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P08203

- ARAD_ECOLI

UniProt

P08203 - ARAD_ECOLI

Protein

L-ribulose-5-phosphate 4-epimerase

Gene

araD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 134 (01 Oct 2014)
      Sequence version 2 (01 Aug 1991)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    L-ribulose 5-phosphate = D-xylulose 5-phosphate.UniRule annotation

    Cofactori

    Binds 1 zinc ion per subunit.1 PublicationUniRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi95 – 951Zinc
    Metal bindingi97 – 971Zinc
    Metal bindingi171 – 1711Zinc

    GO - Molecular functioni

    1. L-ribulose-phosphate 4-epimerase activity Source: EcoCyc
    2. zinc ion binding Source: InterPro

    GO - Biological processi

    1. L-arabinose catabolic process to xylulose 5-phosphate Source: EcoCyc
    2. L-lyxose metabolic process Source: EcoCyc

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Arabinose catabolism, Carbohydrate metabolism

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:RIBULPEPIM-MONOMER.
    ECOL316407:JW0060-MONOMER.
    MetaCyc:RIBULPEPIM-MONOMER.
    SABIO-RKP08203.
    UniPathwayiUPA00145; UER00567.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    L-ribulose-5-phosphate 4-epimeraseUniRule annotation (EC:5.1.3.4UniRule annotation)
    Alternative name(s):
    Phosphoribulose isomeraseUniRule annotation
    Gene namesi
    Name:araDUniRule annotation
    Ordered Locus Names:b0061, JW0060
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10055. araD.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 231231L-ribulose-5-phosphate 4-epimerasePRO_0000162919Add
    BLAST

    Expressioni

    Gene expression databases

    GenevestigatoriP08203.

    Interactioni

    Subunit structurei

    Homotetramer.2 PublicationsUniRule annotation

    Protein-protein interaction databases

    DIPiDIP-9126N.
    IntActiP08203. 4 interactions.
    STRINGi511145.b0061.

    Structurei

    Secondary structure

    1
    231
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1816
    Beta strandi28 – 336
    Turni34 – 374
    Beta strandi38 – 414
    Beta strandi43 – 453
    Turni48 – 503
    Helixi53 – 553
    Beta strandi57 – 604
    Turni61 – 633
    Beta strandi66 – 683
    Helixi77 – 8610
    Beta strandi92 – 954
    Helixi99 – 1079
    Helixi116 – 1194
    Helixi134 – 1385
    Helixi141 – 15515
    Turni160 – 1623
    Beta strandi165 – 1684
    Turni169 – 1713
    Beta strandi172 – 1798
    Helixi180 – 20324
    Helixi212 – 22110

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JDIX-ray2.40A/B/C/D/E/F1-231[»]
    1K0WX-ray2.10A/B/C/D/E/F1-231[»]
    ProteinModelPortaliP08203.
    SMRiP08203. Positions 1-223.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP08203.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the aldolase class II family. AraD/FucA subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0235.
    HOGENOMiHOG000218183.
    KOiK01786.
    OMAiLALPQHN.
    OrthoDBiEOG6358F1.
    PhylomeDBiP08203.

    Family and domain databases

    Gene3Di3.40.225.10. 1 hit.
    HAMAPiMF_00989. AraD_entero.
    InterProiIPR001303. Aldolase_II/adducin_N.
    IPR004661. AraD.
    [Graphical view]
    PfamiPF00596. Aldolase_II. 1 hit.
    [Graphical view]
    SMARTiSM01007. Aldolase_II. 1 hit.
    [Graphical view]
    SUPFAMiSSF53639. SSF53639. 1 hit.
    TIGRFAMsiTIGR00760. araD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P08203-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLEDLKRQVL EANLALPKHN LVTLTWGNVS AVDRERGVFV IKPSGVDYSV    50
    MTADDMVVVS IETGEVVEGT KKPSSDTPTH RLLYQAFPSI GGIVHTHSRH 100
    ATIWAQAGQS IPATGTTHAD YFYGTIPCTR KMTDAEINGE YEWETGNVIV 150
    ETFEKQGIDA AQMPGVLVHS HGPFAWGKNA EDAVHNAIVL EEVAYMGIFC 200
    RQLAPQLPDM QQTLLDKHYL RKHGAKAYYG Q 231
    Length:231
    Mass (Da):25,519
    Last modified:August 1, 1991 - v2
    Checksum:i1753F75958332163
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti50 – 501V → I.
    Natural varianti70 – 701T → A.
    Natural varianti216 – 2161D → N.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M15263 Genomic DNA. Translation: AAA23464.1.
    M35371 Genomic DNA. No translation available.
    M62646 Genomic DNA. Translation: AAA24405.1.
    U00096 Genomic DNA. Translation: AAC73172.1.
    AP009048 Genomic DNA. Translation: BAB96630.1.
    M37727 Genomic DNA. Translation: AAA23683.1.
    M38283 Genomic DNA. Translation: AAA63763.1.
    X56048 Genomic DNA. Translation: CAA39519.1.
    PIRiE64727. ISECP4.
    RefSeqiNP_414603.1. NC_000913.3.
    YP_488367.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73172; AAC73172; b0061.
    BAB96630; BAB96630; BAB96630.
    GeneIDi12934049.
    945294.
    KEGGiecj:Y75_p0061.
    eco:b0061.
    PATRICi32115223. VBIEscCol129921_0063.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M15263 Genomic DNA. Translation: AAA23464.1 .
    M35371 Genomic DNA. No translation available.
    M62646 Genomic DNA. Translation: AAA24405.1 .
    U00096 Genomic DNA. Translation: AAC73172.1 .
    AP009048 Genomic DNA. Translation: BAB96630.1 .
    M37727 Genomic DNA. Translation: AAA23683.1 .
    M38283 Genomic DNA. Translation: AAA63763.1 .
    X56048 Genomic DNA. Translation: CAA39519.1 .
    PIRi E64727. ISECP4.
    RefSeqi NP_414603.1. NC_000913.3.
    YP_488367.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1JDI X-ray 2.40 A/B/C/D/E/F 1-231 [» ]
    1K0W X-ray 2.10 A/B/C/D/E/F 1-231 [» ]
    ProteinModelPortali P08203.
    SMRi P08203. Positions 1-223.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9126N.
    IntActi P08203. 4 interactions.
    STRINGi 511145.b0061.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73172 ; AAC73172 ; b0061 .
    BAB96630 ; BAB96630 ; BAB96630 .
    GeneIDi 12934049.
    945294.
    KEGGi ecj:Y75_p0061.
    eco:b0061.
    PATRICi 32115223. VBIEscCol129921_0063.

