Escherichia coli K-12 substr. MG1655 Polypeptide: alkyl hydroperoxide reductase, AhpF component

Gene: ahpF Accession Numbers: EG11385 (EcoCyc), b0606, ECK0600

Synonyms: alkyl hydroperoxide reductase, F52a subunit

Regulation Summary Diagram: ?

Regulation summary diagram for ahpF

Component of: alkyl hydroperoxide reductase (extended summary available)

AhpF is the peroxiredoxin reductase component of alkyl hydroperoxide reductase.

The N-terminal domain of AhpF belongs to the family of protein-disulfide oxidoreductases, while the C terminus belongs to the thioredoxin reductase family [Bieger01]. By similarity to the enzyme from Salmonella typhimurium, it is thought to channel electrons from NADH to the AhpC component for reduction of the hydroperoxide substrate. An internal redox-active disulfide bridge between two cysteine residues is reduced by electron transfer from NADH via the FAD cofactor. This reduction triggers a cascade of disulfide-exchange reactions, first intramolecularly, then intermolecularly to the disulfide cysteine residues of the AhpC component.

AhpF consists of an N-terminal domain (NTD), an FAD-binding domain and an NADH-binding domain [Dip14]. A crystal structure of the catalytic core of AhpF containing the FAD cofactor has been solved at 1.9 Å resolution [Bieger00, Bieger01]. Crystal structures of the full-length protein have been solved, and the NTD was identified as the AhpC-interacting epitope [Dip14].

Overexpression of AhpF suppresses the formation of aggregated proteins upon streptomycin treatment and increases resistance to aminoglycoside antibiotics [Ling12].

Review: [Poole00]

Citations: [Smillie92, GomezSagasti14]

Gene Citations: [Ferrante95]

Locations: cytosol

Map Position: [638,976 -> 640,541] (13.77 centisomes, 50°)
Length: 1566 bp / 521 aa

Molecular Weight of Polypeptide: 56.177 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002093 , CGSC:31194 , DIP:DIP-9077N , EchoBASE:EB1358 , EcoGene:EG11385 , EcoliWiki:b0606 , ModBase:P35340 , OU-Microarray:b0606 , PortEco:ahpF , PR:PRO_000022071 , Pride:P35340 , Protein Model Portal:P35340 , RefSeq:NP_415139 , RegulonDB:EG11385 , SMR:P35340 , String:511145.b0606 , Swiss-Model:P35340 , UniProt:P35340

Relationship Links: InterPro:IN-FAMILY:IPR000103 , InterPro:IN-FAMILY:IPR001327 , InterPro:IN-FAMILY:IPR002109 , InterPro:IN-FAMILY:IPR008255 , InterPro:IN-FAMILY:IPR012081 , InterPro:IN-FAMILY:IPR012336 , InterPro:IN-FAMILY:IPR013027 , InterPro:IN-FAMILY:IPR023753 , PDB:Structure:1FL2 , PDB:Structure:4O5Q , PDB:Structure:4O5U , Pfam:IN-FAMILY:PF00070 , Pfam:IN-FAMILY:PF07992 , Pfam:IN-FAMILY:PF13192 , Prints:IN-FAMILY:PR00368 , Prints:IN-FAMILY:PR00469 , Prosite:IN-FAMILY:PS00573 , Prosite:IN-FAMILY:PS51354

In Paralogous Gene Group: 40 (11 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for ahpF

GO Terms:

Biological Process: GO:0000302 - response to reactive oxygen species Inferred by computational analysis [GOA01a]
GO:0045454 - cell redox homeostasis Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008785 - alkyl hydroperoxide reductase activity Inferred from experiment Inferred by computational analysis [GOA01a, Seaver01]
GO:0071949 - FAD binding Inferred from experiment [Bieger00]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01a]
GO:0015035 - protein disulfide oxidoreductase activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0050660 - flavin adenine dinucleotide binding Inferred by computational analysis [Bieger01, GOA01a]
GO:0051287 - NAD binding Inferred by computational analysis [GOA01a]
GO:0070402 - NADPH binding Inferred by computational analysis [Bieger01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, LopezCampistrou05, Lasserre06]
GO:0009321 - alkyl hydroperoxide reductase complex Inferred from experiment [Dip14]

