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P50620

- RIR1_BACSU

UniProt

P50620 - RIR1_BACSU

Protein

Ribonucleoside-diphosphate reductase subunit alpha

Gene

nrdE

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides By similarity.By similarity

    Catalytic activityi

    2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

    Enzyme regulationi

    Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction By similarity.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei153 – 1531SubstrateBy similarity
    Sitei170 – 1701Important for hydrogen atom transferBy similarity
    Sitei177 – 1771Allosteric effector bindingBy similarity
    Binding sitei198 – 1981Substrate; via amide nitrogenBy similarity
    Sitei207 – 2071Allosteric effector bindingBy similarity
    Active sitei380 – 3801Proton acceptorBy similarity
    Active sitei382 – 3821Cysteine radical intermediateBy similarity
    Active sitei384 – 3841Proton acceptorBy similarity
    Sitei409 – 4091Important for hydrogen atom transferBy similarity
    Sitei683 – 6831Important for electron transferBy similarity
    Sitei684 – 6841Important for electron transferBy similarity
    Sitei695 – 6951Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei698 – 6981Interacts with thioredoxin/glutaredoxinBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

    GO - Biological processi

    1. DNA replication Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciBSUB:BSU17380-MONOMER.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase subunit alpha (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase large subunit
    Gene namesi
    Name:nrdE
    Synonyms:nrdA
    Ordered Locus Names:BSU17380
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU17380. [Micado]

    Subcellular locationi

    GO - Cellular componenti

    1. ribonucleoside-diphosphate reductase complex Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 700700Ribonucleoside-diphosphate reductase subunit alphaPRO_0000187209Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi170 ↔ 409Redox-activeBy similarity

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiP50620.
    PRIDEiP50620.

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta subunits.By similarity

    Protein-protein interaction databases

    STRINGi224308.BSU17380.

    Structurei

    3D structure databases

    ProteinModelPortaliP50620.
    SMRiP50620. Positions 2-690.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni169 – 1702Substrate bindingBy similarity
    Regioni380 – 3845Substrate bindingBy similarity
    Regioni580 – 5845Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0209.
    HOGENOMiHOG000246165.
    KOiK00525.
    OMAiIYYIRIR.
    OrthoDBiEOG6J48HC.
    PhylomeDBiP50620.

    Family and domain databases

    InterProiIPR013346. NrdE_NrdA.
    IPR026459. RNR_1b_NrdE.
    IPR000788. RNR_lg_C.
    IPR013509. RNR_lsu_N.
    IPR013554. RNR_N.
    IPR008926. RNR_R1-su_N.
    [Graphical view]
    PfamiPF02867. Ribonuc_red_lgC. 1 hit.
    PF00317. Ribonuc_red_lgN. 1 hit.
    PF08343. RNR_N. 1 hit.
    [Graphical view]
    PRINTSiPR01183. RIBORDTASEM1.
    SUPFAMiSSF48168. SSF48168. 1 hit.
    TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
    TIGR04170. RNR_1b_NrdE. 1 hit.
    PROSITEiPS00089. RIBORED_LARGE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P50620-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSQNQVPKWI QLNNEIMIQK DGKFQFDKDK EAVHSYFVDY INQNTVFFHN    50
    LKEKLDYLVE NQYYEEEFLS LYSFEDIKEV FKTAYAKKFR FPSFMSAFKF 100
    YNDYALKTND KKKILERYED RISIVALFFA NGDTEKAKEY VNLMINQEYQ 150
    PSTPTFLNAG RKRRGELVSC FLLEVNDSLN DISRAIDISM QLSKLGGGVS 200
    LNLSKLRAKG EAIKDVENAT KGVVGVMKLL DNAFRYADQM GQRQGSGAAY 250
    LNIFHRDIND FLDTKKISAD EDVRVKTLSI GVVIPDKFVE LAREDKAAYV 300
    FYPHTIYKEY GQHMDEMDMN EMYDKFVDNP RVKKEKINPR KLLEKLAMLR 350
    SESGYPYIMF QDNVNKVHAN NHISKVKFSN LCSEVLQASQ VSSYTDYDEE 400
    DEIGLDISCN LGSLNILNVM EHKSIEKTVK LATDSLTHVS ETTDIRNAPA 450
    VRRANKAMKS IGLGAMNLHG YLAQNGIAYE SPEARDFANT FFMMVNFYSI 500
    QRSAEIAKEK GETFDQYEGS TYATGEYFDK YVSTDFSPKY EKIANLFEGM 550
    HIPTTEDWKK LKAFVAEHGM YHSYRLCIAP TGSISYVQSS TASVMPIMER 600
    IEERTYGNSK TYYPMPGLAS NNWFFYKEAY DMDMFKVVDM IATIQQHIDQ 650
    GISFTLFLKD TMTTRDLNRI DLYAHHRGIK TIYYARTKDT GQDSCLSCVV 700
    Length:700
    Mass (Da):80,689
    Last modified:October 1, 1996 - v1
    Checksum:iD2D4B914B97BBFA6
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z68500 Genomic DNA. Translation: CAA92810.1.
    AL009126 Genomic DNA. Translation: CAB13622.1.
    PIRiB69667.
    RefSeqiNP_389620.1. NC_000964.3.

