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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 vitamin a vitamin B6

Summary:
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

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

InChIKey: InChIKey=NGVDGCNFYWLIFO-UHFFFAOYSA-L

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 Change Formation (ΔfG in kcal/mol): -213.60925 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

4-amino-2-methyl-5-phosphomethylpyrimidine 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-phosphomethylpyrimidine 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 acceptor ↔ pyridoxal 5'-phosphate + an aminated amino group acceptor
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] , hydroxymethylbilane synthase [Miller89] , pyridoxal kinase [White70, Comment 4] , erythrose 4-phosphate dehydrogenase [Comment 5] , 3-phosphoshikimate-1-carboxyvinyltransferase , methanol:MtaC protein Co-methyltransferase [vanderMeijden84] , cholate 12α-hydroxy dehydrogenase [Braun91] , 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: threonine deaminase , threonine synthase , diaminopimelate decarboxylase , selenocysteine synthase , leucine transaminase , isoleucine transaminase , valine transaminase , glutamate-1-semialdehyde aminotransferase , N-succinyldiaminopimelate aminotransferase , acetylornithine aminotransferase , ornithine decarboxylase , ornithine decarboxylase , arginine decarboxylase, biosynthetic , arginine decarboxylase, degradative , lysine decarboxylase , lysine decarboxylase , 2-amino-3-ketobutyrate CoA ligase , 4-aminobutyrate transaminase , 4-aminobutyrate aminotransferase , phosphohydroxythreonine aminotransferase , 3-phosphoserine aminotransferase , alanine racemase , dTDP-4-dehydro-6-deoxy-D-glucose transaminase , 7,8-diaminopelargonic acid synthase , aminodeoxychorismate lyase , glutamate decarboxylase A , glutamate decarboxylase B , UDP-L-Ara4O C-4" transaminase , glycine decarboxylase , acetylornithine transaminase , succinylornithine transaminase , tryptophanase , cystathionine β-lyase , cysteine synthase , O-acetylserine sulfhydrylase , cystathionine-β-lyase , threonine dehydratase , serine deaminase , D-serine ammonia-lyase , glycogen phosphorylase , phenylalanine aminotransferase , tyrosine aminotransferase , leucine aminotransferase , cysteine sulfinate desulfinase , methionine-oxo-acid transaminase , 2,3-diaminopropionate ammonia-lyase , 8-amino-7-oxononanoate synthase , D-cysteine desulfhydrase, PLP-dependent , diamine transaminase , putrescine aminotransferase , selenocysteine lyase , cysteine sulfinate desulfinase , L-cysteine desulfurase , L-cysteine:[protein cysteine] sulfurtransferase , allothreonine acetaldehyde-lyase (glycine-forming) , 5,10-methenyltetrahydrofolate hydrolase , 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase , tryptophan synthase , tryptophan synthase , kynurenine-oxoglutarate transaminase , phenylalanine transaminase , aspartate transaminase , maltodextrin phosphorylase , L-allo-threonine aldolase , phenylserine aldolase , threonine aldolase , 4-hydroxy-L-threonine aldolase , lysine 2,3-aminomutase , valine-pyruvate aminotransferase , O-succinylhomoserine(thiol)-lyase , 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

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


References

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

Braun91: 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.

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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

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

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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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