MultiFun Terms: cell processes protection detoxification

Essentiality data for ahpF 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]

Last-Curated ? 18-Nov-2014 by Keseler I , SRI International

Subunit of: alkyl hydroperoxide reductase

Subunit composition of alkyl hydroperoxide reductase = [AhpC]10[AhpF]4
         alkyl hydroperoxide reductase, AhpC component = AhpC (extended summary available)
         alkyl hydroperoxide reductase, AhpF component = AhpF (extended summary available)

Alkyl hydroperoxide reductase converts alkyl hydroperoxides to their corresponding alcohols. By similarity to the enzyme from Salmonella typhimurium, the AhpC component catalyzes the peroxide reductase reaction, while the AhpF component restores the reduced state of AhpC by transferring electrons from NADH to AhpC. Based on structural data, a model of the catalytic cycle has been proposed [Dip14].

Alkyl hydroperoxide reductase is responsible for scavenging H2O2 at low concentrations, while catalase is responsible for scavenging H2O2 at high concentrations [Seaver01, Seaver01a].

Overexpression of alkyl hydroperoxide reductase leads to increased resistance to cumene hydroperoxide and other redox-cycling agents [Greenberg88]. An ahpCF mutant is more sensitive to the increased endogenous production of peroxides during phosphate starvation [Moreau01] and has a severe growth defect when grown on phenylethylamine [Ravindra13]. An insertion mutant in the ahpC promoter region is cold sensitive [Serina04]. Oxidative stress-related proteins, including AhpC and AhpF, are upregulated when germfree mice inoculated with E. coli are fed a lactose diet. An ahpCF mutant shows increased doubling time under conditions of high osmolality [Rothe12].

Reviews: [Poole05, Imlay08, Mishra12, Rothe13, Lu14c]

Citations: [Ferrante95, Gundlach14]

GO Terms:

Biological Process: GO:0033194 - response to hydroperoxide Inferred from experiment [Seaver01]
GO:0045454 - cell redox homeostasis Inferred from experiment [Seaver01a]
Molecular Function: GO:0008785 - alkyl hydroperoxide reductase activity Inferred from experiment [Dip14a, Dip14]

Last-Curated ? 18-Nov-2014 by Keseler I , SRI International

Enzymatic reaction of: alkyl hydroperoxide reductase

EC Number: 1.8.1.-

an organic hydroperoxide + NADH + H+ <=> an alcohol + NAD+ + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for an organic hydroperoxide: hydrogen peroxide [Dip14 , Seaver01 ]

Cofactors or Prosthetic Groups: FAD [Bieger01]

Sequence Features

Protein sequence of alkyl hydroperoxide reductase, AhpF component with features indicated

Feature Class Location Citations Comment
Acetylation-Modification 16
N6-acetyllysine-Modification 53
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Nucleotide-Phosphate-Binding-Region 214 -> 229
UniProt: FAD; Non-Experimental Qualifier: by similarity;
Disulfide-Bond-Site 345, 348
UniProt: Redox-active; Non-Experimental Qualifier: by similarity;
N6-acetyllysine-Modification 354
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Nucleotide-Phosphate-Binding-Region 357 -> 371
UniProt: NAD or NADP; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 478 -> 488
UniProt: FAD; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b0606 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11385; confirmed by SwissProt match.


