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P0A794

- PDXJ_ECOLI

UniProt

P0A794 - PDXJ_ECOLI

Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

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 89 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate.1 Publication

    Catalytic activityi

    1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei9 – 913-amino-2-oxopropyl phosphate
    Binding sitei20 – 2013-amino-2-oxopropyl phosphate
    Active sitei45 – 451Proton acceptor
    Binding sitei47 – 4711-deoxy-D-xylulose 5-phosphate
    Binding sitei52 – 5211-deoxy-D-xylulose 5-phosphate
    Active sitei72 – 721Proton acceptor
    Binding sitei102 – 10211-deoxy-D-xylulose 5-phosphate
    Sitei153 – 1531Transition state stabilizer
    Active sitei193 – 1931Proton donor
    Binding sitei194 – 19413-amino-2-oxopropyl phosphate; via amide nitrogen

    GO - Molecular functioni

    1. pyridoxine 5'-phosphate synthase activity Source: EcoCyc

    GO - Biological processi

    1. pyridoxine biosynthetic process Source: EcoliWiki

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Pyridoxine biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:PDXJ-MONOMER.
    ECOL316407:JW2548-MONOMER.
    MetaCyc:PDXJ-MONOMER.
    UniPathwayiUPA00244; UER00313.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxine 5'-phosphate synthase (EC:2.6.99.2)
    Short name:
    PNP synthase
    Gene namesi
    Name:pdxJ
    Ordered Locus Names:b2564, JW2548
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10693. pdxJ.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed
    Chaini2 – 243242Pyridoxine 5'-phosphate synthasePRO_0000190114Add
    BLAST

    Proteomic databases

    PaxDbiP0A794.
    PRIDEiP0A794.

    Expressioni

    Gene expression databases

    GenevestigatoriP0A794.

    Interactioni

    Subunit structurei

    Homooctamer; tetramer of dimers.2 Publications

    Protein-protein interaction databases

    DIPiDIP-36215N.
    IntActiP0A794. 5 interactions.
    MINTiMINT-1227457.
    STRINGi511145.b2564.

    Structurei

    Secondary structure

    1
    243
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 95
    Helixi11 – 188
    Beta strandi20 – 223
    Helixi27 – 359
    Turni36 – 383
    Beta strandi40 – 456
    Beta strandi51 – 533
    Helixi55 – 6410
    Beta strandi66 – 738
    Helixi77 – 8610
    Beta strandi89 – 935
    Turni98 – 1003
    Beta strandi103 – 1053
    Helixi110 – 1123
    Helixi113 – 12513
    Beta strandi129 – 1346
    Helixi138 – 1469
    Beta strandi150 – 1556
    Helixi157 – 1615
    Helixi165 – 18420
    Beta strandi188 – 1947
    Turni197 – 1993
    Helixi200 – 2045
    Beta strandi209 – 2146
    Helixi216 – 22510
    Helixi227 – 24216

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HO1X-ray2.00A/B/C/D2-243[»]
    1HO4X-ray2.30A/B/C/D2-243[»]
    1IXNX-ray2.30A/B/C/D2-243[»]
    1IXOX-ray2.30A/B/C/D2-243[»]
    1IXPX-ray2.30A/B/C/D2-243[»]
    1IXQX-ray2.30A/B/C/D2-243[»]
    1M5WX-ray1.96A/B/C/D/E/F/G/H1-243[»]
    ProteinModelPortaliP0A794.
    SMRiP0A794. Positions 2-243.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A794.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni11 – 1221-deoxy-D-xylulose 5-phosphate binding
    Regioni215 – 21623-amino-2-oxopropyl phosphate binding

    Sequence similaritiesi

    Belongs to the PNP synthase family.Curated

    Phylogenomic databases

    eggNOGiCOG0854.
    HOGENOMiHOG000258095.
    KOiK03474.
    OMAiVPETRQE.
    OrthoDBiEOG6M9F0H.
    PhylomeDBiP0A794.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00279. PdxJ.
    InterProiIPR013785. Aldolase_TIM.
    IPR004569. PyrdxlP_synth_PdxJ.
    [Graphical view]
    PfamiPF03740. PdxJ. 1 hit.
    [Graphical view]
    SUPFAMiSSF63892. SSF63892. 1 hit.
    TIGRFAMsiTIGR00559. pdxJ. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P0A794-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAELLLGVNI DHIATLRNAR GTAYPDPVQA AFIAEQAGAD GITVHLREDR    50
    RHITDRDVRI LRQTLDTRMN LEMAVTEEML AIAVETKPHF CCLVPEKRQE 100
    VTTEGGLDVA GQRDKMRDAC KRLADAGIQV SLFIDADEEQ IKAAAEVGAP 150
    FIEIHTGCYA DAKTDAEQAQ ELARIAKAAT FAASLGLKVN AGHGLTYHNV 200
    KAIAAIPEMH ELNIGHAIIG RAVMTGLKDA VAEMKRLMLE ARG 243
    Length:243
    Mass (Da):26,384
    Last modified:January 23, 2007 - v2
    Checksum:iBF513A5B844E8CB2
    GO

