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MetaCyc Enzyme: coproporphyrinogen III oxidase

Gene: hemF Accession Numbers: EG12189 (MetaCyc), b2436, ECK2431

Synonyms: popB, sec

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of coproporphyrinogen III oxidase = [HemF]2
         coproporphyrinogen III oxidase = HemF

Summary:
Coproporphyrinogen III oxidase (HemF) catalyzes the decarboxylation of coproporphyrinogen III to protoporphyrinogen IX. The enzyme is strictly aerobic, requiring molecular oxygen as the electron acceptor and producing hydrogen peroxide [Troup94, Breckau03]. His and Trp residues essential for catalytic activity were identified by kinetic analysis of mutant enzymes [Breckau03].

E. coli contains two coproporphyrinogen III oxidases, one that is active under aerobic conditions, the hemF gene product, and one that is active under anaerobic conditions, the hemN gene product [Troup95].

Overexpression of hemF can suppress the growth defect of a hemG mutant; thus, HemF was hypothesized to be able to oxidize protoporphyrinogen IX as well [Narita99]. However, no such activity was found in vitro [Breckau03].

Locations: cytosol

Map Position: [2,551,247 -> 2,552,146]

Molecular Weight of Polypeptide: 34.323 kD (from nucleotide sequence), 35.0 kD (experimental) [Troup94 ]

Unification Links: ASAP:ABE-0008034 , CGSC:643 , EchoBASE:EB2106 , EcoGene:EG12189 , EcoliWiki:b2436 , ModBase:P36553 , OU-Microarray:b2436 , PortEco:hemF , PR:PRO_000022875 , Pride:P36553 , Protein Model Portal:P36553 , RefSeq:NP_416931 , RegulonDB:EG12189 , SMR:P36553 , String:511145.b2436 , Swiss-Model:P36553 , UniProt:P36553

Relationship Links: InterPro:IN-FAMILY:IPR001260 , InterPro:IN-FAMILY:IPR018375 , Panther:IN-FAMILY:PTHR10755 , Pfam:IN-FAMILY:PF01218 , Prints:IN-FAMILY:PR00073 , Prosite:IN-FAMILY:PS01021

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006783 - heme biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, Troup94]
GO:0019353 - protoporphyrinogen IX biosynthetic process from glutamate Inferred from experiment [Troup94]
GO:0006779 - porphyrin-containing compound biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006782 - protoporphyrinogen IX biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004109 - coproporphyrinogen oxidase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Breckau03]
GO:0030145 - manganese ion binding Inferred from experiment Inferred by computational analysis [GOA06, Breckau03]
GO:0042803 - protein homodimerization activity Inferred from experiment Inferred by computational analysis [GOA06, Breckau03, GOA]
GO:0046906 - tetrapyrrole binding Inferred from experiment [Breckau03]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, Breckau03]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

Credits:
Created in EcoCyc 09-Jul-2009 by Keseler I , SRI International
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: coproporphyrinogen III oxidase

Synonyms: coproporphyrinogenase III oxidate, aerobic, coproporphyrinogenase, coproporphyrinogen oxidase, coprogen oxidase, coproporphyrinogen:oxygen oxidoreductase, CPO

EC Number: 1.3.3.3

coproporphyrinogen III + oxygen + 2 H+ <=> protoporphyrinogen IX + 2 CO2 + 2 H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown. [Breckau03]

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

Summary:
The Ki for the mixed inhibition by protoporphyrin IX is 6 µM [Breckau03].

Cofactors or Prosthetic Groups: Mn2+ [Breckau03]

Inhibitors (Unknown Mechanism): protoporphyrin IX [Breckau03]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
coproporphyrinogen III
3.1
[Macieira03, BRENDA14]
coproporphyrinogen III
2.6
0.003
[Breckau03, BRENDA14]

pH(opt): 7 [BRENDA14, Macieira03], 6 [Breckau03]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 48 -> 57
[UniProt10a]
UniProt: Important for dimerization; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 92
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 96
[UniProt10]
UniProt: Manganese;
Metal-Binding-Site 106
[UniProt10]
UniProt: Manganese;
Active-Site 106
[UniProt10a]
UniProt: Proton donor; Non-Experimental Qualifier: by similarity;
Protein-Segment 108 -> 110
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 145
[UniProt10]
UniProt: Manganese;
Metal-Binding-Site 175
[UniProt10]
UniProt: Manganese;
Protein-Segment 240 -> 275
[UniProt10a]
UniProt: Important for dimerization; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Protein-Segment 258 -> 263
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;

History:
10/20/97 Gene b2436 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12189; confirmed by SwissProt match.


References

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." http://www.brenda-enzymes.org.

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

GOA: GOA "Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity."

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Macieira03: Macieira S, Martins BM, Huber R (2003). "Oxygen-dependent coproporphyrinogen-III oxidase from Escherichia coli: one-step purification and biochemical characterisation." FEMS Microbiol Lett 226(1);31-7. PMID: 13129604

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

Troup94: Troup B, Jahn M, Hungerer C, Jahn D (1994). "Isolation of the hemF operon containing the gene for the Escherichia coli aerobic coproporphyrinogen III oxidase by in vivo complementation of a yeast HEM13 mutant." J Bacteriol 1994;176(3);673-80. PMID: 8300522

Troup95: Troup B, Hungerer C, Jahn D (1995). "Cloning and characterization of the Escherichia coli hemN gene encoding the oxygen-independent coproporphyrinogen III oxidase." J Bacteriol 1995;177(11);3326-31. PMID: 7768836

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

UniProtGOA11a: 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."


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 Sat Dec 20, 2014, biocyc14.