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Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.

Cofactori

FMNNote: Binds 1 FMN per subunit.

Kineticsi

  1. KM=0.3 µM for pyridoxamine 5'-phosphate1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei67 – 671FMN3 Publications
    Binding sitei70 – 701FMN; via amide nitrogen3 Publications
    Binding sitei72 – 721Substrate
    Binding sitei89 – 891FMN3 Publications
    Binding sitei129 – 1291Substrate
    Binding sitei133 – 1331Substrate
    Binding sitei137 – 1371Substrate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi82 – 832FMN3 Publications
    Nucleotide bindingi146 – 1472FMN3 Publications

    GO - Molecular functioni

    • FMN binding Source: EcoCyc
    • oxidoreductase activity Source: EcoliWiki
    • pyridoxamine-phosphate oxidase activity Source: EcoCyc

    GO - Biological processi

    • oxidation-reduction process Source: EcoliWiki
    • pyridoxal 5'-phosphate salvage Source: EcoCyc
    • pyridoxine biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Pyridoxine biosynthesis

    Keywords - Ligandi

    Flavoprotein, FMN

    Enzyme and pathway databases

    BioCyciEcoCyc:PDXH-MONOMER.
    ECOL316407:JW1630-MONOMER.
    MetaCyc:PDXH-MONOMER.
    BRENDAi1.4.3.5. 2026.
    UniPathwayiUPA00190; UER00304.
    UPA00190; UER00305.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC:1.4.3.5)
    Alternative name(s):
    PNP/PMP oxidase
    Short name:
    PNPOx
    Pyridoxal 5'-phosphate synthase
    Gene namesi
    Name:pdxH
    Ordered Locus Names:b1638, JW1630
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11487. pdxH.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi14 – 141R → E: Reduces affinity for substrate about 7-fold, but has no effect on catalytic activity. 1 Publication
    Mutagenesisi14 – 141R → M: Reduces affinity for substrate about 9-fold, but has no effect on catalytic activity. 1 Publication
    Mutagenesisi17 – 171Y → F: Reduces affinity for substrate 3-fold, but has about 5-fold increase in catalytic activity. 1 Publication
    Mutagenesisi49 – 491D → A: Reduces affinity for substrate 3-fold and catalytic activity 2-fold. 1 Publication
    Mutagenesisi197 – 1971R → E: Reduces affinity for substrate 8000-fold and catalytic activity 16-fold. 1 Publication
    Mutagenesisi197 – 1971R → M: Reduces affinity for substrate 300-fold and catalytic activity about 4-fold. 1 Publication
    Mutagenesisi199 – 1991H → A: Reduces affinity for substrate 230-fold, but has no effect on catalytic activity. 1 Publication
    Mutagenesisi199 – 1991H → N: Reduces catalytic activity about 4-fold, but has no effect on affinity for substrate. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 218217Pyridoxine/pyridoxamine 5'-phosphate oxidasePRO_0000167706Add
    BLAST

    Proteomic databases

    PaxDbiP0AFI7.
    PRIDEiP0AFI7.

    Expressioni

    Gene expression databases

    GenevestigatoriP0AFI7.

    Interactioni

    Subunit structurei

    Homodimer.4 Publications

    Protein-protein interaction databases

    DIPiDIP-48024N.
    IntActiP0AFI7. 13 interactions.
    STRINGi511145.b1638.

