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P19624

- PDXA_ECOLI

UniProt

P19624 - PDXA_ECOLI

Protein

4-hydroxythreonine-4-phosphate dehydrogenase

Gene

pdxA

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 133 (01 Oct 2014)
      Sequence version 1 (01 Feb 1991)
      Previous versions | rss
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    Functioni

    Catalyzes the NAD(P)-dependent oxidation of 4-(phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP).2 Publications

    Catalytic activityi

    4-phosphonooxy-L-threonine + NAD+ = 3-amino-2-oxopropyl phosphate + CO2 + NADH.1 Publication

    Cofactori

    Binds 1 divalent metal cation per subunit. Can use ions such as zinc, magnesium or cobalt.2 Publications

    Kineticsi

    1. KM=85 µM for 4-(phosphohydroxy)-L-threonine (at 0.1 M Tris-HCl and pH 7.5)1 Publication
    2. KM=113 µM for 4-(phosphohydroxy)-L-threonine (at 0.1 M phosphate buffer and pH 7.5)1 Publication

    Vmax=2.8 µmol/min/mg enzyme with 4-(phosphohydroxy)-L-threonine as substrate (at 0.1 M Tris-HCl and pH 7.5)1 Publication

    Vmax=0.66 µmol/min/mg enzyme with 4-(phosphohydroxy)-L-threonine as substrate (at 0.1 M phosphate buffer and pH 7.5)1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei136 – 1361Substrate1 Publication
    Binding sitei137 – 1371Substrate1 Publication
    Metal bindingi166 – 1661Divalent metal cation; shared with dimeric partner
    Metal bindingi211 – 2111Divalent metal cation; shared with dimeric partner
    Metal bindingi266 – 2661Divalent metal cation; shared with dimeric partner
    Binding sitei274 – 2741Substrate1 Publication
    Binding sitei283 – 2831Substrate1 Publication
    Binding sitei292 – 2921Substrate1 Publication

    GO - Molecular functioni

    1. 4-hydroxythreonine-4-phosphate dehydrogenase activity Source: EcoCyc
    2. cobalt ion binding Source: UniProtKB-HAMAP
    3. identical protein binding Source: IntAct
    4. magnesium ion binding Source: EcoCyc
    5. NAD binding Source: EcoCyc
    6. zinc ion binding Source: EcoCyc

    GO - Biological processi

    1. pyridoxal phosphate biosynthetic process Source: EcoCyc
    2. pyridoxine biosynthetic process Source: EcoCyc

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Pyridoxine biosynthesis

    Keywords - Ligandi

    Cobalt, Magnesium, Metal-binding, NAD, NADP, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:PDXA-MONOMER.
    ECOL316407:JW0051-MONOMER.
    MetaCyc:PDXA-MONOMER.
    UniPathwayiUPA00244; UER00312.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-hydroxythreonine-4-phosphate dehydrogenase (EC:1.1.1.262)
    Alternative name(s):
    4-(phosphohydroxy)-L-threonine dehydrogenase
    Gene namesi
    Name:pdxA
    Ordered Locus Names:b0052, JW0051
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10691. pdxA.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3293294-hydroxythreonine-4-phosphate dehydrogenasePRO_0000188804Add
    BLAST

    Proteomic databases

    PaxDbiP19624.
    PRIDEiP19624.

    Expressioni

    Gene expression databases

    GenevestigatoriP19624.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-1112869,EBI-1112869

    Protein-protein interaction databases

    DIPiDIP-10448N.
    IntActiP19624. 5 interactions.
    STRINGi511145.b0052.

    Structurei

    Secondary structure

    1
    329
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 105
    Helixi18 – 258
    Beta strandi31 – 388
    Helixi40 – 4910
    Beta strandi55 – 584
    Beta strandi72 – 776
    Helixi93 – 10917
    Beta strandi114 – 1185
    Helixi123 – 1286
    Helixi136 – 1438
    Beta strandi150 – 1578
    Beta strandi159 – 1646
    Helixi169 – 1713
    Helixi172 – 1754
    Helixi178 – 19417
    Beta strandi202 – 2065
    Helixi210 – 2167
    Helixi221 – 2244
    Helixi226 – 23510
    Beta strandi239 – 2446
    Helixi246 – 2494
    Helixi252 – 2554
    Beta strandi259 – 2657
    Helixi266 – 2749
    Beta strandi278 – 2803
    Beta strandi282 – 29413
    Helixi301 – 3033
    Turni304 – 3063
    Helixi312 – 32817

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1PS6X-ray2.25A/B2-329[»]
    1PS7X-ray2.47A/B/C/D1-329[»]
    1PTMX-ray1.96A/B1-329[»]
    ProteinModelPortaliP19624.
    SMRiP19624. Positions 1-329.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP19624.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PdxA family.Curated

    Phylogenomic databases

    eggNOGiCOG1995.
    HOGENOMiHOG000221592.
    KOiK00097.
    OMAiDTLFQDK.
    OrthoDBiEOG6GN6ZC.
    PhylomeDBiP19624.

