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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).3 Publications

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.3 Publications
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.3 Publications

Cofactori

FMN6 PublicationsNote: Binds 1 FMN per subunit.6 Publications

Kineticsi

Kcat is 0.3 sec(-1) for oxidase activity with pyridoxine 5'-phosphate as substrate (at pH 7.6 and 37 degrees Celsius).1 Publication

Manual assertion based on experiment ini

  1. KM=0.3 µM for pyridoxamine 5'-phosphate1 Publication
  2. KM=2 µM for pyridoxine 5'-phosphate (at pH 7.6 and 37 degrees Celsius)2 Publications
  3. KM=105 µM for pyridoxamine 5'-phosphate (at pH 7.6 and 37 degrees Celsius)1 Publication

    Pathwayi: pyridoxal 5'-phosphate salvage

    This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate.
    Proteins known to be involved in this subpathway in this organism are:
    1. Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
    This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

    Pathwayi: pyridoxal 5'-phosphate salvage

    This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.
    Proteins known to be involved in this subpathway in this organism are:
    1. Pyridoxine/pyridoxamine 5'-phosphate oxidase (pdxH)
    This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei72Substrate1 Publication1
    Binding sitei88FMN3 Publications1
    Binding sitei89FMN3 Publications1
    Binding sitei111FMN2 Publications1
    Binding sitei129Substrate1 Publication1
    Binding sitei133Substrate1 Publication1
    Binding sitei137Substrate1 Publication1
    Binding sitei191FMN1 Publication1
    Binding sitei201FMN2 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi67 – 72FMN3 Publications6
    Nucleotide bindingi82 – 83FMN3 Publications2
    Nucleotide bindingi146 – 147FMN3 Publications2

    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.
    UniPathwayiUPA01068; UER00304.
    UPA01068; UER00305.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC:1.4.3.53 Publications)
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11487. pdxH.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi14R → E: Reduces affinity for substrate about 7-fold, but has no effect on catalytic activity. 1 Publication1
    Mutagenesisi14R → M: Reduces affinity for substrate about 9-fold, but has no effect on catalytic activity. 1 Publication1
    Mutagenesisi17Y → F: Reduces affinity for substrate 3-fold, but has about 5-fold increase in catalytic activity. 1 Publication1
    Mutagenesisi49D → A: Reduces affinity for substrate 3-fold and catalytic activity 2-fold. 1 Publication1
    Mutagenesisi197R → E: Reduces affinity for substrate 8000-fold and catalytic activity 16-fold. 1 Publication1
    Mutagenesisi197R → M: Reduces affinity for substrate 300-fold and catalytic activity about 4-fold. 1 Publication1
    Mutagenesisi199H → A: Reduces affinity for substrate 230-fold, but has no effect on catalytic activity. 1 Publication1
    Mutagenesisi199H → N: Reduces catalytic activity about 4-fold, but has no effect on affinity for substrate. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00001677062 – 218Pyridoxine/pyridoxamine 5'-phosphate oxidaseAdd BLAST217

    Proteomic databases

    EPDiP0AFI7.
    PaxDbiP0AFI7.
    PRIDEiP0AFI7.

    Interactioni

    Subunit structurei

    Homodimer.6 Publications

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1218
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi9 – 12Combined sources4
    Helixi24 – 26Combined sources3
    Helixi31 – 44Combined sources14
    Beta strandi52 – 58Combined sources7
    Beta strandi64 – 70Combined sources7
    Beta strandi73 – 75Combined sources3
    Beta strandi78 – 84Combined sources7
    Helixi88 – 95Combined sources8
    Beta strandi98 – 103Combined sources6
    Helixi106 – 108Combined sources3
    Beta strandi110 – 120Combined sources11
    Helixi123 – 130Combined sources8
    Helixi135 – 143Combined sources9
    Helixi154 – 166Combined sources13
    Beta strandi167 – 170Combined sources4
    Beta strandi178 – 183Combined sources6
    Beta strandi186 – 192Combined sources7
    Helixi195 – 197Combined sources3
    Beta strandi200 – 206Combined sources7
    Beta strandi208 – 215Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AFI7.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni14 – 17Substrate binding1 Publication4
    Regioni197 – 199Substrate binding1 Publication3

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4108S7T. Bacteria.
    COG0259. LUCA.
    HOGENOMiHOG000242755.
    InParanoidiP0AFI7.
    KOiK00275.
    OMAiPEHWGGY.
    PhylomeDBiP0AFI7.

    Family and domain databases

    Gene3Di2.30.110.10. 1 hit.
    HAMAPiMF_01629. PdxH. 1 hit.
    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:SF0. PTHR10851:SF0. 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.
    WP_001282319.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74710; AAC74710; b1638.
    BAA15399; BAA15399; BAA15399.
    GeneIDi946806.
    KEGGiecj:JW1630.
    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.
    WP_001282319.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    EPDiP0AFI7.
    PaxDbiP0AFI7.
    PRIDEiP0AFI7.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74710; AAC74710; b1638.
    BAA15399; BAA15399; BAA15399.
    GeneIDi946806.
    KEGGiecj:JW1630.
    eco:b1638.
    PATRICi32118578. VBIEscCol129921_1709.

    Organism-specific databases

    EchoBASEiEB1450.
    EcoGeneiEG11487. pdxH.

    Phylogenomic databases

    eggNOGiENOG4108S7T. Bacteria.
    COG0259. LUCA.
    HOGENOMiHOG000242755.
    InParanoidiP0AFI7.
    KOiK00275.
    OMAiPEHWGGY.
    PhylomeDBiP0AFI7.

    Enzyme and pathway databases

    UniPathwayiUPA01068; UER00304.
    UPA01068; UER00305.
    BioCyciEcoCyc:PDXH-MONOMER.
    ECOL316407:JW1630-MONOMER.
    MetaCyc:PDXH-MONOMER.
    BRENDAi1.4.3.5. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0AFI7.
    PROiP0AFI7.

    Family and domain databases

    Gene3Di2.30.110.10. 1 hit.
    HAMAPiMF_01629. PdxH. 1 hit.
    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:SF0. PTHR10851:SF0. 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...

    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: November 2, 2016
    This is version 100 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

    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 one 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.