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P57276

- RIR1_BUCAI

UniProt

P57276 - RIR1_BUCAI

Protein

Ribonucleoside-diphosphate reductase subunit alpha

Gene

nrdA

Organism
Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 93 (01 Oct 2014)
      Sequence version 1 (01 Dec 2000)
      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 to separate specificity and activation sites on the alpha subunit. 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. Stimulated by ATP and inhibited by dATP binding to the activity site By similarity.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei9 – 91Allosteric activatorBy similarity
    Binding sitei55 – 551Allosteric activatorBy similarity
    Binding sitei91 – 911Allosteric activatorBy similarity
    Binding sitei209 – 2091SubstrateBy similarity
    Sitei225 – 2251Important for hydrogen atom transferBy similarity
    Sitei232 – 2321Allosteric effector bindingBy similarity
    Binding sitei253 – 2531Substrate; via amide nitrogenBy similarity
    Sitei262 – 2621Allosteric effector bindingBy similarity
    Active sitei437 – 4371Proton acceptorBy similarity
    Active sitei439 – 4391Cysteine radical intermediateBy similarity
    Active sitei441 – 4411Proton acceptorBy similarity
    Sitei462 – 4621Important for hydrogen atom transferBy similarity
    Sitei730 – 7301Important for electron transferBy similarity
    Sitei731 – 7311Important for electron transferBy similarity
    Sitei754 – 7541Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei759 – 7591Interacts 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

    BioCyciBAPH107806:GBZJ-178-MONOMER.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase subunit alpha (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase
    Gene namesi
    Name:nrdA
    Ordered Locus Names:BU179
    OrganismiBuchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
    Taxonomic identifieri107806 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeBuchnera
    ProteomesiUP000001806: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. ribonucleoside-diphosphate reductase complex Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 761761Ribonucleoside-diphosphate reductase subunit alphaPRO_0000187206Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi225 ↔ 462Redox-activeBy similarity

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta subunits.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliP57276.
    SMRiP57276. Positions 5-737.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini5 – 9591ATP-conePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni15 – 217Allosteric activator bindingBy similarity
    Regioni224 – 2252Substrate bindingBy similarity
    Regioni437 – 4415Substrate bindingBy similarity
    Regioni621 – 6255Substrate bindingBy similarity

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0209.
    HOGENOMiHOG000278076.
    KOiK00525.
    OMAiLLWQMPS.
    OrthoDBiEOG6J48HC.

    Family and domain databases

    InterProiIPR005144. ATP-cone.
    IPR013346. NrdE_NrdA.
    IPR000788. RNR_lg_C.
    IPR013509. RNR_lsu_N.
    IPR008926. RNR_R1-su_N.
    [Graphical view]
    PfamiPF03477. ATP-cone. 1 hit.
    PF02867. Ribonuc_red_lgC. 1 hit.
    PF00317. Ribonuc_red_lgN. 1 hit.
    [Graphical view]
    PRINTSiPR01183. RIBORDTASEM1.
    SUPFAMiSSF48168. SSF48168. 1 hit.
    TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
    PROSITEiPS51161. ATP_CONE. 1 hit.
    PS00089. RIBORED_LARGE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P57276-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKKNLFVTKR DGRKEKINLD KIHKVLNWAS EGLDDVSVSQ VELCSRIQFY    50
    NNITTINIHE TIIKAAADLI SQDTPDYQYM AARLAIFHLR KKAYGQFEPP 100
    KLYDHVKKMV DLEKYDENLL KNYSYKEFLQ MNSFIDHWRD MNFSYAAVKQ 150
    LEGKYLIQNR VNGKIYESAQ FLYILISACL FSQYPKNVRM NYIHRFYNAI 200
    STFKISLPTP IMSGVRTPTR QFSSCVLIEC GDSLNSINAT TSSIVKYVSQ 250
    RAGIGVNAGQ IRALGSPIRN GEAFHTGCIP FYKHFQSAVK SCSQGGVRGG 300
    AATIFYPIWH LEVESLLVLK NNRGIEENRV RHIDYAIQIN KLMYQRMLSG 350
    DQITLFSPSD VPDLYKAFFS DQKKFKKIYL QYEKNKNIRK KTIKALDLFS 400
    LMMQERTSTG RIYVQNVDHC NLHSAFNPEL SPIRQSNLCL EITLPTKSLN 450
    DVHDTDGEIA LCTLSAFNLG KIKSLDDFKE LSILSVRALD EILDYQNYPV 500
    LAAKKSAISR RSLGIGVINF AYYLAKNKVR YSDGSAHNLT HKTFEAMQYY 550
    LLEASCELAK EKGACSLFNH TNYYLGKLPI DTYKKYIDDI CNEPLHLDWN 600
    LLRSKIKKYG LRNSTLSALM PSETSSQISN ATNGIEPPRG FISIKVSKDG 650
    ILRQVVPEYK KLRLQYELLW DIPNNTGYLQ LAGIMQKFID QSISVNTHYD 700
    PARFLNNKIP MKQLLYDLLL SYKLGLKTLY YQNTRDGSED DQNITSKSIT 750
    EDICESGSCI L 761
    Length:761
    Mass (Da):87,166
    Last modified:December 1, 2000 - v1
    Checksum:i700A2A4AA426AC76
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000003 Genomic DNA. Translation: BAB12896.1.
    RefSeqiNP_240010.1. NC_002528.1.

    Genome annotation databases

    EnsemblBacteriaiBAB12896; BAB12896; BAB12896.
    GeneIDi1109622.
    KEGGibuc:BU179.
    PATRICi21243876. VBIBucAph127364_0190.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000003 Genomic DNA. Translation: BAB12896.1 .
    RefSeqi NP_240010.1. NC_002528.1.

    3D structure databases

    ProteinModelPortali P57276.
    SMRi P57276. Positions 5-737.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAB12896 ; BAB12896 ; BAB12896 .
    GeneIDi 1109622.
    KEGGi buc:BU179.
    PATRICi 21243876. VBIBucAph127364_0190.

    Phylogenomic databases

    eggNOGi COG0209.
    HOGENOMi HOG000278076.
    KOi K00525.
    OMAi LLWQMPS.
    OrthoDBi EOG6J48HC.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci BAPH107806:GBZJ-178-MONOMER.

    Family and domain databases

    InterProi IPR005144. ATP-cone.
    IPR013346. NrdE_NrdA.
    IPR000788. RNR_lg_C.
    IPR013509. RNR_lsu_N.
    IPR008926. RNR_R1-su_N.
    [Graphical view ]
    Pfami PF03477. ATP-cone. 1 hit.
    PF02867. Ribonuc_red_lgC. 1 hit.
    PF00317. Ribonuc_red_lgN. 1 hit.
    [Graphical view ]
    PRINTSi PR01183. RIBORDTASEM1.
    SUPFAMi SSF48168. SSF48168. 1 hit.
    TIGRFAMsi TIGR02506. NrdE_NrdA. 1 hit.
    PROSITEi PS51161. ATP_CONE. 1 hit.
    PS00089. RIBORED_LARGE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS."
      Shigenobu S., Watanabe H., Hattori M., Sakaki Y., Ishikawa H.
      Nature 407:81-86(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: APS.

    Entry informationi

    Entry nameiRIR1_BUCAI
    AccessioniPrimary (citable) accession number: P57276
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: December 1, 2000
    Last modified: October 1, 2014
    This is version 93 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. Buchnera aphidicola (subsp. Acyrthosiphon pisum)
      Buchnera aphidicola (subsp. Acyrthosiphon pisum): entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3