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Escherichia coli K-12 substr. MG1655 Enzyme: coproporphyrinogen III oxidase



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

Synonyms: popB, sec

Regulation Summary Diagram: ?

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] (54.99 centisomes)
Length: 900 bp / 299 aa

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: ?

Genetic Regulation 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

Essentiality data for hemF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Created 09-Jul-2009 by Keseler I , SRI International
Last-Curated ? 09-Jul-2009 by Keseler I , 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: heme biosynthesis I (aerobic) , superpathway of heme biosynthesis from uroporphyrinogen-III

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;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

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


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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 EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, BIOCYC14A.