EzCatDB: S00071

DB codeS00071
CATH domainDomain 12.30.110.10Catalytic domain
E.C.1.4.3.5
CSA1g79


Enzyme Name
Swiss-protKEGG

P0AFI7P38075Q9NVS9
Protein namePyridoxine/pyridoxamine 5''-phosphate oxidasePyridoxamine 5''-phosphate oxidasePyridoxine-5''-phosphate oxidasepyridoxal 5'-phosphate synthase
pyridoxamine 5'-phosphate oxidase
pyridoxamine phosphate oxidase
pyridoxine (pyridoxamine)phosphate oxidase
pyridoxine (pyridoxamine) 5'-phosphate oxidase
pyridoxaminephosphate oxidase (EC 1.4.3.5: deaminating)
PMP oxidase
pyridoxol-5'-phosphate:oxygen oxidoreductase (deaminating)(incorrect)
pyridoxamine-phosphate oxidase
PdxH
SynonymsEC 1.4.3.5
PNP/PMP oxidase
PNPOx
Pyridoxal 5''-phosphate synthase
EC 1.4.3.5
PNP/PMP oxidase
PNPOx
EC 1.4.3.5
Pyridoxamine-phosphate oxidase

KEGG pathways
MAP codePathways
MAP00750Vitamin B6 metabolism

Swiss-prot:Accession NumberP0AFI7P38075Q9NVS9
Entry namePDXH_ECOLIPDX3_YEASTPNPO_HUMAN
ActivityPyridoxamine 5''-phosphate + H(2)O + O(2) = pyridoxal 5''-phosphate + NH(3) + H(2)O(2).,Pyridoxine 5''-phosphate + O(2) = pyridoxal 5''- phosphate + H(2)O(2).Pyridoxamine 5''-phosphate + H(2)O + O(2) = pyridoxal 5''-phosphate + NH(3) + H(2)O(2).,Pyridoxine 5''-phosphate + O(2) = pyridoxal 5''- phosphate + H(2)O(2).Pyridoxamine 5''-phosphate + H(2)O + O(2) = pyridoxal 5''-phosphate + NH(3) + H(2)O(2).,Pyridoxine 5''-phosphate + O(2) = pyridoxal 5''- phosphate + H(2)O(2).
SubunitHomodimer.Homodimer (By similarity).Homodimer.
Subcellular location


CofactorBinds 1 FMN per subunit.Binds 1 FMN per subunit.Binds 1 FMN per subunit.


CofactorsSubstratesProducts
KEGG-idC00061C00647C00627C00001C00007C00018C00014C00027
CompoundFMNPyridoxamine 5'-phosphatePyridoxine 5'-phosphateH2OO2Pyridoxal 5'-phosphateNH3H2O2
Typeamide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,phosphate group/phosphate ionamine group,aromatic ring (with nitrogen atoms),phosphate group/phosphate ioncarbohydrate,aromatic ring (with nitrogen atoms),phosphate group/phosphate ionH2Oothersaromatic ring (with nitrogen atoms),phosphate group/phosphate ionamine group,organic ionothers
1dnlABound:FMNUnboundUnbound
UnboundUnboundUnboundUnbound
1g76ABound:FMNUnboundUnbound
UnboundBound:PLPUnboundUnbound
1g77ABound:FMNUnboundUnbound
UnboundBound:PLPUnboundUnbound
1g78ABound:FMNUnboundUnbound
UnboundBound:PLPUnboundUnbound
1g79ABound:FMNUnboundUnbound
UnboundBound:PLPUnboundUnbound
1jnwABound:FMNUnboundUnbound
UnboundBound:PLPUnboundUnbound
1wv4ABound:FMNUnboundUnbound
UnboundUnboundUnboundUnbound
1wv4BBound:FMNUnboundUnbound
UnboundUnboundUnboundUnbound
1ci0ABound:FMNUnboundUnbound
UnboundUnboundUnboundUnbound
1ci0BBound:FMNUnboundUnbound
UnboundUnboundUnboundUnbound
1nrgABound:FMNUnboundUnbound
UnboundBound:PLPUnboundUnbound