    Genome annotation databases

    EnsemblBacteriaiCAB13622; CAB13622; BSU17380.
    GeneIDi940091.
    KEGGibsu:BSU17380.
    PATRICi18975287. VBIBacSub10457_1835.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z68500 Genomic DNA. Translation: CAA92810.1 .
    AL009126 Genomic DNA. Translation: CAB13622.1 .
    PIRi B69667.
    RefSeqi NP_389620.1. NC_000964.3.

    3D structure databases

    ProteinModelPortali P50620.
    SMRi P50620. Positions 2-690.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU17380.

    Proteomic databases

    PaxDbi P50620.
    PRIDEi P50620.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB13622 ; CAB13622 ; BSU17380 .
    GeneIDi 940091.
    KEGGi bsu:BSU17380.
    PATRICi 18975287. VBIBacSub10457_1835.

    Organism-specific databases

    GenoListi BSU17380. [Micado ]

    Phylogenomic databases

    eggNOGi COG0209.
    HOGENOMi HOG000246165.
    KOi K00525.
    OMAi IYYIRIR.
    OrthoDBi EOG6J48HC.
    PhylomeDBi P50620.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci BSUB:BSU17380-MONOMER.

    Family and domain databases

    InterProi IPR013346. NrdE_NrdA.
    IPR026459. RNR_1b_NrdE.
    IPR000788. RNR_lg_C.
    IPR013509. RNR_lsu_N.
    IPR013554. RNR_N.
    IPR008926. RNR_R1-su_N.
    [Graphical view ]
    Pfami PF02867. Ribonuc_red_lgC. 1 hit.
    PF00317. Ribonuc_red_lgN. 1 hit.
    PF08343. RNR_N. 1 hit.
    [Graphical view ]
    PRINTSi PR01183. RIBORDTASEM1.
    SUPFAMi SSF48168. SSF48168. 1 hit.
    TIGRFAMsi TIGR02506. NrdE_NrdA. 1 hit.
    TIGR04170. RNR_1b_NrdE. 1 hit.
    PROSITEi PS00089. RIBORED_LARGE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The Bacillus subtilis genes for ribonucleotide reductase are similar to the genes for the second class I NrdE/NrdF enzymes of Enterobacteriaceae."
      Scotti C., Valbuzzi A., Perego M., Galizzi A., Albertini A.M.
      Microbiology 142:2995-3004(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.

    Entry informationi

    Entry nameiRIR1_BACSU
    AccessioniPrimary (citable) accession number: P50620
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 104 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

    Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3