PDXH_ECOLI
ID PDXH_ECOLI Reviewed; 218 AA.
AC P0AFI7; P28225;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Pyridoxine/pyridoxamine 5'-phosphate oxidase;
DE EC=1.4.3.5 {ECO:0000269|PubMed:11786019, ECO:0000269|PubMed:7860596, ECO:0000269|PubMed:9693059};
DE AltName: Full=PNP/PMP oxidase;
DE Short=PNPOx;
DE AltName: Full=Pyridoxal 5'-phosphate synthase;
GN Name=pdxH; OrderedLocusNames=b1638, JW1630;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1356963; DOI=10.1128/jb.174.19.6033-6045.1992;
RA Lam H.-M., Winkler M.E.;
RT "Characterization of the complex pdxH-tyrS operon of Escherichia coli K-12
RT and pleiotropic phenotypes caused by pdxH insertion mutations.";
RL J. Bacteriol. 174:6033-6045(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, COFACTOR, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=7860596; DOI=10.1128/jb.177.4.883-891.1995;
RA Zhao G., Winkler M.E.;
RT "Kinetic limitation and cellular amount of pyridoxine (pyridoxamine) 5'-
RT phosphate oxidase of Escherichia coli K-12.";
RL J. Bacteriol. 177:883-891(1995).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND
RP SUBUNIT.
RX PubMed=9693059; DOI=10.1006/prep.1998.0904;
RA di Salvo M., Yang E., Zhao G., Winkler M.E., Schirch V.;
RT "Expression, purification, and characterization of recombinant Escherichia
RT coli pyridoxine 5'-phosphate oxidase.";
RL Protein Expr. Purif. 13:349-356(1998).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 20-218 IN COMPLEX WITH FMN,
RP COFACTOR, AND SUBUNIT.
RX PubMed=10903950; DOI=10.1016/s0969-2126(00)00162-3;
RA Safo M.K., Mathews I., Musayev F.N., di Salvo M.L., Thiel D.J.,
RA Abraham D.J., Schirch V.;
RT "X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase
RT complexed with FMN at 1.8-A resolution.";
RL Structure 8:751-762(2000).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL
RP 5'-PHOSPHATE AND FMN, COFACTOR, AND SUBUNIT.
RX PubMed=11453690; DOI=10.1006/jmbi.2001.4734;
RA Safo M.K., Musayev F.N., di Salvo M.L., Schirch V.;
RT "X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase
RT complexed with pyridoxal 5'-phosphate at 2.0 A resolution.";
RL J. Mol. Biol. 310:817-826(2001).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL
RP 5'-PHOSPHATE AND FMN, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT,
RP BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ARG-14; TYR-17; ASP-49;
RP ARG-197 AND HIS-199, AND COFACTOR.
RX PubMed=11786019; DOI=10.1006/jmbi.2001.5254;
RA di Salvo M.L., Ko T.-P., Musayev F.N., Raboni S., Schirch V., Safo M.K.;
RT "Active site structure and stereospecificity of Escherichia coli
RT pyridoxine-5'-phosphate oxidase.";
RL J. Mol. Biol. 315:385-397(2002).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL
RP 5'-PHOSPHATE AND FMN, COFACTOR, AND SUBUNIT.
RX PubMed=15858270; DOI=10.1107/s0907444905005512;
RA Safo M.K., Musayev F.N., Schirch V.;
RT "Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a
RT tetragonal crystal form: insights into the mechanistic pathway of the
RT enzyme.";
RL Acta Crystallogr. D 61:599-604(2005).
CC -!- FUNCTION: Catalyzes the oxidation of either pyridoxine 5'-phosphate
CC (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate
CC (PLP). {ECO:0000269|PubMed:11786019, ECO:0000269|PubMed:7860596,
CC ECO:0000269|PubMed:9693059}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + O2 + pyridoxamine 5'-phosphate = H2O2 + NH4(+) +
CC pyridoxal 5'-phosphate; Xref=Rhea:RHEA:15817, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16240, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:58451, ChEBI:CHEBI:597326; EC=1.4.3.5;
CC Evidence={ECO:0000269|PubMed:11786019, ECO:0000269|PubMed:7860596,
CC ECO:0000269|PubMed:9693059};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate;
CC Xref=Rhea:RHEA:15149, ChEBI:CHEBI:15379, ChEBI:CHEBI:16240,
CC ChEBI:CHEBI:58589, ChEBI:CHEBI:597326; EC=1.4.3.5;
CC Evidence={ECO:0000269|PubMed:11786019, ECO:0000269|PubMed:7860596,
CC ECO:0000269|PubMed:9693059};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:10903950, ECO:0000269|PubMed:11453690,
CC ECO:0000269|PubMed:11786019, ECO:0000269|PubMed:15858270,
CC ECO:0000269|PubMed:7860596, ECO:0000269|PubMed:9693059};
CC Note=Binds 1 FMN per subunit. {ECO:0000269|PubMed:10903950,
CC ECO:0000269|PubMed:11453690, ECO:0000269|PubMed:11786019,
CC ECO:0000269|PubMed:15858270, ECO:0000269|PubMed:7860596,
CC ECO:0000269|PubMed:9693059};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.3 uM for pyridoxamine 5'-phosphate
CC {ECO:0000269|PubMed:11786019};
CC KM=2 uM for pyridoxine 5'-phosphate (at pH 7.6 and 37 degrees
CC Celsius) {ECO:0000269|PubMed:7860596, ECO:0000269|PubMed:9693059};
CC KM=105 uM for pyridoxamine 5'-phosphate (at pH 7.6 and 37 degrees
CC Celsius) {ECO:0000269|PubMed:7860596};
CC Note=kcat is 0.3 sec(-1) for oxidase activity with pyridoxine 5'-
CC phosphate as substrate (at pH 7.6 and 37 degrees Celsius).
