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P25539

- RIBD_ECOLI

UniProt

P25539 - RIBD_ECOLI

Protein

Riboflavin biosynthesis protein RibD

Gene

ribD

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 134 (01 Oct 2014)
      Sequence version 1 (01 May 1992)
      Previous versions | rss
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    Functioni

    Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.

    Catalytic activityi

    2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H2O = 5-amino-6-(5-phosphoribosylamino)uracil + NH3.
    5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP+ = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH.

    Cofactori

    Binds 1 zinc ion.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi50 – 501Zinc; catalyticBy similarity
    Active sitei52 – 521Proton donorBy similarity
    Metal bindingi75 – 751Zinc; catalyticBy similarity
    Metal bindingi84 – 841Zinc; catalyticBy similarity
    Binding sitei168 – 1681Substrate
    Binding sitei170 – 1701NADP
    Binding sitei184 – 1841Substrate
    Binding sitei196 – 1961NADP
    Binding sitei200 – 2001NADP
    Binding sitei204 – 2041Substrate; via amide nitrogen
    Binding sitei207 – 2071Substrate
    Binding sitei234 – 2341NADP
    Binding sitei299 – 2991Substrate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi161 – 1644NADP
    Nucleotide bindingi301 – 3044NADP

    GO - Molecular functioni

    1. 5-amino-6-(5-phosphoribosylamino)uracil reductase activity Source: EcoCyc
    2. diaminohydroxyphosphoribosylaminopyrimidine deaminase activity Source: EcoCyc
    3. NADP binding Source: EcoCyc
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. riboflavin biosynthetic process Source: EcoCyc

    Keywords - Molecular functioni

    Hydrolase, Oxidoreductase

    Keywords - Biological processi

    Riboflavin biosynthesis

    Keywords - Ligandi

    Metal-binding, NADP, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:RIBOFLAVINSYNDEAM-MONOMER.
    ECOL316407:JW0404-MONOMER.
    MetaCyc:RIBOFLAVINSYNDEAM-MONOMER.
    UniPathwayiUPA00275; UER00401.
    UPA00275; UER00402.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Riboflavin biosynthesis protein RibD
    Including the following 2 domains:
    Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC:3.5.4.26)
    Short name:
    DRAP deaminase
    Alternative name(s):
    Riboflavin-specific deaminase
    5-amino-6-(5-phosphoribosylamino)uracil reductase (EC:1.1.1.193)
    Alternative name(s):
    HTP reductase
    Gene namesi
    Name:ribD
    Synonyms:ribG, ybaE
    Ordered Locus Names:b0414, JW0404
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11321. ribD.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 367367Riboflavin biosynthesis protein RibDPRO_0000171721Add
    BLAST

    Proteomic databases

    PaxDbiP25539.
    PRIDEiP25539.

    Expressioni

    Gene expression databases

    GenevestigatoriP25539.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-10708N.
    IntActiP25539. 34 interactions.
    MINTiMINT-1221612.
    STRINGi511145.b0414.

    Structurei

    Secondary structure

    1
    367
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi2 – 1413
    Helixi15 – 173
    Turni18 – 203
    Beta strandi28 – 336
    Beta strandi36 – 427
    Beta strandi46 – 483
    Helixi51 – 599
    Helixi60 – 634
    Beta strandi64 – 663
    Beta strandi68 – 725
    Helixi85 – 917
    Beta strandi96 – 1005
    Helixi111 – 1177
    Beta strandi122 – 1243
    Helixi128 – 1347
    Helixi136 – 1438
    Beta strandi144 – 1463
    Beta strandi148 – 1569
    Helixi174 – 18512
    Beta strandi187 – 1937
    Helixi194 – 2007
    Helixi208 – 2103
    Helixi214 – 2174
    Helixi221 – 2233
    Beta strandi228 – 2325
    Helixi243 – 2453
    Beta strandi247 – 2493
    Beta strandi251 – 2577
    Beta strandi267 – 2715
    Helixi281 – 29010
    Beta strandi295 – 2984
    Helixi302 – 31110
    Beta strandi315 – 3239
    Beta strandi349 – 3568
    Beta strandi359 – 3657

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2G6VX-ray2.60A/B2-367[»]
    2O7PX-ray3.00A/B2-367[»]
    2OBCX-ray3.00A/B2-367[»]
    ProteinModelPortaliP25539.
    SMRiP25539. Positions 2-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP25539.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 145145DeaminaseAdd
    BLAST
    Regioni146 – 367222ReductaseAdd
    BLAST

    Sequence similaritiesi

    In the N-terminal section; belongs to the cytidine and deoxycytidylate deaminase family.Curated
    In the C-terminal section; belongs to the HTP reductase family.Curated

    Phylogenomic databases

    eggNOGiCOG0117.
    HOGENOMiHOG000257442.
    KOiK11752.
    OMAiQINSVWV.
    OrthoDBiEOG66F07R.
    PhylomeDBiP25539.

