia coli is mediated by the aerobic coproporphyrinogen oxidase." Mol Gen Genet 1999;261(6);1012-20. PMID: 10485293

Nishimura95: Nishimura K, Nakayashiki T, Inokuchi H (1995). "Cloning and identification of the hemG gene encoding protoporphyrinogen oxidase (PPO) of Escherichia coli K-12." DNA Res 1995;2(1);1-8. PMID: 7788523

Sasarman79: Sasarman A, Chartrand P, Lavoie M, Tardif D, Proschek R, Lapointe C (1979). "Mapping of a new hem gene in Escherichia coli K12." J Gen Microbiol 113(2);297-303. PMID: 390093

Sasarman93: Sasarman A, Letowski J, Czaika G, Ramirez V, Nead MA, Jacobs JM, Morais R (1993). "Nucleotide sequence of the hemG gene involved in the protoporphyrinogen oxidase activity of Escherichia coli K12." Can J Microbiol 39(12);1155-61. PMID: 7916647

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 21, 2014, BIOCYC13B.