Active-site residues
resource
literature [13]
pdbCatalytic residuesModified residues
1dnlAARG 197
MSE 53;MSE 79;MSE 113;MSE 127(modified with selenium)
1g76AARG 197

1g77AARG 197
MSE 53;MSE 79;MSE 113;MSE 127(modified with selenium)
1g78AARG 197
MSE 53;MSE 79;MSE 113;MSE 127(modified with selenium)
1g79AARG 197

1jnwAARG 197
MSE 53;MSE 79;MSE 113;MSE 127(modified with selenium)
1wv4AARG 197

1wv4BARG 197

1ci0AARG 205

1ci0BARG 205

1nrgAARG 225


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[11]Fig.1, p.758-760
[12]p.824-825
[13]Scheme 1, Scheme 2, Fig.5, p.392-394
[14]FIg.2, p.81

references
[1]
PubMed ID187217
JournalBiochemistry
Year1976
Volume15
Pages5458-66
AuthorsKorytnyk W, Hakala MT, Potti PG, Angelino N, Chang SC
TitleOn the inhibitory activity of 4-vinyl analogues of pyridoxal: enzyme and cell culture studies.
[2]
PubMed ID475395
JournalArch Biochem Biophys
Year1979
Volume195
Pages325-35
AuthorsHoriike K, Merrill AH Jr, McCormick DB
TitleActivation and inactivation of rabbit liver pyridoxamine (pyridoxine) 5'-phosphate oxidase activity by urea and other solutes.
[3]
PubMed ID476073
JournalBiochemistry
Year1979
Volume18
Pages3635-41
AuthorsMerrill AH Jr, Kasai S, Matsui K, Tsuge H, McCormick DB
TitleSpectroscopic studies of pyridoxamine (pyridoxine) 5'-phosphate oxidase. Equilibrium dissociation constants and spectra for riboflavin 5'-phosphate and analogues.
[4]
PubMed ID440132
JournalMethods Enzymol
Year1979
Volume62
Pages568-74
AuthorsMerrill AH, Kazarinoff MN, Tsuge H, Horiike K, McCormick DB
TitlePyridoxamine (pyridoxine) 5'-phosphate oxidase from rabbit liver.
[5]
PubMed ID7459383
JournalBiochim Biophys Acta
Year1980
Volume626
Pages57-63
AuthorsMerrill AH Jr, Korytnyk W, Horiike K, McCormick DB
TitleSpectroscopic studies of complexes between pyridoxamine (pyridoxine)-5'-phosphate oxidase and pyridoxyl 5'-phosphate compounds differing at position 4'.
[6]
PubMed ID6244277
JournalJ Biol Chem
Year1980
Volume255
Pages2355-9
AuthorsGregory JF 3rd
TitleEffects of epsilon-pyridoxyllysine and related compounds on liver and brain pyridoxal kinase and liver pyridoxamine (pyridoxine) 5'-phosphate oxidase.
[7]
PubMed ID4019487
JournalJ Biol Chem
Year1985
Volume260
Pages9580-2
AuthorsBowers-Komro DM, McCormick DB
TitlePyridoxamine-5'-phosphate oxidase exhibits no specificity in prochiral hydrogen abstraction from substrate.
[8]
CommentsCHARACTERIZATION
Medline ID98359888
PubMed ID9693059
JournalProtein Expr Purif
Year1998
Volume13
Pages349-56
AuthorsDi Salvo M, Yang E, Zhao G, Winkler ME, Schirch V
TitleExpression, purification, and characterization of recombinant Escherichia coli pyridoxine 5'-phosphate oxidase.
Related Swiss-protP0AFI7
[9]
PubMed ID10479623
JournalJ Struct Biol
Year1999
Volume127
Pages88-91
AuthorsMusayev FN, Safo MK, Di Salvo ML, Schirch V, Abraham DJ
TitleCrystallization and preliminary X-ray crystallographic analysis of pyridoxine 5'-phosphate oxidase complexed with flavin mononucleotide.
[10]
PubMed ID10775448
JournalArch Biochem Biophys
Year2000
Volume377
Pages109-14
AuthorsYang ES, Schirch V
