DB code: S00071

CATH domain 2.30.110.10 : Pnp Oxidase; Chain A Catalytic domain
E.C. 1.4.3.5
CSA 1g79
M-CSA 1g79
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0AFI7 Pyridoxine/pyridoxamine 5''-phosphate oxidase
EC 1.4.3.5
PNP/PMP oxidase
PNPOx
Pyridoxal 5''-phosphate synthase
NP_416155.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489902.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF10590 (PNPOx_C)
PF01243 (Pyridox_oxidase)
[Graphical View]
P38075 Pyridoxamine 5''-phosphate oxidase
EC 1.4.3.5
PNP/PMP oxidase
PNPOx
NP_009591.1 (Protein)
NM_001178383.1 (DNA/RNA sequence)
PF10590 (PNPOx_C)
PF01243 (Pyridox_oxidase)
[Graphical View]
Q9NVS9 Pyridoxine-5''-phosphate oxidase
EC 1.4.3.5
Pyridoxamine-phosphate oxidase
NP_060599.1 (Protein)
NM_018129.3 (DNA/RNA sequence)
PF10590 (PNPOx_C)
PF01243 (Pyridox_oxidase)
[Graphical View]

KEGG enzyme name
pyridoxal 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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0AFI7 PDXH_ECOLI 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). Homodimer. Binds 1 FMN per subunit.
P38075 PDX3_YEAST 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). Homodimer (By similarity). Binds 1 FMN per subunit.
Q9NVS9 PNPO_HUMAN 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). Homodimer. Binds 1 FMN per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00750 Vitamin B6 metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00061 C00647 C00627 C00001 C00007 C00018 C00014 C00027
E.C.
Compound FMN Pyridoxamine 5'-phosphate Pyridoxine 5'-phosphate H2O O2 Pyridoxal 5'-phosphate NH3 H2O2
Type amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,phosphate group/phosphate ion amine group,aromatic ring (with nitrogen atoms),phosphate group/phosphate ion carbohydrate,aromatic ring (with nitrogen atoms),phosphate group/phosphate ion H2O others aromatic ring (with nitrogen atoms),phosphate group/phosphate ion amine group,organic ion others
ChEBI 17621
18335
28803
15377
15379
26689
27140
18405
16134
16240
PubChem 643976
1053
1055
22247451
962
977
1051
222
22326046
784
1dnlA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1g76A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Bound:PLP Unbound Unbound
1g77A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Bound:PLP Unbound Unbound
1g78A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Bound:PLP Unbound Unbound
1g79A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Bound:PLP Unbound Unbound
1jnwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Bound:PLP Unbound Unbound
1wv4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1wv4B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1ci0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1ci0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1nrgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Bound:PLP Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [13]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dnlA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 197 MSE 53;MSE 79;MSE 113;MSE 127(modified with selenium)
1g76A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 197
1g77A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 197 MSE 53;MSE 79;MSE 113;MSE 127(modified with selenium)
1g78A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 197 MSE 53;MSE 79;MSE 113;MSE 127(modified with selenium)
1g79A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 197
1jnwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 197 MSE 53;MSE 79;MSE 113;MSE 127(modified with selenium)
1wv4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 197
1wv4B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 197
1ci0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 205
1ci0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 205
1nrgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 225

