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MetaCyc Compound: pyridoxal 5'-phosphate

Abbrev Name: PLP

Synonyms: PLP, pyridoxal phosphate, pyridoxal-5P, pyridoxal 5-phosphate, pyridoxal-P, vitamin B6

Superclasses: a vitamina vitamin B6

Pyridoxal-5'-phosphate (PLP, vitamin B6) is an essential cofactor in all living systems [John95]. It plays an important role in amino acid and carbohydrate metabolism and has recently been implicated in singlet oxygen resistance [Daub00].

Most bacteria, archaebacteria, fungi, and plants synthesize PLP in a single reaction, as described in pyridoxal 5'-phosphate biosynthesis II. Some anaerobic bacteria use a longer, more complex pathway (see pyridoxal 5'-phosphate biosynthesis I).

Chemical Formula: C8H8NO6P

Molecular Weight: 245.13 Daltons

Monoisotopic Molecular Weight: 247.0245735688 Daltons

pyridoxal 5'-phosphate compound structure

SMILES: CC1(N=CC(=C(C=1O)C=O)COP(=O)([O-])[O-])

InChI: InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)/p-2


Unification Links: CAS:54-47-7, ChEBI:597326, ChemSpider:559203, HMDB:HMDB01491, IAF1260:33526, KEGG:C00018, MetaboLights:MTBLC597326, PubChem:644168

Standard Gibbs Free Energy of Formation (ΔfG in kcal/mol): -213.60925Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis (yeast) :
[an HMP-P synthase]-L-histidine + pyridoxal 5'-phosphate → 4-amino-2-methyl-5-phosphomethylpyrimidine + an HMP-P synthase

pyridoxal 5'-phosphate salvage II (plants) :
pyridoxal 5'-phosphate + H2O → pyridoxal + phosphate

Reactions known to produce the compound:

4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis (yeast) :
pyridoxine 5'-phosphate + oxygen → hydrogen peroxide + pyridoxal 5'-phosphate
pyridoxal + ATP → pyridoxal 5'-phosphate + ADP + H+

pyridoxal 5'-phosphate biosynthesis I :
pyridoxine 5'-phosphate + oxygen → hydrogen peroxide + pyridoxal 5'-phosphate

pyridoxal 5'-phosphate biosynthesis II :
keto-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine → pyridoxal 5'-phosphate + L-glutamate + phosphate + 3 H2O + H+

pyridoxal 5'-phosphate salvage I :
pyridoxine 5'-phosphate + oxygen → hydrogen peroxide + pyridoxal 5'-phosphate
pyridoxal + ATP → pyridoxal 5'-phosphate + ADP + H+
pyridoxamine 5'-phosphate + oxygen + H2O → ammonium + hydrogen peroxide + pyridoxal 5'-phosphate

pyridoxal 5'-phosphate salvage II (plants) :
pyridoxine 5'-phosphate + oxygen → hydrogen peroxide + pyridoxal 5'-phosphate
pyridoxal + ATP → pyridoxal 5'-phosphate + ADP + H+
pyridoxamine 5'-phosphate + oxygen + H2O → ammonium + hydrogen peroxide + pyridoxal 5'-phosphate

Reactions known to both consume and produce the compound:

Not in pathways:
pyridoxamine 5'-phosphate + 2-oxoglutarate ↔ pyridoxal 5'-phosphate + D-glutamate
pyridoxamine 5'-phosphate + a deaminated amino group donor ↔ pyridoxal 5'-phosphate + an aminated amino group donor
D-alanine + pyridoxal 5'-phosphate ↔ pyruvate + pyridoxamine 5'-phosphate

In Reactions of unknown directionality:

Not in pathways:
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + ammonium = pyridoxal 5'-phosphate + phosphate + H+ + 4 H2O

Enzymes activated by pyridoxal 5'-phosphate, sorted by the type of activation, are:

