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P38075

- PDX3_YEAST

UniProt

P38075 - PDX3_YEAST

Protein

Pyridoxamine 5'-phosphate oxidase

Gene

PDX3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 134 (01 Oct 2014)
      Sequence version 1 (01 Oct 1994)
      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.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei73 – 731FMN1 Publication
    Binding sitei76 – 761FMN; via amide nitrogen1 Publication
    Binding sitei78 – 781SubstrateBy similarity
    Binding sitei96 – 961FMN1 Publication
    Binding sitei136 – 1361SubstrateBy similarity
    Binding sitei140 – 1401SubstrateBy similarity
    Binding sitei144 – 1441SubstrateBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi88 – 892FMN1 Publication
    Nucleotide bindingi153 – 1542FMN1 Publication

    GO - Molecular functioni

    1. FMN binding Source: InterPro
    2. pyridoxamine-phosphate oxidase activity Source: SGD

    GO - Biological processi

    1. pyridoxal 5'-phosphate salvage Source: SGD
    2. pyridoxine biosynthetic process Source: UniProtKB-KW

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Pyridoxine biosynthesis

    Keywords - Ligandi

    Flavoprotein, FMN

    Enzyme and pathway databases

    BioCyciMetaCyc:YBR035C-MONOMER.
    YEAST:YBR035C-MONOMER.
    ReactomeiREACT_189056. Vitamins B6 activation to pyridoxal phosphate.
    UniPathwayiUPA00190; UER00304.
    UPA00190; UER00305.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxamine 5'-phosphate oxidase (EC:1.4.3.5)
    Alternative name(s):
    PNP/PMP oxidase
    Short name:
    PNPOx
    Gene namesi
    Name:PDX3
    Ordered Locus Names:YBR035C
    ORF Names:YBR0321
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome II

    Organism-specific databases

    CYGDiYBR035c.
    SGDiS000000239. PDX3.

    Subcellular locationi

    GO - Cellular componenti

    1. mitochondrial intermembrane space Source: SGD

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 228228Pyridoxamine 5'-phosphate oxidasePRO_0000167787Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

    Keywords - PTMi

    Isopeptide bond, Ubl conjugation

    Proteomic databases

    MaxQBiP38075.
    PaxDbiP38075.
    PeptideAtlasiP38075.

    Expressioni

    Gene expression databases

    GenevestigatoriP38075.

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    BioGridi32736. 107 interactions.
    DIPiDIP-4324N.
    IntActiP38075. 1 interaction.
    MINTiMINT-528829.
    STRINGi4932.YBR035C.

    Structurei

    Secondary structure

    1
    228
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi28 – 303
    Helixi35 – 4814
    Beta strandi57 – 648
    Turni65 – 684
    Beta strandi69 – 768
    Beta strandi82 – 909
    Beta strandi92 – 943
    Helixi95 – 1028
    Beta strandi105 – 1128
    Turni113 – 1164
    Beta strandi117 – 12711
    Helixi130 – 13910
    Helixi142 – 1509
    Beta strandi156 – 1583
    Helixi160 – 17314
    Beta strandi186 – 20015
    Beta strandi208 – 2136
    Beta strandi222 – 2265

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1CI0X-ray2.70A/B1-228[»]
    ProteinModelPortaliP38075.
    SMRiP38075. Positions 24-228.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP38075.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni205 – 2073Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0259.
    GeneTreeiENSGT00390000011219.
    HOGENOMiHOG000242755.
    KOiK00275.
    OMAiELDHRGF.
    OrthoDBiEOG7WDNF3.

    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.