    Sequence cautioni

    The sequence D64044 differs from that shown. Reason: Frameshift at several positions.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti194 – 1941G → S in pdxH null mutation suppressor. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M76470 Genomic DNA. Translation: AAA21845.1.
    M74526 Genomic DNA. Translation: AAA24315.1.
    D64044 Genomic DNA. No translation available.
    U36841 Genomic DNA. Translation: AAA79826.1.
    U00096 Genomic DNA. Translation: AAC75617.1.
    AP009048 Genomic DNA. Translation: BAE76740.1.
    PIRiA42293.
    RefSeqiNP_417059.1. NC_000913.3.
    YP_490792.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75617; AAC75617; b2564.
    BAE76740; BAE76740; BAE76740.
    GeneIDi12931607.
    947039.
    KEGGiecj:Y75_p2517.
    eco:b2564.
    PATRICi32120527. VBIEscCol129921_2666.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M76470 Genomic DNA. Translation: AAA21845.1 .
    M74526 Genomic DNA. Translation: AAA24315.1 .
    D64044 Genomic DNA. No translation available.
    U36841 Genomic DNA. Translation: AAA79826.1 .
    U00096 Genomic DNA. Translation: AAC75617.1 .
    AP009048 Genomic DNA. Translation: BAE76740.1 .
    PIRi A42293.
    RefSeqi NP_417059.1. NC_000913.3.
    YP_490792.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1HO1 X-ray 2.00 A/B/C/D 2-243 [» ]
    1HO4 X-ray 2.30 A/B/C/D 2-243 [» ]
    1IXN X-ray 2.30 A/B/C/D 2-243 [» ]
    1IXO X-ray 2.30 A/B/C/D 2-243 [» ]
    1IXP X-ray 2.30 A/B/C/D 2-243 [» ]
    1IXQ X-ray 2.30 A/B/C/D 2-243 [» ]
    1M5W X-ray 1.96 A/B/C/D/E/F/G/H 1-243 [» ]
    ProteinModelPortali P0A794.
    SMRi P0A794. Positions 2-243.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-36215N.
    IntActi P0A794. 5 interactions.
    MINTi MINT-1227457.
    STRINGi 511145.b2564.

    Proteomic databases

    PaxDbi P0A794.
    PRIDEi P0A794.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75617 ; AAC75617 ; b2564 .
    BAE76740 ; BAE76740 ; BAE76740 .
    GeneIDi 12931607.
    947039.
    KEGGi ecj:Y75_p2517.
    eco:b2564.
    PATRICi 32120527. VBIEscCol129921_2666.

    Organism-specific databases

    EchoBASEi EB0687.
    EcoGenei EG10693. pdxJ.

    Phylogenomic databases

    eggNOGi COG0854.
    HOGENOMi HOG000258095.
    KOi K03474.
    OMAi VPETRQE.
    OrthoDBi EOG6M9F0H.
    PhylomeDBi P0A794.

    Enzyme and pathway databases

    UniPathwayi UPA00244 ; UER00313 .
    BioCyci EcoCyc:PDXJ-MONOMER.
    ECOL316407:JW2548-MONOMER.
    MetaCyc:PDXJ-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0A794.
    PROi P0A794.

    Gene expression databases

    Genevestigatori P0A794.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_00279. PdxJ.
    InterProi IPR013785. Aldolase_TIM.
    IPR004569. PyrdxlP_synth_PdxJ.
    [Graphical view ]
    Pfami PF03740. PdxJ. 1 hit.
    [Graphical view ]
    SUPFAMi SSF63892. SSF63892. 1 hit.
    TIGRFAMsi TIGR00559. pdxJ. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon."
      Takiff H.E., Baker T., Copeland T., Chen S.-M., Court D.L.
      J. Bacteriol. 174:1544-1553(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: K12.
    2. "Suppression of insertions in the complex pdxJ operon of Escherichia coli K-12 by lon and other mutations."
      Lam H.-M., Tancula E., Dempsey W.B., Winkler M.E.
      J. Bacteriol. 174:1554-1567(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. Nashimoto H., Saito N.
      Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "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.
    6. "Isolation of a pdxJ point mutation that bypasses the requirement for the PdxH oxidase in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12."
      Man T.K., Zhao G., Winkler M.E.
      J. Bacteriol. 178:2445-2449(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT SER-194.
    7. "Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein."
      Laber B., Maurer W., Scharf S., Stepusin K., Schmidt F.S.
      FEBS Lett. 449:45-48(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
      Strain: K12 / ATCC 35607 / JM83.
    8. "Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme."
      Garrido Franco M., Huber R., Schmidt F.S., Laber B., Clausen T.
      Acta Crystallogr. D 56:1045-1048(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION.
    9. "Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and beyond."
      Garrido-Franco M.
      Biochim. Biophys. Acta 1647:92-97(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    10. "Structural basis for the function of pyridoxine 5'-phosphate synthase."
      Garrido Franco M., Laber B., Huber R., Clausen T.
      Structure 9:245-253(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH PRODUCT, SUBUNIT.
    11. "Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate."
      Yeh J.I., Du S., Pohl E., Cane D.E.
      Biochemistry 41:11649-11657(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF APOENZYME AND COMPLEX WITH SUBSTRATE, SUBUNIT.
    12. "Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis."
      Garrido-Franco M., Laber B., Huber R., Clausen T.
      J. Mol. Biol. 321:601-612(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE AND SUBSTRATE ANALOG, REACTION MECHANISM.

    Entry informationi

    Entry nameiPDXJ_ECOLI
    AccessioniPrimary (citable) accession number: P0A794
    Secondary accession number(s): P24223, Q2MAG6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    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

    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