Activator (Allosteric) of: histidine-pyruvate aminotransferase [Emes73], pyridoxamine-pyruvate aminotransferase Activator (Mechanism unknown) of: glucose-1-phosphate adenylyltransferase [Gardiol90, Figueroa11], β-cyano-L-alanine synthase [Ikegami88], urocanase [Kaminskas70]

Enzymes inhibited by pyridoxal 5'-phosphate, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: L-glutamine:D-fructose-6-phosphate aminotransferase [GolinelliPimpan91, Comment 1], pyridoxamine 5'-phosphate oxidase [Comment 2], pyridoxine 5'-phosphate oxidase [Zhao95a, Comment 2], glucose-6-phosphate 1-dehydrogenase [Haghighi82] Inhibitor (Noncompetitive) of: kynurenine 3-monooxygenase [Breton00], porphobilinogen synthase [Van71] Inhibitor (Mechanism unknown) of: L-glutamine:D-fructose-6-phosphate aminotransferase [GolinelliPimpan91, Comment 3], 3-phosphoshikimate-1-carboxyvinyltransferase, hydroxymethylbilane synthase [Miller89], pyridoxal kinase [White70, Comment 4], erythrose 4-phosphate dehydrogenase [Comment 5], methanol:MtaC protein Co-methyltransferase [vanderMeijden84], cholate 12α-hydroxy dehydrogenase [Braun91a], mimosine synthase [Ikegami90], methanol:5-hydroxybenzimidazolylcobamide Co-methyltransferase [vanderMeijden84], trehalose phosphorylase [Aisaka98], willardiine synthase [Ahmmad84], isowillardiine synthase [Ahmmad84] Inhibitor (Other types) of: glutamate dehydrogenase [Blumenthal73]

