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P0AFI7

- PDXH_ECOLI

UniProt

P0AFI7 - PDXH_ECOLI

Protein

Pyridoxine/pyridoxamine 5'-phosphate oxidase

Gene

pdxH

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 84 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    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

    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

    1. FMN binding Source: EcoCyc
    2. oxidoreductase activity Source: EcoliWiki
    3. pyridoxamine-phosphate oxidase activity Source: EcoCyc

    GO - Biological processi

    1. oxidation-reduction process Source: EcoliWiki
    2. pyridoxal 5'-phosphate salvage Source: EcoCyc
    3. pyridoxine biosynthetic process Source: EcoCyc

    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.
    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: Chromosome, UP000000625: 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 – 124
    Helixi24 – 263
    Helixi31 – 4414
    Beta strandi52 – 587
    Beta strandi64 – 707
    Beta strandi73 – 753
    Beta strandi78 – 847
    Helixi88 – 958
    Beta strandi98 – 1036
    Helixi106 – 1083
    Beta strandi110 – 12011
    Helixi123 – 1308
    Helixi135 – 1439
    Helixi154 – 16613
    Beta strandi167 – 1704
    Beta strandi178 – 1836
    Beta strandi186 – 1927
    Helixi195 – 1973
    Beta strandi200 – 2067
    Beta strandi208 – 2158

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    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.
    KOiK00275.
    OMAiNMGSRKA.
    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

    MSDNDELQQI AHLRREYTKG GLRRRDLPAD PLTLFERWLS QACEAKLADP    50
    TAMVVATVDE HGQPYQRIVL LKHYDEKGMV FYTNLGSRKA HQIENNPRVS 100
    LLFPWHTLER QVMVIGKAER LSTLEVMKYF HSRPRDSQIG AWVSKQSSRI 150
    SARGILESKF LELKQKFQQG EVPLPSFWGG FRVSLEQIEF WQGGEHRLHD 200
    RFLYQRENDA WKIDRLAP 218
    Length:218
    Mass (Da):25,545
    Last modified:January 23, 2007 - v2
    Checksum:i8B47CEEEA6CEF5F9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_489902.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74710; AAC74710; b1638.
    BAA15399; BAA15399; BAA15399.
    GeneIDi12934494.
    946806.
    KEGGiecj:Y75_p1615.
    eco:b1638.
    PATRICi32118578. VBIEscCol129921_1709.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M92351 Genomic DNA. Translation: AAA24709.1 .
    U00096 Genomic DNA. Translation: AAC74710.1 .
    AP009048 Genomic DNA. Translation: BAA15399.1 .
    PIRi B43261.
    RefSeqi NP_416155.1. NC_000913.3.
    YP_489902.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DNL X-ray 1.80 A 20-218 [» ]
    1G76 X-ray 2.20 A 1-218 [» ]
    1G77 X-ray 2.10 A 1-218 [» ]
    1G78 X-ray 2.20 A 1-218 [» ]
    1G79 X-ray 2.00 A 1-218 [» ]
    1JNW X-ray 2.07 A 1-218 [» ]
    1WV4 X-ray 2.60 A/B 1-218 [» ]
    DisProti DP00165.
    ProteinModelPortali P0AFI7.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48024N.
    IntActi P0AFI7. 13 interactions.
    STRINGi 511145.b1638.

    Proteomic databases

    PaxDbi P0AFI7.
    PRIDEi P0AFI7.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74710 ; AAC74710 ; b1638 .
    BAA15399 ; BAA15399 ; BAA15399 .
    GeneIDi 12934494.
    946806.
    KEGGi ecj:Y75_p1615.
    eco:b1638.
    PATRICi 32118578. VBIEscCol129921_1709.

    Organism-specific databases

    EchoBASEi EB1450.
    EcoGenei EG11487. pdxH.

    Phylogenomic databases

    eggNOGi COG0259.
    HOGENOMi HOG000242755.
    KOi K00275.
    OMAi NMGSRKA.
    OrthoDBi EOG60KN2Z.
    PhylomeDBi P0AFI7.

    Enzyme and pathway databases

    UniPathwayi UPA00190 ; UER00304 .
    UPA00190 ; UER00305 .
    BioCyci EcoCyc:PDXH-MONOMER.
    ECOL316407:JW1630-MONOMER.
    MetaCyc:PDXH-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0AFI7.
    PROi P0AFI7.

    Gene expression databases

    Genevestigatori P0AFI7.

    Family and domain databases

    Gene3Di 2.30.110.10. 1 hit.
    HAMAPi MF_01629. PdxH.
    InterProi IPR000659. Pyridox_Oxase.
    IPR019740. Pyridox_Oxase_CS.
    IPR011576. Pyridox_Oxase_FMN-bd.
    IPR019576. Pyridoxamine_oxidase_dimer_C.
    IPR012349. Split_barrel_FMN-bd.
    [Graphical view ]
    PANTHERi PTHR10851. PTHR10851. 1 hit.
    Pfami PF10590. PNPOx_C. 1 hit.
    PF01243. Pyridox_oxidase. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000190. Pyd_amn-ph_oxd. 1 hit.
    SUPFAMi SSF50475. SSF50475. 1 hit.
    TIGRFAMsi TIGR00558. pdxH. 1 hit.
    PROSITEi PS01064. PYRIDOX_OXIDASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 84 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