CC {ECO:0000269|PubMed:9693059};
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1.
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10903950,
CC ECO:0000269|PubMed:11453690, ECO:0000269|PubMed:11786019,
CC ECO:0000269|PubMed:15858270, ECO:0000269|PubMed:7860596,
CC ECO:0000269|PubMed:9693059}.
CC -!- MISCELLANEOUS: Can bind a second molecule of pyridoxamine 5'-phosphate
CC at a non-catalytic site in a cleft at the protein surface.
CC -!- SIMILARITY: Belongs to the pyridoxamine 5'-phosphate oxidase family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; M92351; AAA24709.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74710.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15399.1; -; Genomic_DNA.
DR PIR; B43261; B43261.
DR RefSeq; NP_416155.1; NC_000913.3.
DR RefSeq; WP_001282319.1; NZ_STEB01000003.1.
DR PDB; 1DNL; X-ray; 1.80 A; A=20-218.
DR PDB; 1G76; X-ray; 2.20 A; A=1-218.
DR PDB; 1G77; X-ray; 2.10 A; A=1-218.
DR PDB; 1G78; X-ray; 2.20 A; A=1-218.
DR PDB; 1G79; X-ray; 2.00 A; A=1-218.
DR PDB; 1JNW; X-ray; 2.07 A; A=1-218.
DR PDB; 1WV4; X-ray; 2.60 A; A/B=1-218.
DR PDB; 6YLZ; X-ray; 1.56 A; AAA=1-218.
DR PDB; 6YMH; X-ray; 2.42 A; AAA/BBB=1-218.
DR PDBsum; 1DNL; -.
DR PDBsum; 1G76; -.
DR PDBsum; 1G77; -.
DR PDBsum; 1G78; -.
DR PDBsum; 1G79; -.
DR PDBsum; 1JNW; -.
DR PDBsum; 1WV4; -.
DR PDBsum; 6YLZ; -.
DR PDBsum; 6YMH; -.
DR AlphaFoldDB; P0AFI7; -.
DR SMR; P0AFI7; -.
DR BioGRID; 4263488; 16.
DR BioGRID; 851147; 1.
DR DIP; DIP-48024N; -.
DR IntAct; P0AFI7; 13.
DR STRING; 511145.b1638; -.
DR DrugBank; DB03247; Flavin mononucleotide.
DR DrugBank; DB03345; Mercaptoethanol.
DR jPOST; P0AFI7; -.
DR PaxDb; P0AFI7; -.
DR PRIDE; P0AFI7; -.
DR EnsemblBacteria; AAC74710; AAC74710; b1638.
DR EnsemblBacteria; BAA15399; BAA15399; BAA15399.
DR GeneID; 58462440; -.
DR GeneID; 946806; -.
DR KEGG; ecj:JW1630; -.
DR KEGG; eco:b1638; -.
DR PATRIC; fig|1411691.4.peg.622; -.
DR EchoBASE; EB1450; -.
DR eggNOG; COG0259; Bacteria.
DR InParanoid; P0AFI7; -.
DR OMA; PEPNAMV; -.
DR PhylomeDB; P0AFI7; -.
DR BioCyc; EcoCyc:PDXH-MON; -.
DR BioCyc; MetaCyc:PDXH-MON; -.
DR BRENDA; 1.4.3.5; 2026.
DR SABIO-RK; P0AFI7; -.
DR UniPathway; UPA01068; UER00304.
DR UniPathway; UPA01068; UER00305.
DR EvolutionaryTrace; P0AFI7; -.
DR PRO; PR:P0AFI7; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0032991; C:protein-containing complex; IDA:CAFA.
DR GO; GO:0010181; F:FMN binding; IDA:EcoCyc.
DR GO; GO:0016491; F:oxidoreductase activity; IDA:EcoliWiki.
DR GO; GO:0042301; F:phosphate ion binding; IDA:CAFA.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:CAFA.
DR GO; GO:0004733; F:pyridoxamine-phosphate oxidase activity; IDA:EcoCyc.
DR GO; GO:1902444; F:riboflavin binding; IDA:CAFA.
DR GO; GO:0036001; P:'de novo' pyridoxal 5'-phosphate biosynthetic process; IMP:EcoCyc.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 2.30.110.10; -; 1.
DR HAMAP; MF_01629; PdxH; 1.
DR InterPro; IPR000659; Pyridox_Oxase.
DR InterPro; IPR019740; Pyridox_Oxase_CS.