    Family and domain databases

    Gene3Di3.40.430.10. 1 hit.
    InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
    IPR002125. CMP_dCMP_Zn-bd.
    IPR016193. Cytidine_deaminase-like.
    IPR024072. DHFR-like_dom.
    IPR004794. Eubact_RibD.
    IPR011549. RibD_C.
    IPR002734. RibDG_C.
    [Graphical view]
    PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
    PF01872. RibD_C. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006769. RibD. 1 hit.
    SUPFAMiSSF53597. SSF53597. 1 hit.
    SSF53927. SSF53927. 1 hit.
    TIGRFAMsiTIGR00326. eubact_ribD. 1 hit.
    TIGR00227. ribD_Cterm. 1 hit.
    PROSITEiPS00903. CYT_DCMP_DEAMINASES. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P25539-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQDEYYMARA LKLAQRGRFT THPNPNVGCV IVKDGEIVGE GYHQRAGEPH    50
    AEVHALRMAG EKAKGATAYV TLEPCSHHGR TPPCCDALIA AGVARVVASM 100
    QDPNPQVAGR GLYRLQQAGI DVSHGLMMSE AEQLNKGFLK RMRTGFPYIQ 150
    LKLGASLDGR TAMASGESQW ITSPQARRDV QLLRAQSHAI LTSSATVLAD 200
    DPALTVRWSE LDEQTQALYP QQNLRQPIRI VIDSQNRVTP VHRIVQQPGE 250
    TWFARTQEDS REWPETVRTL LIPEHKGHLD LVVLMMQLGK QQINSIWVEA 300
    GPTLAGALLQ AGLVDELIVY IAPKLLGSDA RGLCTLPGLE KLADAPQFKF 350
    KEIRHVGPDV CLHLVGA 367
    Length:367
    Mass (Da):40,338
    Last modified:May 1, 1992 - v1
    Checksum:iB19CEF474D48D14D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X64395 Genomic DNA. Translation: CAA45735.1.
    U82664 Genomic DNA. Translation: AAB40170.1.
    U00096 Genomic DNA. Translation: AAC73517.1.
    AP009048 Genomic DNA. Translation: BAE76194.1.
    PIRiS26201.
    RefSeqiNP_414948.1. NC_000913.3.
    YP_488706.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73517; AAC73517; b0414.
    BAE76194; BAE76194; BAE76194.
    GeneIDi12934255.
    945620.
    KEGGiecj:Y75_p0402.
    eco:b0414.
    PATRICi32115977. VBIEscCol129921_0430.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X64395 Genomic DNA. Translation: CAA45735.1 .
    U82664 Genomic DNA. Translation: AAB40170.1 .
    U00096 Genomic DNA. Translation: AAC73517.1 .
    AP009048 Genomic DNA. Translation: BAE76194.1 .
    PIRi S26201.
    RefSeqi NP_414948.1. NC_000913.3.
    YP_488706.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2G6V X-ray 2.60 A/B 2-367 [» ]
    2O7P X-ray 3.00 A/B 2-367 [» ]
    2OBC X-ray 3.00 A/B 2-367 [» ]
    ProteinModelPortali P25539.
    SMRi P25539. Positions 2-367.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10708N.
    IntActi P25539. 34 interactions.
    MINTi MINT-1221612.
    STRINGi 511145.b0414.

    Proteomic databases

    PaxDbi P25539.
    PRIDEi P25539.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73517 ; AAC73517 ; b0414 .
    BAE76194 ; BAE76194 ; BAE76194 .
    GeneIDi 12934255.
    945620.
    KEGGi ecj:Y75_p0402.
    eco:b0414.
    PATRICi 32115977. VBIEscCol129921_0430.

    Organism-specific databases

    EchoBASEi EB1297.
    EcoGenei EG11321. ribD.

    Phylogenomic databases

    eggNOGi COG0117.
    HOGENOMi HOG000257442.
    KOi K11752.
    OMAi QINSVWV.
    OrthoDBi EOG66F07R.
    PhylomeDBi P25539.

    Enzyme and pathway databases

    UniPathwayi UPA00275 ; UER00401 .
    UPA00275 ; UER00402 .
    BioCyci EcoCyc:RIBOFLAVINSYNDEAM-MONOMER.
    ECOL316407:JW0404-MONOMER.
    MetaCyc:RIBOFLAVINSYNDEAM-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P25539.
    PROi P25539.

    Gene expression databases

    Genevestigatori P25539.

    Family and domain databases

    Gene3Di 3.40.430.10. 1 hit.
    InterProi IPR016192. APOBEC/CMP_deaminase_Zn-bd.
    IPR002125. CMP_dCMP_Zn-bd.
    IPR016193. Cytidine_deaminase-like.
    IPR024072. DHFR-like_dom.
    IPR004794. Eubact_RibD.
    IPR011549. RibD_C.
    IPR002734. RibDG_C.
    [Graphical view ]
    Pfami PF00383. dCMP_cyt_deam_1. 1 hit.
    PF01872. RibD_C. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF006769. RibD. 1 hit.
    SUPFAMi SSF53597. SSF53597. 1 hit.
    SSF53927. SSF53927. 1 hit.
    TIGRFAMsi TIGR00326. eubact_ribD. 1 hit.
    TIGR00227. ribD_Cterm. 1 hit.
    PROSITEi PS00903. CYT_DCMP_DEAMINASES. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Insertional disruption of the nusB (ssyB) gene leads to cold-sensitive growth of Escherichia coli and suppression of the secY24 mutation."
      Taura T., Ueguchi C., Shiba K., Ito K.
      Mol. Gen. Genet. 234:429-432(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Sequence of minutes 4-25 of Escherichia coli."
      Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
      Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    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 riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis."
      Richter G., Fischer M., Krieger C., Eberhardt S., Luttgen H., Gerstenschlager I., Bacher A.
      J. Bacteriol. 179:2022-2028(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    6. "The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism."
      Stenmark P., Moche M., Gurmu D., Nordlund P.
      J. Mol. Biol. 373:48-64(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEXES WITH RIBOSE-5-PHOSPHATE AND NADP, SUBUNIT.

    Entry informationi

    Entry nameiRIBD_ECOLI
    AccessioniPrimary (citable) accession number: P25539
    Secondary accession number(s): Q2MC12
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: May 1, 1992
    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 programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Multifunctional enzyme, 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