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

Bieger00: Bieger B, Essen LO (2000). "Crystallization and preliminary X-ray analysis of the catalytic core of the alkylhydroperoxide reductase component AhpF from Escherichia coli." Acta Crystallogr D Biol Crystallogr 2000;56 ( Pt 1);92-4. PMID: 10666639

Bieger01: Bieger B, Essen LO (2001). "Crystal structure of the catalytic core component of the alkylhydroperoxide reductase AhpF from Escherichia coli." J Mol Biol 307(1);1-8. PMID: 11243797

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

Dip14: Dip PV, Kamariah N, Subramanian Manimekalai MS, Nartey W, Balakrishna AM, Eisenhaber F, Eisenhaber B, Gruber G (2014). "Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli." Acta Crystallogr D Biol Crystallogr 70(Pt 11);2848-62. PMID: 25372677

Dip14a: Dip PV, Kamariah N, Nartey W, Beushausen C, Kostyuchenko VA, Ng TS, Lok SM, Saw WG, Eisenhaber F, Eisenhaber B, Gruber G (2014). "Key roles of the Escherichia coli AhpC C-terminus in assembly and catalysis of alkylhydroperoxide reductase, an enzyme essential for the alleviation of oxidative stress." Biochim Biophys Acta 1837(12);1932-1943. PMID: 25193562

Ferrante95: Ferrante AA, Augliera J, Lewis K, Klibanov AM (1995). "Cloning of an organic solvent-resistance gene in Escherichia coli: the unexpected role of alkylhydroperoxide reductase." Proc Natl Acad Sci U S A 92(17);7617-21. PMID: 7644465

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."

GomezSagasti14: Gomez-Sagasti MT, Becerril JM, Martin I, Epelde L, Garbisu C (2014). "cDNA microarray assessment of early gene expression profiles in Escherichia coli cells exposed to a mixture of heavy metals." Cell Biol Toxicol 30(4);207-32. PMID: 24952731

Greenberg88: Greenberg JT, Demple B (1988). "Overproduction of peroxide-scavenging enzymes in Escherichia coli suppresses spontaneous mutagenesis and sensitivity to redox-cycling agents in oxyR-mutants." EMBO J 7(8);2611-7. PMID: 2847922

Gundlach14: Gundlach J, Winter J (2014). "Evolution of Escherichia coli for maximum HOCl resistance through constitutive expression of the OxyR regulon." Microbiology 160(Pt 8);1690-704. PMID: 24899627

Imlay08: Imlay JA (2008). "Cellular defenses against superoxide and hydrogen peroxide." Annu Rev Biochem 77;755-76. PMID: 18173371

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Ling12: Ling J, Cho C, Guo LT, Aerni HR, Rinehart J, Soll D (2012). "Protein aggregation caused by aminoglycoside action is prevented by a hydrogen peroxide scavenger." Mol Cell 48(5);713-22. PMID: 23122414

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

Lu14c: Lu J, Holmgren A (2014). "The thioredoxin antioxidant system." Free Radic Biol Med 66;75-87. PMID: 23899494

Mishra12: Mishra S, Imlay J (2012). "Why do bacteria use so many enzymes to scavenge hydrogen peroxide?." Arch Biochem Biophys 525(2);145-60. PMID: 22609271

Moreau01: Moreau PL, Gerard F, Lutz NW, Cozzone P (2001). "Non-growing Escherichia coli cells starved for glucose or phosphate use different mechanisms to survive oxidative stress." Mol Microbiol 39(4);1048-60. PMID: 11251823

Poole00: Poole LB, Reynolds CM, Wood ZA, Karplus PA, Ellis HR, Li Calzi M (2000). "AhpF and other NADH:peroxiredoxin oxidoreductases, homologues of low Mr thioredoxin reductase." Eur J Biochem 267(20);6126-33. PMID: 11012664

Poole05: Poole LB (2005). "Bacterial defenses against oxidants: mechanistic features of cysteine-based peroxidases and their flavoprotein reductases." Arch Biochem Biophys 433(1);240-54. PMID: 15581580

Ravindra13: Ravindra Kumar S, Imlay JA (2013). "How Escherichia coli tolerates profuse hydrogen peroxide formation by a catabolic pathway." J Bacteriol 195(20);4569-79. PMID: 23913322