DR InterPro; IPR011576; Pyridox_Oxase_put.
DR InterPro; IPR019576; Pyridoxamine_oxidase_dimer_C.
DR InterPro; IPR012349; Split_barrel_FMN-bd.
DR PANTHER; PTHR10851; PTHR10851; 1.
DR Pfam; PF10590; PNP_phzG_C; 1.
DR Pfam; PF01243; Putative_PNPOx; 1.
DR PIRSF; PIRSF000190; Pyd_amn-ph_oxd; 1.
DR TIGRFAMs; TIGR00558; pdxH; 1.
DR PROSITE; PS01064; PYRIDOX_OXIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Flavoprotein; FMN; Oxidoreductase;
KW Pyridoxine biosynthesis; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7860596"
FT CHAIN 2..218
FT /note="Pyridoxine/pyridoxamine 5'-phosphate oxidase"
FT /id="PRO_0000167706"
FT BINDING 14..17
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11786019"
FT BINDING 67..72
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:10903950,
FT ECO:0000269|PubMed:11453690, ECO:0000269|PubMed:15858270"
FT BINDING 72
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11453690"
FT BINDING 82..83
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:10903950,
FT ECO:0000269|PubMed:11453690, ECO:0000269|PubMed:15858270"
FT BINDING 88
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:10903950,
FT ECO:0000269|PubMed:11453690, ECO:0000269|PubMed:15858270"
FT BINDING 89
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:10903950,
FT ECO:0000269|PubMed:11453690, ECO:0000269|PubMed:15858270"
FT BINDING 111
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:11786019,
FT ECO:0000269|PubMed:15858270"
FT BINDING 129
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11453690"
FT BINDING 133
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11453690"
FT BINDING 137
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11453690"
FT BINDING 146..147
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:10903950,
FT ECO:0000269|PubMed:11453690, ECO:0000269|PubMed:15858270"
FT BINDING 191
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:15858270"
FT BINDING 197..199
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11786019"
FT BINDING 201
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:11786019,
FT ECO:0000269|PubMed:15858270"
FT MUTAGEN 14
FT /note="R->E: Reduces affinity for substrate about 7-fold,
FT but has no effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:11786019"
FT MUTAGEN 14
FT /note="R->M: Reduces affinity for substrate about 9-fold,
FT but has no effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:11786019"
FT MUTAGEN 17
FT /note="Y->F: Reduces affinity for substrate 3-fold, but has
FT about 5-fold increase in catalytic activity."
FT /evidence="ECO:0000269|PubMed:11786019"
FT MUTAGEN 49
FT /note="D->A: Reduces affinity for substrate 3-fold and
FT catalytic activity 2-fold."
FT /evidence="ECO:0000269|PubMed:11786019"
FT MUTAGEN 197
FT /note="R->E: Reduces affinity for substrate 8000-fold and
FT catalytic activity 16-fold."
FT /evidence="ECO:0000269|PubMed:11786019"
FT MUTAGEN 197
FT /note="R->M: Reduces affinity for substrate 300-fold and
FT catalytic activity about 4-fold."
FT /evidence="ECO:0000269|PubMed:11786019"
FT MUTAGEN 199
FT /note="H->A: Reduces affinity for substrate 230-fold, but
FT has no effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:11786019"
FT MUTAGEN 199
FT /note="H->N: Reduces catalytic activity about 4-fold, but
FT has no effect on affinity for substrate."
FT /evidence="ECO:0000269|PubMed:11786019"
FT HELIX 9..12
FT /evidence="ECO:0007829|PDB:1JNW"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:1DNL"
FT HELIX 31..44
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 64..70
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 73..75
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 78..84
FT /evidence="ECO:0007829|PDB:1DNL"
FT HELIX 88..95
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 98..103
FT /evidence="ECO:0007829|PDB:1DNL"
FT HELIX 106..108
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 110..120
FT /evidence="ECO:0007829|PDB:1DNL"
FT HELIX 123..130
FT /evidence="ECO:0007829|PDB:1DNL"
FT HELIX 135..143
FT /evidence="ECO:0007829|PDB:1DNL"
FT HELIX 154..166
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 167..170
FT /evidence="ECO:0007829|PDB:1G79"
FT STRAND 178..183
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 186..192
FT /evidence="ECO:0007829|PDB:1DNL"
FT HELIX 195..197
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 200..206
FT /evidence="ECO:0007829|PDB:1DNL"
FT STRAND 208..215
FT /evidence="ECO:0007829|PDB:1DNL"
SQ SEQUENCE 218 AA; 25545 MW; 8B47CEEEA6CEF5F9 CRC64;
MSDNDELQQI AHLRREYTKG GLRRRDLPAD PLTLFERWLS QACEAKLADP TAMVVATVDE
HGQPYQRIVL LKHYDEKGMV FYTNLGSRKA HQIENNPRVS LLFPWHTLER QVMVIGKAER
LSTLEVMKYF HSRPRDSQIG AWVSKQSSRI SARGILESKF LELKQKFQQG EVPLPSFWGG
FRVSLEQIEF WQGGEHRLHD RFLYQRENDA WKIDRLAP