TitleTight binding of pyridoxal 5'-phosphate to recombinant Escherichia coli pyridoxine 5'-phosphate oxidase.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 19-217
Medline ID20366584
PubMed ID10903950
JournalStructure Fold Des
Year2000
Volume8
Pages751-62
AuthorsSafo MK, Mathews I, Musayev FN, di Salvo ML, Thiel DJ, Abraham DJ, Schirch V
TitleX-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8 A resolution.
Related PDB1dnl
Related Swiss-protP0AFI7
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 19-217
Medline ID21348190
PubMed ID11453690
JournalJ Mol Biol
Year2001
Volume310
Pages817-26
AuthorsSafo MK, Musayev FN, di Salvo ML, Schirch V
TitleX-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution.
Related PDB1g76,1g77,1g78,1g79
Related Swiss-protP0AFI7
[13]
PubMed ID11786019
JournalJ Mol Biol
Year2002
Volume315
Pages385-97
Authorsdi Salvo ML, Ko TP, Musayev FN, Raboni S, Schirch V, Safo MK
TitleActive site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase.
[14]
PubMed ID12686112
JournalBiochim Biophys Acta
Year2003
Volume1647
Pages76-82
Authorsdi Salvo ML, Safo MK, Musayev FN, Bossa F, Schirch V
TitleStructure and mechanism of Escherichia coli pyridoxine 5'-phosphate oxidase.
[15]
PubMed ID12824491
JournalProtein Sci
Year2003
Volume12
Pages1455-63
AuthorsMusayev FN, Di Salvo ML, Ko TP, Schirch V, Safo MK
TitleStructure and properties of recombinant human pyridoxine 5'-phosphate oxidase.
Related PDB1nrg
[16]
PubMed ID15502343
JournalActa Crystallogr D Biol Crystallogr
Year2004
Volume60
Pages2110-3
AuthorsParsons JF, Calabrese K, Eisenstein E, Ladner JE
TitleStructure of the phenazine biosynthesis enzyme PhzG.
[17]
CommentsX-ray crystallography
PubMed ID15858270
JournalActa Crystallogr D Biol Crystallogr
Year2005
Volume61
Pages599-604
AuthorsSafo MK, Musayev FN, Schirch V
TitleStructure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme.
Related PDB1wv4

comments
According to the literature [11], this enzyme catalyzes three distinct reactions.
(A) Oxidation of either pyridoxamine 5'-phosphate (PMP) or pyridoxine 5'-phosphate (PNP) to form either PLP or Schiff-base form of PLP at C4' (Hydride transfer from the substrate to FMN).
(B) FMNH2 + O2=> FMN + H2O2 (Hydride transfer from FMNH2 to O2).
(C) (In the case of PMP as the fisrt substrate), exchange of double-bonded atoms (change from Schiff-base to aldehyde). The catalytic mechanism of this reaction has not been elucidated.
###
According to the literature [11], [12], [13] & [14], for the reaction (A), there have been two proposed mechanisms:
(a) Direct hydride transfer from the substrate C4' carbon to N5 atom of FMN.
(b) Carbanion pathway, which involves a covalent adduct of the substrate with FMN. This mechanism requires a general base, which deprotonates the hydrogen atom from the C4' carbon.
All the literature [11]-[14] supported the mechanism (a), direct hydride transfer, since such a base could not be identified.

createdupdated
2004-01-302009-03-16


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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