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Escherichia coli K-12 substr. MG1655 Enzyme: lipid hydroperoxide peroxidase



Gene: tpx Accession Numbers: G6660 (EcoCyc), b1324, ECK1320

Synonyms: yzzJ, p20, scavengase, scavengase p20, thiol peroxidase

Regulation Summary Diagram: ?

Subunit composition of lipid hydroperoxide peroxidase = [Tpx]2
         lipid hydroperoxide peroxidase = Tpx

Summary:
Tpx is a thioredoxin 1-dependent thiol peroxidase that belongs to the family of atypical 2-Cys peroxidases [Baker03a, Choi03]. In vivo, Tpx appears to function as a lipid hydroperoxide peroxidase and acts as the principal antioxidant under anaerobic conditions [Cha04].

Osmotic shock experiments initially indicated that the enzyme was located in the periplasm [Cha95]. However, no signal sequence for transport into the periplasm is evident, and in vivo interaction with thioredoxin 1 indicates that the enzyme is located in the cytoplasm [Tao08a].

Kinetic analysis shows a bisubstrate ping-pong catalytic mechanism [Baker03a]. The enzyme is a dimer in solution, and this form is independent of the redox state; electrophoresis data is consistent with intrasubunit disulfide bond formation [Baker03a]. A crystal structure of Tpx in the oxidized state has been solved at 2.2 Å resolution [Choi03].

A tpx deletion mutant is more sensitive to oxidative stress than wild type [Cha96]. Cys61 is the peroxidatic residue and is essential for catalytic activity [Zhou97a, Baker03a]. A Cys95 mutant has partial activity [Baker03a]. Expression of tpx is induced under aerobic conditions [Kim96d, Kim99a] and by low pH [Stancik02], but not oxidative stress [Cha04].

Tpx: "thiol peroxidase" [Kim96d]

Reviews: [Mishra12, Fourquet08, Wood03, Hofmann02]

Locations: periplasmic space, cytosol

Map Position: [1,386,329 <- 1,386,835] (29.88 centisomes)
Length: 507 bp / 168 aa

Molecular Weight of Polypeptide: 17.835 kD (from nucleotide sequence), 20.0 kD (experimental) [Cha95 ]

Unification Links: ASAP:ABE-0004442 , DIP:DIP-31857N , EchoBASE:EB2538 , EcoGene:EG12672 , EcoliWiki:b1324 , ModBase:P0A862 , OU-Microarray:b1324 , PortEco:tpx , PR:PRO_000024095 , Pride:P0A862 , Protein Model Portal:P0A862 , RefSeq:NP_415840 , RegulonDB:G6660 , SMR:P0A862 , String:511145.b1324 , UniProt:P0A862

Relationship Links: InterPro:IN-FAMILY:IPR002065 , InterPro:IN-FAMILY:IPR012336 , InterPro:IN-FAMILY:IPR013740 , InterPro:IN-FAMILY:IPR018219 , PDB:Structure:1QXH , PDB:Structure:3HVS , PDB:Structure:3HVV , PDB:Structure:3HVX , PDB:Structure:3I43 , PDB:Structure:4AF2 , Pfam:IN-FAMILY:PF08534 , Prosite:IN-FAMILY:PS01265 , Prosite:IN-FAMILY:PS51352

In Paralogous Gene Group: 420 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0034599 - cellular response to oxidative stress Inferred from experiment [Cha96]
GO:0045454 - cell redox homeostasis Inferred by computational analysis [GOA06]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Kumar04]
GO:0008379 - thioredoxin peroxidase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Cha95]
GO:0032843 - hydroperoxide reductase activity Inferred from experiment [Baker03a]
GO:0004601 - peroxidase activity Inferred by computational analysis [UniProtGOA11]
GO:0016209 - antioxidant activity Inferred by computational analysis [UniProtGOA11]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0016684 - oxidoreductase activity, acting on peroxide as acceptor Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Tao08a]
GO:0005829 - cytosol Inferred from experiment [Ishihama08, LopezCampistrou05, Tao08a]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: cell processes protection detoxification

Essentiality data for tpx 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:
Created 08-Dec-2008 by Keseler I , SRI International
Last-Curated ? 09-Dec-2008 by Keseler I , SRI International


Enzymatic reaction of: lipid hydroperoxide peroxidase

Synonyms: thiol peroxidase

EC Number: 1.11.1.15

an organic hydroperoxide + a reduced thioredoxin <=> an alcohol + an oxidized thioredoxin + 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.

Alternative Substrates for an organic hydroperoxide: hydrogen peroxide [Baker03a ] , tertiary butyl hydroperoxide [Cha95 ] , cumene hydroperoxide [Baker03a ]

Summary:
The enzyme was first shown to be active with H2O2 and alkyl hydroperoxides, with t-butyl hydroperoxide appearing to be the better substrate [Cha95]. The KM for cumene hydroperoxide is 9.1 µM, while the KM for H2O2 is 1730 µM [Baker03a].

