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Q9SJ20

- RIR1_ARATH

UniProt

Q9SJ20 - RIR1_ARATH

Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

RNR1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 106 (01 Oct 2014)
      Sequence version 1 (01 May 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. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide.1 Publication

    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 large 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 sitei5 – 51Allosteric activatorBy similarity
    Binding sitei53 – 531Allosteric activatorBy similarity
    Binding sitei88 – 881Allosteric activatorBy similarity
    Binding sitei202 – 2021SubstrateBy similarity
    Sitei218 – 2181Important for hydrogen atom transferBy similarity
    Sitei226 – 2261Allosteric effector binding, determines substrate specificityBy similarity
    Binding sitei247 – 2471Substrate; via amide nitrogenBy similarity
    Sitei256 – 2561Allosteric effector binding, determines substrate specificityBy similarity
    Active sitei427 – 4271Proton acceptorBy similarity
    Active sitei429 – 4291Cysteine radical intermediateBy similarity
    Active sitei431 – 4311Proton acceptorBy similarity
    Sitei444 – 4441Important for hydrogen atom transferBy similarity
    Sitei756 – 7561Important for electron transferBy similarity
    Sitei757 – 7571Important for electron transferBy similarity
    Sitei811 – 8111Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei814 – 8141Interacts with thioredoxin/glutaredoxinBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. deoxyribonucleoside triphosphate biosynthetic process Source: TAIR
    2. deoxyribonucleotide biosynthetic process Source: UniProtKB
    3. DNA replication Source: TAIR
    4. response to cadmium ion Source: TAIR

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciARA:AT2G21790-MONOMER.
    MetaCyc:AT2G21790-MONOMER.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase large subunit (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleoside-diphosphate reductase R1 subunit
    Short name:
    AtRNR1
    Gene namesi
    Name:RNR1
    Ordered Locus Names:At2g21790
    ORF Names:F7D8.11
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 2

    Organism-specific databases

    TAIRiAT2G21790.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. ribonucleoside-diphosphate reductase complex Source: InterPro

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 816816Ribonucleoside-diphosphate reductase large subunitPRO_0000187195Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi218 ↔ 444Redox-activeBy similarity

    Post-translational modificationi

    Contains a disulfide bonds Probable. Binding of the substrate occurs primarily when the active-site cysteines are reduced.Curated

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiQ9SJ20.
    PRIDEiQ9SJ20.

    Expressioni

    Inductioni

    Basal expression regulated by ATR/RAD3. Can be induced by another pathway when dNTPs levels are low.1 Publication

    Gene expression databases

    ArrayExpressiQ9SJ20.
    GenevestigatoriQ9SJ20.

    Interactioni

    Subunit structurei

    Heterotetramer of two large/R1 and two small/R2 subunits. A radical transfer pathway may occur between 'Tyr-125' of protein R2 and R1.1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliQ9SJ20.
    SMRiQ9SJ20. Positions 1-762.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 9292ATP-conePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni11 – 177Allosteric activator bindingBy similarity
    Regioni217 – 2182Substrate bindingBy similarity
    Regioni285 – 2884Allosteric effector binding, determines substrate specificityBy similarity
    Regioni427 – 4315Substrate bindingBy similarity
    Regioni622 – 6265Substrate bindingBy similarity

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0209.
    HOGENOMiHOG000057035.
    InParanoidiQ9SJ20.
    KOiK10807.
    OMAiLLWQMPS.
    PhylomeDBiQ9SJ20.

    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.