This compound has been characterized as a cofactor or prosthetic group of the following enzymes: D-serine ammonia-lyase, ornithine decarboxylase, ornithine decarboxylase, arginine decarboxylase, biosynthetic, arginine decarboxylase, degradative, lysine decarboxylase, lysine decarboxylase, 2-amino-3-ketobutyrate CoA ligase, threonine deaminase, N-acetylornithine aminotransferase, 4-aminobutyrate transaminase, 4-aminobutyrate aminotransferase, L-cysteine:[protein cysteine] sulfurtransferase, aminodeoxychorismate lyase, alanine racemase, alanine racemase, 7,8-diaminopelargonic acid synthase, threonine synthase, glutamate decarboxylase A, glutamate decarboxylase B, glutamate-1-semialdehyde aminotransferase, diaminopimelate decarboxylase, N-succinyldiaminopimelate aminotransferase, N-acetylornithine aminotransferase, leucine transaminase, isoleucine transaminase, valine transaminase, UDP-L-Ara4O C-4" transaminase, dTDP-4-dehydro-6-deoxy-D-glucose transaminase, N-succinyldiaminopimelate aminotransferase, phosphohydroxythreonine aminotransferase, 3-phosphoserine aminotransferase, glycine decarboxylase, threonine dehydratase, serine deaminase, tryptophanase, cystathionine β-lyase, cysteine synthase, O-acetylserine sulfhydrylase, cystathionine-β-lyase, N-acetylornithine aminotransferase, succinylornithine transaminase, selenocysteine synthase, glycogen phosphorylase, tryptophan synthase, tryptophan synthase, 2,3-diaminopropionate ammonia-lyase, 8-amino-7-oxononanoate synthase, lysine 2,3-aminomutase, valine-pyruvate aminotransferase, kynurenine-oxoglutarate transaminase, phenylalanine transaminase, aspartate transaminase, phenylalanine aminotransferase, tyrosine aminotransferase, leucine aminotransferase, D-cysteine desulfhydrase, PLP-dependent, methionine-oxo-acid transaminase, cysteine sulfinate desulfinase, selenocysteine lyase, cysteine sulfinate desulfinase, L-cysteine desulfurase, maltodextrin phosphorylase, diamine transaminase, putrescine aminotransferase, L-allo-threonine aldolase, phenylserine aldolase, threonine aldolase, 4-hydroxy-L-threonine aldolase, allothreonine acetaldehyde-lyase (glycine-forming), 5,10-methenyltetrahydrofolate hydrolase, 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase, O-succinylhomoserine(thiol)-lyase, (2S,3R)-4-(2-aminophenyl)-2-amino-3-hydroxy-4-oxobutanoate aminotransferase, hydroxykynureninase, hydroxykynureninase, dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose transaminase, 8-amino-3,8-dideoxy-D-manno-octulosonate transaminase, glutamate 2,3-aminomutase, (S)-3-aminotridecan-4-one synthase, 3-aminotridec-2-en-4-one synthase, methliin lyase, S-alk(en)-L-cysteine sulfoxide lyase, alliin lyase, GDP-3-dehydro-6-deoxymannose aminotransferase, 2-furaldehyde phosphate aminotransferase, 3-benzyl-3,6 -bis(cysteinyl)- 6-(hydroxymethyl)-diketopiperazine lyase, hercynylcysteine S-oxide lyase, (S)-3-acetyloctanal aminotransferase, ketoacyl synthase, 5-aminolevulinate synthase, 5-aminolevulinyl-CoA cyclase, D-fructose-6-phosphate-L-glutamate transaminase, aspartate 1-decarboxylase, 4-amino-4-deoxychorismate lyase, 4-amino-4-deoxychorismate lyase, serine dehydratase, L-threonine deaminase, L-threonine deaminase, UDP-acetamido-4-amino-6-deoxygalactopyranose transaminase, alanine aminotransferase, dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose aminotransferase, cystathionine γ-lyase, CMP-5'-3-aminopropylphosphonate synthase, dTDP-3-amino-3,6-dideoxy-α-D-glucopyranose transaminase, 2-aminoadipate-2-oxoglutarate aminotransferase, alanine racemase, D-serine ammonia-lyase, dTDP-3-amino-3,6-dideoxy-α-D-glucopyranose transaminase, dTDP-4-amino-4,6-dideoxy-D-glucose transaminase, D-glucosaminate 6-phosphate ammonia-lyase, CysO-thiocarboxylate-dependent cysteine synthase, hercynylcysteine S-oxide lyase, [cysteine desulfurase]-S-sulfanylcysteine:[acceptor protein]-cysteine sulfurtransferase, [cysteine desulfurase]-S-sulfanylcysteine:[acceptor protein]-cysteine sulfurtransferase, L-cysteine desulfurase, [cysteine desulfurase]-S-sulfanylcysteine:[acceptor protein]-cysteine sulfurtransferase, L-cysteine desulfurase, 8-amino-7-oxononanoate synthase, phytosphingosine 1-phosphate aldolase, dihydrosphingosine phosphate lyase, serine C-palmitoyltransferase, valine decarboxylase, isobutanal:L-alanine aminotransferase, PLP-dependent decarboxylase, phenylacetaldehyde synthase, phenylacetaldehyde synthase, arginine decarboxylase, carboxyspermidine decarboxylase, UDP-4-amino-4,6-dideoxy-α-D-N-acetyl-D-glucosamine transaminase, L-glutamyl-[BtrI acyl-carrier protein] decarboxylase, glutamate--6'-oxoparomomycin aminotransferase, glutamate--6'-dehydroparomanine aminotransferase, glutamate--2'-deamino-2'-hydroxy-6'-dehydroparomamine aminotransferase, glutamate--6'-dehydroparomanine aminotransferase, glutamate--6'-oxoneomycin C aminotransferase, L-glutamine:5-amino-2,3,4-trihydroxycyclohexanone aminotransferase, L-glutamine:2-deoxy-scyllo-inosose aminotransferase, L-glutamine:2-deoxy-scyllo-inosose aminotransferase, glycogen