    Structurei

    Secondary structure

    1
    218
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 124Combined sources
    Helixi24 – 263Combined sources
    Helixi31 – 4414Combined sources
    Beta strandi52 – 587Combined sources
    Beta strandi64 – 707Combined sources
    Beta strandi73 – 753Combined sources
    Beta strandi78 – 847Combined sources
    Helixi88 – 958Combined sources
    Beta strandi98 – 1036Combined sources
    Helixi106 – 1083Combined sources
    Beta strandi110 – 12011Combined sources
    Helixi123 – 1308Combined sources
    Helixi135 – 1439Combined sources
    Helixi154 – 16613Combined sources
    Beta strandi167 – 1704Combined sources
    Beta strandi178 – 1836Combined sources
    Beta strandi186 – 1927Combined sources
    Helixi195 – 1973Combined sources
    Beta strandi200 – 2067Combined sources
    Beta strandi208 – 2158Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DNLX-ray1.80A20-218[»]
    1G76X-ray2.20A1-218[»]
    1G77X-ray2.10A1-218[»]
    1G78X-ray2.20A1-218[»]
    1G79X-ray2.00A1-218[»]
    1JNWX-ray2.07A1-218[»]
    1WV4X-ray2.60A/B1-218[»]
    DisProtiDP00165.
    ProteinModelPortaliP0AFI7.
    SMRiP0AFI7. Positions 5-218.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AFI7.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni14 – 174Substrate binding
    Regioni197 – 1993Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0259.
    HOGENOMiHOG000242755.
    InParanoidiP0AFI7.
    KOiK00275.
    OMAiPHWGGFR.
    OrthoDBiEOG60KN2Z.
    PhylomeDBiP0AFI7.

    Family and domain databases

    Gene3Di2.30.110.10. 1 hit.
    HAMAPiMF_01629. PdxH.
    InterProiIPR000659. Pyridox_Oxase.
    IPR019740. Pyridox_Oxase_CS.
    IPR011576. Pyridox_Oxase_FMN-bd.
    IPR019576. Pyridoxamine_oxidase_dimer_C.
    IPR012349. Split_barrel_FMN-bd.
    [Graphical view]
    PANTHERiPTHR10851. PTHR10851. 1 hit.
    PfamiPF10590. PNPOx_C. 1 hit.
    PF01243. Pyridox_oxidase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
    SUPFAMiSSF50475. SSF50475. 1 hit.
    TIGRFAMsiTIGR00558. pdxH. 1 hit.
    PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P0AFI7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSDNDELQQI AHLRREYTKG GLRRRDLPAD PLTLFERWLS QACEAKLADP
    60 70 80 90 100
    TAMVVATVDE HGQPYQRIVL LKHYDEKGMV FYTNLGSRKA HQIENNPRVS
    110 120 130 140 150
    LLFPWHTLER QVMVIGKAER LSTLEVMKYF HSRPRDSQIG AWVSKQSSRI
    160 170 180 190 200
    SARGILESKF LELKQKFQQG EVPLPSFWGG FRVSLEQIEF WQGGEHRLHD
    210
    RFLYQRENDA WKIDRLAP
    Length:218
    Mass (Da):25,545
    Last modified:January 23, 2007 - v2
    Checksum:i8B47CEEEA6CEF5F9
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M92351 Genomic DNA. Translation: AAA24709.1.
    U00096 Genomic DNA. Translation: AAC74710.1.
    AP009048 Genomic DNA. Translation: BAA15399.1.
    PIRiB43261.
    RefSeqiNP_416155.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC74710; AAC74710; b1638.
    BAA15399; BAA15399; BAA15399.
    GeneIDi946806.
    KEGGiecj:Y75_p1615.
    eco:b1638.
    PATRICi32118578. VBIEscCol129921_1709.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M92351 Genomic DNA. Translation: AAA24709.1.
    U00096 Genomic DNA. Translation: AAC74710.1.
    AP009048 Genomic DNA. Translation: BAA15399.1.
    PIRiB43261.
    RefSeqiNP_416155.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DNLX-ray1.80A20-218[»]
    1G76X-ray2.20A1-218[»]
    1G77X-ray2.10A1-218[»]
    1G78X-ray2.20A1-218[»]
    1G79X-ray2.00A1-218[»]
    1JNWX-ray2.07A1-218[»]
    1WV4X-ray2.60A/B1-218[»]
    DisProtiDP00165.
    ProteinModelPortaliP0AFI7.
    SMRiP0AFI7. Positions 5-218.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-48024N.
    IntActiP0AFI7. 13 interactions.
    STRINGi511145.b1638.

