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Escherichia coli K-12 substr. MG1655 Enzyme: porphyrinogen peroxidase



Gene: yfeX Accession Numbers: G7266 (EcoCyc), b2431, ECK2426

Synonyms: dye-decolorizing peroxidase

Regulation Summary Diagram: ?

Summary:
YfeX belongs to the family of dye-decolorizing (DyP-type) peroxidases and is able to oxidize both protoporphyrinogen IX and coproporphyrinogen III to their corresponding porphyrins [Dailey11].

The authors of [Dailey11] were unable to reproduce dechelation of iron from protoheme or mesoheme, disputing the results of [Letoffe09], described below:

Due to the lack of an outer membrane receptor for heme, E. coli K-12 is unable to utilize heme as a source of iron [Sasarman68, McConville79]. However, expression of the heme receptor protein HasR from Serratia marcescens enables utilization of heme as a source of iron. This requires the presence of either the Dpp dipeptide ABC transporter or of the EfeUO transporter, which is not functional in E. coli K-12 due to a frameshift mutation disrupting efeU. Once transported to the cytoplasm, the YfeX protein is able to release iron from hemin without destroying the tetrapyrrol ring. The EfeB protein, although it is normally transported to the periplasm, is able to catalyze the same cytoplasmic reaction. A yfeX efeB double mutant in a HasR-expressing strain is unable to use heme as an external source of iron [Letoffe09].

Purified YfeX binds both hemin and protoporphyrin IX; the H215 residue is the predicted iron ligand and is required for binding of both substrates [Letoffe09].

YfeX expression is upregulated under glucose-limited fed-batch conditions [Raman05].

Gene Citations: [Rhodius05]

Locations: cytosol

Map Position: [2,547,668 <- 2,548,567] (54.91 centisomes)
Length: 900 bp / 299 aa

Molecular Weight of Polypeptide: 33.052 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008015 , DIP:DIP-47971N , EchoBASE:EB3917 , EcoGene:EG14165 , EcoliWiki:b2431 , OU-Microarray:b2431 , PortEco:yfeX , Pride:P76536 , Protein Model Portal:P76536 , RefSeq:NP_416926 , RegulonDB:G7266 , SMR:P76536 , String:511145.b2431 , UniProt:P76536

Relationship Links: InterPro:IN-FAMILY:IPR006314 , InterPro:IN-FAMILY:IPR011008 , Pfam:IN-FAMILY:PF04261 , Prosite:IN-FAMILY:PS51404

In Paralogous Gene Group: 242 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01a]
Molecular Function: GO:0004601 - peroxidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01a, Dailey11]
GO:0020037 - heme binding Inferred from experiment Inferred by computational analysis [GOA01a, Dailey11, Letoffe09]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Letoffe09]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

Gene Class: UNCLASSIFIED

Essentiality data for yfeX 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]

Credits:
Last-Curated ? 21-Nov-2011 by Keseler I , SRI International


Enzymatic reaction of: deferrochelatase (porphyrinogen peroxidase)

protoheme IX + 2 H+ <=> protoporphyrin IX + Fe2+

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.

Summary:
The Kd for hemin is 3.9 nM, and the Kd for protoporphyrin IX is 4.8 nM [Letoffe09].


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 215
[Letoffe09, UniProt12]
Alternate sequence: H → A; UniProt: Strong decrease in affinity for heme and protoporphyrin.
Metal-Binding-Site 215
[UniProt10]
UniProt: Iron (heme proximal ligand); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

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

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

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

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Letoffe09: Letoffe S, Heuck G, Delepelaire P, Lange N, Wandersman C (2009). "Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact." Proc Natl Acad Sci U S A 106(28):11719-24. PMID: 19564607

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

McConville79: McConville ML, Charles HP (1979). "Mutants of Escherichia coli K12 permeable to haemin." J Gen Microbiol 113(1);165-8. PMID: 387910

Raman05: Raman B, Nandakumar MP, Muthuvijayan V, Marten MR (2005). "Proteome analysis to assess physiological changes in Escherichia coli grown under glucose-limited fed-batch conditions." Biotechnol Bioeng 92(3);384-92. PMID: 16180237

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Sasarman68: Sasarman A, Surdeanu M, Szegli G, Horodniceanu T, Greceanu V, Dumitrescu A (1968). "Hemin-deficient mutants of Escherichia coli K-12." J Bacteriol 96(2);570-2. PMID: 4877132

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Rezuchova03: Rezuchova B, Miticka H, Homerova D, Roberts M, Kormanec J (2003). "New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system." FEMS Microbiol Lett 225(1);1-7. PMID: 12900013


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 Sun Dec 28, 2014, biocyc12.