phosphorylase, dTDP-3-oxo-3,4,6-trideoxy-α-D-glucopyranose transaminase, dTDP-3-oxo-3,4,6-trideoxy-α-D-glucopyranose transaminase, dTDP-4-amino-4,6-dideoxy-D-glucose transaminase, molybdenum cofactor sulfurtransferase, dTDP-4-amino-2,3,4,6-tetradeoxy-D-glucose:2-oxoglutarate aminotransferase, histidine-2-oxoglutarate aminotransferase, 2-amino-4-oxopentanoate thiolase, serine hydroxymethyltransferase, 8-amino-7-oxononanoate synthase, tryptophanase, tryptophanase, tryptophanase, O-acetylhomoserine sulfhydrylase, methionine γ-lyase, β-cyano-L-alanine synthase, β-alanine transaminase, β-alanine aminotransferase, taurine:α-ketoglutarate aminotransferase, diaminobutyrate aminotransferase, PLP-dependent GDP-4-amino-4,6-dideoxy-α-D-N-acetylglucosamine aminotransferase, cystathionine β-lyase, cystathionine γ-synthase, 2-aminoethylphosphonate aminotransferase, arginine decarboxylase, sulfinoalanine decarboxylase, serine hydroxymethyltransferase, L-serine ammonia-lyase, ornithine aminotransferase, lysine decarboxylase, glycine decarboxylase, L-tyrosine decarboxylase, β-cyano-L-alanine synthase, mimosine synthase, β-pyrazole-1-ylalanine synthase, lysine--8-amino-7-oxononanoate transaminase, ureidoglycine aminotransferase, O-acetyl-L-homoserine sulfhydrylase, L-erythro-3-hydroxyaspartate aldolase, D-threo-3-hydroxyaspartate aldolase, D-threo-3-hydroxyaspartate ammonia-lyase, L-threo-3-hydroxy aspartate dehydratase, D-erythro-3-hydroxyaspartate aldolase, L-erythro-3-hydroxyaspartate ammonia-lyase, 4-fluorothreonine transaldolase, cysteate aminotransferase, phosphoserine aminotransferase, cysteate synthase, L-cysteate sulfo-lyase, gamma-aminobutyrate transaminase, γ-aminobutyrate transaminase (pyruvate dependent), L,L-diaminopimelate aminotransferase, dihydroxyacetone phosphate transaminase, serine racemase, L-alanine:D-1-guanidino-1-deoxy-3-dehydro-scyllo-inositol transaminase, lysine decarboxylase, tyrosine aminotransferase, 3-O-methyl-dopa transaminase, L-lysine decarboxylase, 5-aminovalerate aminotransferase, homotaurine:2-oxoglutarate aminotransferase, kynurenine hydrolase, 3-hydroxy-L-kynurenine hydrolase, glutamine-phenylpyruvate transaminase, cysteine conjugate β-lyase, kynurenine aminotransferase, Sep-tRNA:Cys-tRNA synthase, L-tryptophan decarboxylase, L-tryptophan decarboxylase, selenocysteine synthase, O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase, histidine decarboxylase, L-tryptophan:pyruvate aminotransferase, L-tryptophan:2-oxoglutarate aminotransferase, L-histidine decarboxylase, threonine synthase, UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose aminotransferase, S-methyl-L-methionine decarboxylase, 3-amino-5-hydroxybenzoate synthase, 8-amino-7-oxononanoate synthase, L-glutamine:2-keto-myo-inositol aminotransferase, O-succinyl-L-homoserine sulfhydrylase, carboxynorspermidine decarboxylase, glycogen phosphorylase, L-allo-threonine aldolase, L-threonine aldolase, alanine--glyoxylate aminotransferase, cystathionine β-synthase, cystathionine β-lyase, nocardicin C-9'-epimerase, L-arginine:pyruvate transaminase, GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase, isopenicillin N epimerase, serine-pyruvate aminotransferase, aspartate aminotransferase, aspartate aminotransferase, aspartate aminotransferase, aspartate aminotransferase, L-threonine-O-3-phosphate decarboxylase, L-allo-threonine aldolase, dopa decarboxylase, methionine γ-lyase, alanine aminotransferase, ornithine racemase, L-lysine:pyruvate aminotransferase, lysine ε-aminotransferase, L-lysine 6-aminotransferase, lysine 2,3-aminomutase, lysine 5,6-aminomutase, α-aminoadipate aminotransferase, tyrosine aminotransferase, tyrosine aminotransferase, serine palmitoyltransferase, branched-chain-amino-acid aminotransferase, L,L-diaminopimelate aminotransferase, L-serine:glyoxylate aminotransferase, methionine-oxo-acid transaminase, cystathionine γ-lyase, diaminopimelate decarboxylase, N-succinyldiaminopimelate-aminotransferase, ornithine aminotransferase, dopa decarboxylase, taurine:pyruvate aminotransferase, kynureninase, willardiine synthase, isowillardiine synthase, L-phenylalanine:2-oxoglutarate aminotransferase, acetylornithine aminotransferase, serine hydroxymethyltransferase, ornithine δ-aminotransferase, L-tryptophan aminotransferase, tryptophan decarboxylase, L-tryptophan decarboxylase, L-tryptophan transaminase, N6-acetyllysine aminotransferase, cystathionine β-synthase, D-ornithine aminomutase, O-acetylhomoserine sulfhydrylase, asparagine aminotransferase, L-isoleucine:2-oxoglutarate aminotransferase, L-valine:2-oxoglutarate aminotransferase, indole-3-acetaldoxime dehydratase, 5-aminolevulinate synthase, tryptophan decarboxylase, arginine-α-ketoglutarate transaminase, L-arginine decarboxyoxidase, arginine racemase, L-2,4-diaminobutyrate decarboxylase, lathyrine synthase, putrescine aminotransferase, polyamine aminotransferase, 4-aminobutyrate aminotransferase, glutamate decarboxylase, glutamate decarboxylase, ornithine decarboxylase