    Family and domain databases

    Gene3Di3.40.718.10. 1 hit.
    HAMAPiMF_00536. PdxA.
    InterProiIPR024084. IsoPropMal-DH-like_dom.
    IPR005255. PdxA.
    [Graphical view]
    PfamiPF04166. PdxA. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00557. pdxA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P19624-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVKTQRVVIT PGEPAGIGPD LVVQLAQREW PVELVVCADA TLLTNRAAML    50
    GLPLTLRPYS PNSPAQPQTA GTLTLLPVAL RAPVTAGQLA VENGHYVVET 100
    LARACDGCLN GEFAALITGP VHKGVINDAG IPFTGHTEFF EERSQAKKVV 150
    MMLATEELRV ALATTHLPLR DIADAITPAL LHEVIAILHH DLRTKFGIAE 200
    PRILVCGLNP HAGEGGHMGT EEIDTIIPVL NELRAQGMKL NGPLPADTLF 250
    QPKYLDNADA VLAMYHDQGL PVLKYQGFGR GVNITLGLPF IRTSVDHGTA 300
    LELAGRGKAD VGSFITALNL AIKMIVNTQ 329
    Length:329
    Mass (Da):35,114
    Last modified:February 1, 1991 - v1
    Checksum:i44E1FEE233C86233
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M68521 Genomic DNA. Translation: AAA24305.1.
    U00096 Genomic DNA. Translation: AAC73163.1.
    AP009048 Genomic DNA. Translation: BAB96619.1.
    PIRiJV0026. BVECXA.
    RefSeqiNP_414594.1. NC_000913.3.
    YP_488358.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73163; AAC73163; b0052.
    BAB96619; BAB96619; BAB96619.
    GeneIDi12932019.
    944919.
    KEGGiecj:Y75_p0052.
    eco:b0052.
    PATRICi32115203. VBIEscCol129921_0053.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M68521 Genomic DNA. Translation: AAA24305.1 .
    U00096 Genomic DNA. Translation: AAC73163.1 .
    AP009048 Genomic DNA. Translation: BAB96619.1 .
    PIRi JV0026. BVECXA.
    RefSeqi NP_414594.1. NC_000913.3.
    YP_488358.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1PS6 X-ray 2.25 A/B 2-329 [» ]
    1PS7 X-ray 2.47 A/B/C/D 1-329 [» ]
    1PTM X-ray 1.96 A/B 1-329 [» ]
    ProteinModelPortali P19624.
    SMRi P19624. Positions 1-329.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10448N.
    IntActi P19624. 5 interactions.
    STRINGi 511145.b0052.

    Proteomic databases

    PaxDbi P19624.
    PRIDEi P19624.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73163 ; AAC73163 ; b0052 .
    BAB96619 ; BAB96619 ; BAB96619 .
    GeneIDi 12932019.
    944919.
    KEGGi ecj:Y75_p0052.
    eco:b0052.
    PATRICi 32115203. VBIEscCol129921_0053.

    Organism-specific databases

    EchoBASEi EB0685.
    EcoGenei EG10691. pdxA.

    Phylogenomic databases

    eggNOGi COG1995.
    HOGENOMi HOG000221592.
    KOi K00097.
    OMAi DTLFQDK.
    OrthoDBi EOG6GN6ZC.
    PhylomeDBi P19624.

    Enzyme and pathway databases

    UniPathwayi UPA00244 ; UER00312 .
    BioCyci EcoCyc:PDXA-MONOMER.
    ECOL316407:JW0051-MONOMER.
    MetaCyc:PDXA-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P19624.
    PROi P19624.

    Gene expression databases

    Genevestigatori P19624.

    Family and domain databases

    Gene3Di 3.40.718.10. 1 hit.
    HAMAPi MF_00536. PdxA.
    InterProi IPR024084. IsoPropMal-DH-like_dom.
    IPR005255. PdxA.
    [Graphical view ]
    Pfami PF04166. PdxA. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR00557. pdxA. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of Escherichia coli K-12."
      Roa B.B., Connolly D.M., Winkler M.E.
      J. Bacteriol. 171:4767-4777(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
      Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
      Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12.
    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. "Biosynthesis of vitamin B6: the oxidation of 4-hydroxy-L-threonine 4-phosphate by pdxA."
      Cane D.E., Hsiung Y., Cornish J.A., Robinson J.K., Spenser I.D.
      J. Am. Chem. Soc. 120:1936-1937(1998)
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR.
    6. "Biosynthesis of vitamin B6: direct identification of the product of the PdxA-catalyzed oxidation of 4-hydroxy-L-threonine-4-phosphate using electrospray ionization mass spectrometry."
      Banks J., Cane D.E.
      Bioorg. Med. Chem. Lett. 14:1633-1636(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    7. "Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway."
      Sivaraman J., Li Y., Banks J., Cane D.E., Matte A., Cygler M.
      J. Biol. Chem. 278:43682-43690(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND ZINC IONS, COFACTOR, SUBUNIT.

    Entry informationi

    Entry nameiPDXA_ECOLI
    AccessioniPrimary (citable) accession number: P19624
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1991
    Last sequence update: February 1, 1991
    Last modified: October 1, 2014
    This is version 133 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The active site is located at the dimer interface.
    According to PubMed:15026039, PdxA may catalyze both oxidation and decarboxylation reactions that directly lead to AHAP.

    Keywords - Technical termi

    3D-structure, Complete proteome, 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