    Organism-specific databases

    EchoBASEi EB0053.
    EcoGenei EG10055. araD.

    Phylogenomic databases

    eggNOGi COG0235.
    HOGENOMi HOG000218183.
    KOi K01786.
    OMAi LALPQHN.
    OrthoDBi EOG6358F1.
    PhylomeDBi P08203.

    Enzyme and pathway databases

    UniPathwayi UPA00145 ; UER00567 .
    BioCyci EcoCyc:RIBULPEPIM-MONOMER.
    ECOL316407:JW0060-MONOMER.
    MetaCyc:RIBULPEPIM-MONOMER.
    SABIO-RK P08203.

    Miscellaneous databases

    EvolutionaryTracei P08203.
    PROi P08203.

    Gene expression databases

    Genevestigatori P08203.

    Family and domain databases

    Gene3Di 3.40.225.10. 1 hit.
    HAMAPi MF_00989. AraD_entero.
    InterProi IPR001303. Aldolase_II/adducin_N.
    IPR004661. AraD.
    [Graphical view ]
    Pfami PF00596. Aldolase_II. 1 hit.
    [Graphical view ]
    SMARTi SM01007. Aldolase_II. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53639. SSF53639. 1 hit.
    TIGRFAMsi TIGR00760. araD. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The organization of the araBAD operon of Escherichia coli."
      Lee N., Gielow W., Martin R., Hamilton E., Fowler A.
      Gene 47:231-244(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: B.
    2. "Nucleotide sequence and deletion analysis of the polB gene of Escherichia coli."
      Chen H., Sun Y., Stark T., Beattie W., Moses R.E.
      DNA Cell Biol. 9:631-635(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. "Nucleotide sequence of the araD gene of Escherichia coli K12 encoding the L-ribulose 5-phosphate 4-epimerase."
      Mineno J., Fukui H., Ishino Y., Kato I., Shinagawa H.
      Nucleic Acids Res. 18:6722-6722(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    4. "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.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    6. "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.
    7. "Purification and preliminary X-ray crystallographic studies of recombinant L-ribulose-5-phosphate 4-epimerase from Escherichia coli."
      Andersson A., Schneider G., Lindqvist Y.
      Protein Sci. 4:1648-1650(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-8, PRELIMINARY CRYSTALLIZATION.
    8. "Escherichia coli DNA polymerase II is homologous to alpha-like DNA polymerases."
      Iwasaki H., Ishino Y., Toh H., Nakata A., Shinagawa H.
      Mol. Gen. Genet. 226:24-33(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 158-231.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    9. "DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli."
      Bonner C.A., Hays S., McEntee K., Goodman M.F.
      Proc. Natl. Acad. Sci. U.S.A. 87:7663-7667(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 222-231.
      Strain: K12.
    10. "Crystalline L-ribulose 5-phosphate 4-epimerase from Escherichia coli."
      Lee N., Patrick J.W., Masson M.
      J. Biol. Chem. 243:4700-4705(1968) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
      Strain: B/R.
    11. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    12. "The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization."
      Luo Y., Samuel J., Mosimann S.C., Lee J.E., Tanner M.E., Strynadka N.C.
      Biochemistry 40:14763-14771(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH ZINC IONS, COFACTOR, SUBUNIT.

    Entry informationi

    Entry nameiARAD_ECOLI
    AccessioniPrimary (citable) accession number: P08203
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: August 1, 1991
    Last modified: October 1, 2014
    This is version 134 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