This compound has been characterized as an alternative substrate of the following enzymes: thiamine monophosphate phosphatase, phosphoglycolate phosphatase

Revised 15-Mar-2010 by Caspi R, SRI International


Ahmmad84: Ahmmad, Mohammad A.S., Maskall, C. Sidney, Brown, Eric G. (1984). "Partial purification and properties of willardiine and isowillardiine synthase activity from Pisum sativum." Phytochemistry, 1984, 23(2):265-270.

Aisaka98: Aisaka K, Masuda T, Chikamune T, Kamitori K (1998). "Purification and characterization of trehalose phosphorylase from Catellatospora ferruginea." Biosci Biotechnol Biochem 62(4);782-7. PMID: 9614710

Blumenthal73: Blumenthal KM, Smith EL (1973). "Nicotinamide adenine dinucleotide phosphate-specific glutamate dehydrogenase of Neurospora. I. Isolation, subunits, amino acid composition, sulfhydryl groups, and identification of a lysine residue reactive with pyridoxal phosphate and N-ethylmaleimide." J Biol Chem 248(17);6002-8. PMID: 4146914

Braun91a: Braun M, Lunsdorf H, Buckmann AF (1991). "12 alpha-hydroxysteroid dehydrogenase from Clostridium group P, strain C 48-50. Production, purification and characterization." Eur J Biochem 196(2);439-50. PMID: 2007406

Breton00: Breton J, Avanzi N, Magagnin S, Covini N, Magistrelli G, Cozzi L, Isacchi A (2000). "Functional characterization and mechanism of action of recombinant human kynurenine 3-hydroxylase." Eur J Biochem 267(4);1092-9. PMID: 10672018

Daub00: Daub ME, Ehrenshaft M (2000). "THE PHOTOACTIVATED CERCOSPORA TOXIN CERCOSPORIN: Contributions to Plant Disease and Fundamental Biology." Annu Rev Phytopathol 38;461-490. PMID: 11701851

Emes73: Emes AV, Hassall H (1973). "The degradation of L-histidine in the rat. The formation of imidazolylpyruvate, imidazolyl-lactate and imidazolylpropionate." Biochem J 136(3);649-58. PMID: 4360716