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 187217
Journal Biochemistry
Year 1976
Volume 15
Pages 5458-66
Authors Korytnyk W, Hakala MT, Potti PG, Angelino N, Chang SC
Title On the inhibitory activity of 4-vinyl analogues of pyridoxal: enzyme and cell culture studies.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 475395
Journal Arch Biochem Biophys
Year 1979
Volume 195
Pages 325-35
Authors Horiike K, Merrill AH Jr, McCormick DB
Title Activation and inactivation of rabbit liver pyridoxamine (pyridoxine) 5'-phosphate oxidase activity by urea and other solutes.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 476073
Journal Biochemistry
Year 1979
Volume 18
Pages 3635-41
Authors Merrill AH Jr, Kasai S, Matsui K, Tsuge H, McCormick DB
Title Spectroscopic studies of pyridoxamine (pyridoxine) 5'-phosphate oxidase. Equilibrium dissociation constants and spectra for riboflavin 5'-phosphate and analogues.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 440132
Journal Methods Enzymol
Year 1979
Volume 62
Pages 568-74
Authors Merrill AH, Kazarinoff MN, Tsuge H, Horiike K, McCormick DB
Title Pyridoxamine (pyridoxine) 5'-phosphate oxidase from rabbit liver.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7459383
Journal Biochim Biophys Acta
Year 1980
Volume 626
Pages 57-63
Authors Merrill AH Jr, Korytnyk W, Horiike K, McCormick DB
Title Spectroscopic studies of complexes between pyridoxamine (pyridoxine)-5'-phosphate oxidase and pyridoxyl 5'-phosphate compounds differing at position 4'.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 6244277
Journal J Biol Chem
Year 1980
Volume 255
Pages 2355-9
Authors Gregory JF 3rd
Title Effects of epsilon-pyridoxyllysine and related compounds on liver and brain pyridoxal kinase and liver pyridoxamine (pyridoxine) 5'-phosphate oxidase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 4019487
Journal J Biol Chem
Year 1985
Volume 260
Pages 9580-2
Authors Bowers-Komro DM, McCormick DB
Title Pyridoxamine-5'-phosphate oxidase exhibits no specificity in prochiral hydrogen abstraction from substrate.
Related PDB
Related UniProtKB
[8]
Resource
Comments CHARACTERIZATION
Medline ID 98359888
PubMed ID 9693059
Journal Protein Expr Purif
Year 1998
Volume 13
Pages 349-56
Authors Di Salvo M, Yang E, Zhao G, Winkler ME, Schirch V
Title Expression, purification, and characterization of recombinant Escherichia coli pyridoxine 5'-phosphate oxidase.
Related PDB
Related UniProtKB P0AFI7
[9]
Resource
Comments
Medline ID
PubMed ID 10479623
Journal J Struct Biol
Year 1999
Volume 127
Pages 88-91
Authors Musayev FN, Safo MK, Di Salvo ML, Schirch V, Abraham DJ
Title Crystallization and preliminary X-ray crystallographic analysis of pyridoxine 5'-phosphate oxidase complexed with flavin mononucleotide.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10775448
Journal Arch Biochem Biophys
Year 2000
Volume 377
Pages 109-14
Authors Yang ES, Schirch V
Title Tight binding of pyridoxal 5'-phosphate to recombinant Escherichia coli pyridoxine 5'-phosphate oxidase.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 19-217
Medline ID 20366584
PubMed ID 10903950
Journal Structure Fold Des
Year 2000
Volume 8
Pages 751-62
Authors Safo MK, Mathews I, Musayev FN, di Salvo ML, Thiel DJ, Abraham DJ, Schirch V
Title X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8 A resolution.
Related PDB 1dnl
Related UniProtKB P0AFI7
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 19-217
Medline ID 21348190
PubMed ID 11453690
Journal J Mol Biol
Year 2001
Volume 310
Pages 817-26
Authors Safo MK, Musayev FN, di Salvo ML, Schirch V
Title X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution.
Related PDB 1g76 1g77 1g78 1g79
Related UniProtKB P0AFI7
[13]
Resource
Comments
Medline ID
PubMed ID 11786019
Journal J Mol Biol
Year 2002
Volume 315
Pages 385-97
Authors di Salvo ML, Ko TP, Musayev FN, Raboni S, Schirch V, Safo MK
Title Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 12686112
Journal Biochim Biophys Acta
Year 2003
Volume 1647
Pages 76-82
Authors di Salvo ML, Safo MK, Musayev FN, Bossa F, Schirch V
Title Structure and mechanism of Escherichia coli pyridoxine 5'-phosphate oxidase.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 12824491
Journal Protein Sci
Year 2003
Volume 12
Pages 1455-63
Authors Musayev FN, Di Salvo ML, Ko TP, Schirch V, Safo MK
Title Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase.
Related PDB 1nrg
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 15502343
Journal Acta Crystallogr D Biol Crystallogr
Year 2004
Volume 60
Pages 2110-3
Authors Parsons JF, Calabrese K, Eisenstein E, Ladner JE
Title Structure of the phenazine biosynthesis enzyme PhzG.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 15858270
Journal Acta Crystallogr D Biol Crystallogr
Year 2005
Volume 61
Pages 599-604
Authors Safo MK, Musayev FN, Schirch V
Title Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme.
Related PDB 1wv4
Related UniProtKB

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.

Created Updated
2004-01-30 2009-03-16