    P38075-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTKQAEETQK PIIFAPETYQ YDKFTLNEKQ LTDDPIDLFT KWFNEAKEDP    50
    RETLPEAITF SSAELPSGRV SSRILLFKEL DHRGFTIYSN WGTSRKAHDI 100
    ATNPNAAIVF FWKDLQRQVR VEGITEHVNR ETSERYFKTR PRGSKIGAWA 150
    SRQSDVIKNR EELDELTQKN TERFKDAEDI PCPDYWGGLR IVPLEIEFWQ 200
    GRPSRLHDRF VYRRKTENDP WKVVRLAP 228
    Length:228
    Mass (Da):26,908
    Last modified:October 1, 1994 - v1
    Checksum:i8B648A219763160E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X76078 Genomic DNA. Translation: CAA53690.1.
    X76992 Genomic DNA. Translation: CAA54295.1.
    Z35904 Genomic DNA. Translation: CAA84977.1.
    AY557712 Genomic DNA. Translation: AAS56038.1.
    BK006936 Genomic DNA. Translation: DAA07155.1.
    PIRiS41301.
    RefSeqiNP_009591.1. NM_001178383.1.

    Genome annotation databases

    EnsemblFungiiYBR035C; YBR035C; YBR035C.
    GeneIDi852323.
    KEGGisce:YBR035C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X76078 Genomic DNA. Translation: CAA53690.1 .
    X76992 Genomic DNA. Translation: CAA54295.1 .
    Z35904 Genomic DNA. Translation: CAA84977.1 .
    AY557712 Genomic DNA. Translation: AAS56038.1 .
    BK006936 Genomic DNA. Translation: DAA07155.1 .
    PIRi S41301.
    RefSeqi NP_009591.1. NM_001178383.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1CI0 X-ray 2.70 A/B 1-228 [» ]
    ProteinModelPortali P38075.
    SMRi P38075. Positions 24-228.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32736. 107 interactions.
    DIPi DIP-4324N.
    IntActi P38075. 1 interaction.
    MINTi MINT-528829.
    STRINGi 4932.YBR035C.

    Proteomic databases

    MaxQBi P38075.
    PaxDbi P38075.
    PeptideAtlasi P38075.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YBR035C ; YBR035C ; YBR035C .
    GeneIDi 852323.
    KEGGi sce:YBR035C.

    Organism-specific databases

    CYGDi YBR035c.
    SGDi S000000239. PDX3.

    Phylogenomic databases

    eggNOGi COG0259.
    GeneTreei ENSGT00390000011219.
    HOGENOMi HOG000242755.
    KOi K00275.
    OMAi ELDHRGF.
    OrthoDBi EOG7WDNF3.

    Enzyme and pathway databases

    UniPathwayi UPA00190 ; UER00304 .
    UPA00190 ; UER00305 .
    BioCyci MetaCyc:YBR035C-MONOMER.
    YEAST:YBR035C-MONOMER.
    Reactomei REACT_189056. Vitamins B6 activation to pyridoxal phosphate.

    Miscellaneous databases

    EvolutionaryTracei P38075.
    NextBioi 971023.
    PROi P38075.

    Gene expression databases

    Genevestigatori P38075.

    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. "Sterol uptake induced by an impairment of pyridoxal phosphate synthesis in Saccharomyces cerevisiae: cloning and sequencing of the PDX3 gene encoding pyridoxine (pyridoxamine) phosphate oxidase."
      Loubbardi A., Karst F., Guilloton M., Marcireau C.
      J. Bacteriol. 177:1817-1823(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The complete sequence of a 33 kb fragment on the right arm of chromosome II from Saccharomyces cerevisiae reveals 16 open reading frames, including ten new open reading frames, five previously identified genes and a homologue of the SCO1 gene."
      Smits P.H.M., de Haan M., Maat C., Grivell L.A.
      Yeast 10:S75-S80(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. "Complete DNA sequence of yeast chromosome II."
      Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
      , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
      EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    6. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-29.
      Strain: SUB592.
    7. "The structure of PNP oxidase from S. cerevisiae."
      New York structural genomix research consortium (NYSGXRC)
      Submitted (JAN-2005) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH FMN.

    Entry informationi

    Entry nameiPDX3_YEAST
    AccessioniPrimary (citable) accession number: P38075
    Secondary accession number(s): D6VQ35
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: October 1, 2014
    This is version 134 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome II
      Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

    External Data

    Dasty 3