Figueroa11: Figueroa CM, Esper MC, Bertolo A, Demonte AM, Aleanzi M, Iglesias AA, Ballicora MA (2011). "Understanding the allosteric trigger for the fructose-1,6-bisphosphate regulation of the ADP-glucose pyrophosphorylase from Escherichia coli." Biochimie 93(10);1816-23. PMID: 21741429

Gardiol90: Gardiol A, Preiss J (1990). "Escherichia coli E-39 ADPglucose synthetase has different activation kinetics from the wild-type allosteric enzyme." Arch Biochem Biophys 280(1);175-80. PMID: 2162151

GolinelliPimpan91: Golinelli-Pimpaneau B, Badet B (1991). "Possible involvement of Lys603 from Escherichia coli glucosamine-6-phosphate synthase in the binding of its substrate fructose 6-phosphate." Eur J Biochem 1991;201(1);175-82. PMID: 1915361

Haghighi82: Haghighi B, Flynn TG, Levy HR (1982). "Glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides. Isolation and sequence of a peptide containing an essential lysine." Biochemistry 21(25);6415-20. PMID: 6817791

Ikegami88: Ikegami, Fumio, Takayama, Kyoko, Tajima, Chiho, Murakoshi, Isamu (1988). "Purification and properties of β-cyano-L-alanine synthase from Spinacia oleracea." Phytochemistry, 1988, 27(7):2011-2016.

Ikegami90: Ikegami, Fumio, Mizuno, Masahiko, Kihara, Miyuki, Murakoshi, Isamu (1990). "Enzymatic synthesis of the thyrotoxic amino acid mimosine by cysteine synthase." Phytochemistry, 1990, 29(11):3461-3465.

John95: John RA (1995). "Pyridoxal phosphate-dependent enzymes." Biochim Biophys Acta 1248(2);81-96. PMID: 7748903

Kaminskas70: Kaminskas E, Kimhi Y, Magasanik B (1970). "Urocanase and N-formimino-L-glutamate formiminohydrolase of Bacillus subtilis, two enzymes of the histidine degradation pathway." J Biol Chem 1970;245(14);3536-44. PMID: 4990470

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Miller89: Miller AD, Packman LC, Hart GJ, Alefounder PR, Abell C, Battersby AR (1989). "Evidence that pyridoxal phosphate modification of lysine residues (Lys-55 and Lys-59) causes inactivation of hydroxymethylbilane synthase (porphobilinogen deaminase)." Biochem J 1989;262(1);119-24. PMID: 2510713

Sivaraman03: Sivaraman J, Li Y, Banks J, Cane DE, Matte A, Cygler M (2003). "Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway." J Biol Chem 278(44);43682-90. PMID: 12896974

Van71: Van Heyningen S, Shemin D (1971). "Inhibition of delta-aminolaevulate dehydratase by pyridoxal derivatives and by cyanide." Biochem J 124(5);68P. PMID: 5130998

vanderMeijden84: van der Meijden P, te Brommelstroet BW, Poirot CM, van der Drift C, Vogels GD (1984). "Purification and properties of methanol:5-hydroxybenzimidazolylcobamide methyltransferase from Methanosarcina barkeri." J Bacteriol 1984;160(2);629-35. PMID: 6438059

White70: White RS, Dempsey WB (1970). "Purification and properties of vitamin B6 kinase from Escherichia coli B." Biochemistry 1970;9(21);4057-64. PMID: 4917899

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Zhao95: Zhao G, Pease AJ, Bharani N, Winkler ME (1995). "Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis." J Bacteriol 1995;177(10);2804-12. PMID: 7751290

Zhao95a: Zhao G, Winkler ME (1995). "Kinetic limitation and cellular amount of pyridoxine (pyridoxamine) 5'-phosphate oxidase of Escherichia coli K-12." J Bacteriol 1995;177(4);883-91. PMID: 7860596

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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