    Proteomic databases

    PaxDbiP0AFI7.
    PRIDEiP0AFI7.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74710; AAC74710; b1638.
    BAA15399; BAA15399; BAA15399.
    GeneIDi946806.
    KEGGiecj:Y75_p1615.
    eco:b1638.
    PATRICi32118578. VBIEscCol129921_1709.

    Organism-specific databases

    EchoBASEiEB1450.
    EcoGeneiEG11487. pdxH.

    Phylogenomic databases

    eggNOGiCOG0259.
    HOGENOMiHOG000242755.
    InParanoidiP0AFI7.
    KOiK00275.
    OMAiPHWGGFR.
    OrthoDBiEOG60KN2Z.
    PhylomeDBiP0AFI7.

    Enzyme and pathway databases

    UniPathwayiUPA00190; UER00304.
    UPA00190; UER00305.
    BioCyciEcoCyc:PDXH-MONOMER.
    ECOL316407:JW1630-MONOMER.
    MetaCyc:PDXH-MONOMER.
    BRENDAi1.4.3.5. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0AFI7.
    PROiP0AFI7.

    Gene expression databases

    GenevestigatoriP0AFI7.

    Family and domain databases

    Gene3Di2.30.110.10. 1 hit.
    HAMAPiMF_01629. PdxH.
    InterProiIPR000659. Pyridox_Oxase.
    IPR019740. Pyridox_Oxase_CS.
    IPR011576. Pyridox_Oxase_FMN-bd.
    IPR019576. Pyridoxamine_oxidase_dimer_C.
    IPR012349. Split_barrel_FMN-bd.
    [Graphical view]
    PANTHERiPTHR10851. PTHR10851. 1 hit.
    PfamiPF10590. PNPOx_C. 1 hit.
    PF01243. Pyridox_oxidase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
    SUPFAMiSSF50475. SSF50475. 1 hit.
    TIGRFAMsiTIGR00558. pdxH. 1 hit.
    PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Characterization of the complex pdxH-tyrS operon of Escherichia coli K-12 and pleiotropic phenotypes caused by pdxH insertion mutations."
      Lam H.-M., Winkler M.E.
      J. Bacteriol. 174:6033-6045(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Kinetic limitation and cellular amount of pyridoxine (pyridoxamine) 5'-phosphate oxidase of Escherichia coli K-12."
      Zhao G., Winkler M.E.
      J. Bacteriol. 177:883-891(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-11, CHARACTERIZATION.
      Strain: K12.
    6. "Expression, purification, and characterization of recombinant Escherichia coli pyridoxine 5'-phosphate oxidase."
      di Salvo M., Yang E., Zhao G., Winkler M.E., Schirch V.
      Protein Expr. Purif. 13:349-356(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    7. "X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8-A resolution."
      Safo M.K., Mathews I., Musayev F.N., di Salvo M.L., Thiel D.J., Abraham D.J., Schirch V.
      Structure 8:751-762(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 20-218 IN COMPLEX WITH FMN, SUBUNIT.
    8. "X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution."
      Safo M.K., Musayev F.N., di Salvo M.L., Schirch V.
      J. Mol. Biol. 310:817-826(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT.
    9. "Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase."
      di Salvo M.L., Ko T.-P., Musayev F.N., Raboni S., Schirch V., Safo M.K.
      J. Mol. Biol. 315:385-397(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ARG-14; TYR-17; ASP-49; ARG-197 AND HIS-199.
    10. "Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme."
      Safo M.K., Musayev F.N., Schirch V.
      Acta Crystallogr. D 61:599-604(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL 5'-PHOSPHATE AND FMN, SUBUNIT.

    Entry informationi

    Entry nameiPDXH_ECOLI
    AccessioniPrimary (citable) accession number: P0AFI7
    Secondary accession number(s): P28225
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: January 23, 2007
    Last modified: May 27, 2015
    This is version 89 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Can bind a second molecule of pyridoxamine 5'-phosphate at a non-catalytic site in a cleft at the protein surface.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.