Kinetic Parameters:

Substrate
Km (μM)
Citations
hydrogen peroxide
1730.0
[Baker03a]
a reduced thioredoxin
22.5
[Baker03a]
cumene hydroperoxide
9.1
[Baker03a]


Sequence Features

Feature Class Location Common Name Citations Comment
Cleavage-of-Initial-Methionine 1  
[Pasquali94, Link97, Cha95, Baker03a]
 
Chain 2 -> 168  
[UniProt09]
UniProt: Thiol peroxidase;
Conserved-Region 19 -> 168  
[UniProt09]
UniProt: Thioredoxin;
Acetylation-Modification 33  
[Yu08]
 
Sequence-Conflict 61  
[Cha95, UniProt10a]
Alternate sequence: C → Y; UniProt: (in Ref. 1; AAC43517);
Intrachain-Disulfide-Bond 61, 95  
[Baker03a]
 
Active-Site 61 peroxidatic center
[Baker03a]
 


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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

Baker03a: Baker LM, Poole LB (2003). "Catalytic mechanism of thiol peroxidase from Escherichia coli. Sulfenic acid formation and overoxidation of essential CYS61." J Biol Chem 278(11);9203-11. PMID: 12514184

Cha04: Cha MK, Kim WC, Lim CJ, Kim K, Kim IH (2004). "Escherichia coli periplasmic thiol peroxidase acts as lipid hydroperoxide peroxidase and the principal antioxidative function during anaerobic growth." J Biol Chem 279(10);8769-78. PMID: 14676195

Cha95: Cha MK, Kim HK, Kim IH (1995). "Thioredoxin-linked "thiol peroxidase" from periplasmic space of Escherichia coli." J Biol Chem 1995;270(48);28635-41. PMID: 7499381

Cha96: Cha MK, Kim HK, Kim IH (1996). "Mutation and Mutagenesis of thiol peroxidase of Escherichia coli and a new type of thiol peroxidase family." J Bacteriol 1996;178(19);5610-4. PMID: 8824604

Choi03: Choi J, Choi S, Choi J, Cha MK, Kim IH, Shin W (2003). "Crystal structure of Escherichia coli thiol peroxidase in the oxidized state: insights into intramolecular disulfide formation and substrate binding in atypical 2-Cys peroxiredoxins." J Biol Chem 278(49);49478-86. PMID: 14506251

Dyson90: Dyson HJ, Gippert GP, Case DA, Holmgren A, Wright PE (1990). "Three-dimensional solution structure of the reduced form of Escherichia coli thioredoxin determined by nuclear magnetic resonance spectroscopy." Biochemistry 1990;29(17);4129-36. PMID: 2193685

Eklund84: Eklund H, Cambillau C, Sjoberg BM, Holmgren A, Jornvall H, Hoog JO, Branden CI (1984). "Conformational and functional similarities between glutaredoxin and thioredoxins." EMBO J 1984;3(7);1443-9. PMID: 6378624

Fourquet08: Fourquet S, Huang ME, D'Autreaux B, Toledano MB (2008). "The dual functions of thiol-based peroxidases in H2O2 scavenging and signaling." Antioxid Redox Signal 10(9);1565-76. PMID: 18498222

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

Gleason88: Gleason FK, Holmgren A (1988). "Thioredoxin and related proteins in procaryotes." FEMS Microbiol Rev 1988;4(4);271-97. PMID: 3152490

Gleason90: Gleason FK, Lim CJ, Gerami-Nejad M, Fuchs JA (1990). "Characterization of Escherichia coli thioredoxins with altered active site residues." Biochemistry 1990;29(15);3701-9. PMID: 2187529

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."

Hofmann02: Hofmann B, Hecht HJ, Flohe L (2002). "Peroxiredoxins." Biol Chem 383(3-4);347-64. PMID: 12033427

Holmgren85: Holmgren A (1985). "Thioredoxin." Annu Rev Biochem 1985;54;237-71. PMID: 3896121

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

Katti90: Katti SK, LeMaster DM, Eklund H (1990). "Crystal structure of thioredoxin from Escherichia coli at 1.68 A resolution." J Mol Biol 1990;212(1);167-84. PMID: 2181145

Kim96d: Kim HK, Kim SJ, Lee JW, Lee JW, Cha MK, Kim IH (1996). "Identification of promoter in the 5'-flanking region of the E. coli thioredoxin-linked thiol peroxidase gene: evidence for the existence of oxygen-related transcriptional regulatory protein." Biochem Biophys Res Commun 1996;221(3);641-6. PMID: 8630014

Kim99a: Kim SJ, Han YH, Kim IH, Kim HK (1999). "Involvement of ArcA and Fnr in expression of Escherichia coli thiol peroxidase gene." IUBMB Life 1999;48(2);215-8. PMID: 10794600

Kumar04: Kumar JK, Tabor S, Richardson CC (2004). "Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli." Proc Natl Acad Sci U S A 101(11);3759-64. PMID: 15004283

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

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

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

Nikkola93: Nikkola M, Gleason FK, Fuchs JA, Eklund H (1993). "Crystal structure analysis of a mutant Escherichia coli thioredoxin in which lysine 36 is replaced by glutamic acid." Biochemistry 1993;32(19);5093-8. PMID: 8098620

Pasquali94: Pasquali C., Sanchez J.-C., Ravier F., Golaz O., Hughes G.J., Frutiger S., Paquet N., Wilkins M., Appel R.D., Bairoch A., Hochstrasser D.F. (1994). Data submission to UniProtKB on 1994-09.

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Stancik02: Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN, Slonczewski JL (2002). "pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli." J Bacteriol 184(15);4246-58. PMID: 12107143

Tao08a: Tao K (2008). "Subcellular localization and in vivo oxidation-reduction kinetics of thiol peroxidase in Escherichia coli." FEMS Microbiol Lett 289(1);41-5. PMID: 19054092

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

Wood03: Wood ZA, Schroder E, Robin Harris J, Poole LB (2003). "Structure, mechanism and regulation of peroxiredoxins." Trends Biochem Sci 28(1);32-40. PMID: 12517450

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

Zhou97a: Zhou Y, Wan XY, Wang HL, Yan ZY, Hou YD, Jin DY (1997). "Bacterial scavengase p20 is structurally and functionally related to peroxiredoxins." Biochem Biophys Res Commun 1997;233(3);848-52. PMID: 9168946


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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