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

Rothe12: Rothe M, Alpert C, Engst W, Musiol S, Loh G, Blaut M (2012). "Impact of nutritional factors on the proteome of intestinal Escherichia coli: induction of OxyR-dependent proteins AhpF and Dps by a lactose-rich diet." Appl Environ Microbiol 78(10);3580-91. PMID: 22427493

Rothe13: Rothe M, Blaut M (2013). "Evolution of the gut microbiota and the influence of diet." Benef Microbes 4(1);31-7. PMID: 23257016

Seaver01: Seaver LC, Imlay JA (2001). "Alkyl hydroperoxide reductase is the primary scavenger of endogenous hydrogen peroxide in Escherichia coli." J Bacteriol 183(24);7173-81. PMID: 11717276

Seaver01a: Seaver LC, Imlay JA (2001). "Hydrogen peroxide fluxes and compartmentalization inside growing Escherichia coli." J Bacteriol 183(24);7182-9. PMID: 11717277

Serina04: Serina S, Nozza F, Nicastro G, Faggioni F, Mottl H, Deho G, Polissi A (2004). "Scanning the Escherichia coli chromosome by random transposon mutagenesis and multiple phenotypic screening." Res Microbiol 155(8);692-701. PMID: 15380559

Smillie92: Smillie DA, Hayward RS, Suzuki T, Fujita N, Ishihama A (1992). "Locations of genes encoding alkyl hydroperoxide reductase on the physical map of the Escherichia coli K-12 genome." J Bacteriol 174(11);3826-7. PMID: 1592833

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

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

Zhang09: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Baez13a: Baez A, Shiloach J (2013). "Escherichia coli avoids high dissolved oxygen stress by activation of SoxRS and manganese-superoxide dismutase." Microb Cell Fact 12;23. PMID: 23497217

Campos07: Campos E, Montella C, Garces F, Baldoma L, Aguilar J, Badia J (2007). "Aerobic L-ascorbate metabolism and associated oxidative stress in Escherichia coli." Microbiology 153(Pt 10);3399-408. PMID: 17906139

Jung03: Jung IL, Kim IG (2003). "Transcription of ahpC, katG, and katE genes in Escherichia coli is regulated by polyamines: polyamine-deficient mutant sensitive to H2O2-induced oxidative damage." Biochem Biophys Res Commun 301(4);915-22. PMID: 12589799

Liu01a: Liu R, Blackwell TW, States DJ (2001). "Conformational model for binding site recognition by the E.coli MetJ transcription factor." Bioinformatics 17(7);622-33. PMID: 11448880

Ozyamak13: Ozyamak E, de Almeida C, de Moura AP, Miller S, Booth IR (2013). "Integrated stress response of Escherichia coli to methylglyoxal: transcriptional readthrough from the nemRA operon enhances protection through increased expression of glyoxalase I." Mol Microbiol 88(5);936-50. PMID: 23646895

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

Storz90: Storz G, Tartaglia LA, Ames BN (1990). "Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation." Science 1990;248(4952);189-94. PMID: 2183352

Tartaglia89: Tartaglia LA, Storz G, Ames BN (1989). "Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress." J Mol Biol 1989;210(4);709-19. PMID: 2693740

Tartaglia92: Tartaglia LA, Gimeno CJ, Storz G, Ames BN (1992). "Multidegenerate DNA recognition by the OxyR transcriptional regulator." J Biol Chem 267(3);2038-45. PMID: 1730735

Toledano94: Toledano MB, Kullik I, Trinh F, Baird PT, Schneider TD, Storz G (1994). "Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection." Cell 78(5);897-909. PMID: 8087856

Zheng01: Zheng M, Wang X, Doan B, Lewis KA, Schneider TD, Storz G (2001). "Computation-directed identification of OxyR DNA binding sites in Escherichia coli." J Bacteriol 183(15);4571-9. PMID: 11443092

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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 19.0 on Fri Oct 9, 2015, biocyc14.