    Q9SJ20-1 [UniParc]FASTAAdd to Basket

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    MYVVKRDGRQ ETVHFDKITA RLKKLSYGLS SDHCDPVLVA QKVCAGVYKG    50
    VTTSQLDELA AETAAAMTCN HPDYASLAAR IAVSNLHKNT KKSFSETIKD 100
    MFYHVNDRSG LKSPLIADDV FEIIMQNAAR LDSEIIYDRD FEYDYFGFKT 150
    LERSYLLKVQ GTVVERPQHM LMRVAVGIHK DDIDSVIQTY HLMSQRWFTH 200
    ASPTLFNAGT PRPQLSSCFL VCMKDDSIEG IYETLKECAV ISKSAGGIGV 250
    SVHNIRATGS YIRGTNGTSN GIVPMLRVFN DTARYVDQGG GKRKGAFAVY 300
    LEPWHADVYE FLELRKNHGK EEHRARDLFY ALWLPDLFME RVQNNGQWSL 350
    FCPNEAPGLA DCWGAEFETL YTKYEREGKA KKVVQAQQLW YEILTSQVET 400
    GTPYMLFKDS CNRKSNQQNL GTIKSSNLCT EIIEYTSPTE TAVCNLASIA 450
    LPRFVREKGV PLDSHPPKLA GSLDSKNRYF DFEKLAEVTA TVTVNLNKII 500
    DVNYYPVETA KTSNMRHRPI GIGVQGLADA FILLGMPFDS PEAQQLNKDI 550
    FETIYYHALK ASTELAARLG PYETYAGSPV SKGILQPDMW NVIPSDRWDW 600
    AVLRDMISKN GVRNSLLVAP MPTASTSQIL GNNECFEPYT SNIYSRRVLS 650
    GEFVVVNKHL LHDLTDMGLW TPTLKNKLIN ENGSIVNVAE IPDDLKAIYR 700
    TVWEIKQRTV VDMAADRGCY IDQSQSLNIH MDKPNFAKLT SLHFYTWKKG 750
    LKTGMYYLRS RAAADAIKFT VDTAMLKEKP SVAEGDKEVE EEDNETKLAQ 800
    MVCSLTNPEE CLACGS 816
    Length:816
    Mass (Da):91,816
    Last modified:May 1, 2000 - v1
    Checksum:iA6769E2F210488EA
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti37 – 371V → I in AAC61773. (PubMed:10542051)Curated
    Sequence conflicti233 – 2331E → G in AAC61773. (PubMed:10542051)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF092841 mRNA. Translation: AAC61773.1.
    AC007019 Genomic DNA. Translation: AAD20398.1.
    CP002685 Genomic DNA. Translation: AEC07222.1.
    AY035080 mRNA. Translation: AAK59585.1.
    BT008573 mRNA. Translation: AAP40400.1.
    PIRiB84605.
    T51813.
    RefSeqiNP_179770.1. NM_127748.3.
    UniGeneiAt.115.

    Genome annotation databases

    EnsemblPlantsiAT2G21790.1; AT2G21790.1; AT2G21790.
    GeneIDi816715.
    KEGGiath:AT2G21790.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF092841 mRNA. Translation: AAC61773.1 .
    AC007019 Genomic DNA. Translation: AAD20398.1 .
    CP002685 Genomic DNA. Translation: AEC07222.1 .
    AY035080 mRNA. Translation: AAK59585.1 .
    BT008573 mRNA. Translation: AAP40400.1 .
    PIRi B84605.
    T51813.
    RefSeqi NP_179770.1. NM_127748.3.
    UniGenei At.115.

    3D structure databases

    ProteinModelPortali Q9SJ20.
    SMRi Q9SJ20. Positions 1-762.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PaxDbi Q9SJ20.
    PRIDEi Q9SJ20.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT2G21790.1 ; AT2G21790.1 ; AT2G21790 .
    GeneIDi 816715.
    KEGGi ath:AT2G21790.

    Organism-specific databases

    GeneFarmi 2079.
    TAIRi AT2G21790.

    Phylogenomic databases

    eggNOGi COG0209.
    HOGENOMi HOG000057035.
    InParanoidi Q9SJ20.
    KOi K10807.
    OMAi LLWQMPS.
    PhylomeDBi Q9SJ20.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci ARA:AT2G21790-MONOMER.
    MetaCyc:AT2G21790-MONOMER.

    Miscellaneous databases

    PROi Q9SJ20.

    Gene expression databases

    ArrayExpressi Q9SJ20.
    Genevestigatori Q9SJ20.

    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. "An active ribonucleotide reductase from Arabidopsis thaliana cloning, expression and characterization of the large subunit."
      Sauge-Merle S., Falconet D., Fontecave M.
      Eur. J. Biochem. 266:62-69(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE, FUNCTION, SUBUNIT, ENZYME REGULATION.
      Tissue: Callus.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "ATR regulates a G2-phase cell-cycle checkpoint in Arabidopsis thaliana."
      Culligan K., Tissier A., Britt A.
      Plant Cell 16:1091-1104(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.

    Entry informationi

    Entry nameiRIR1_ARATH
    AccessioniPrimary (citable) accession number: Q9SJ20
    Secondary accession number(s): O82573
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 21, 2004
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 106 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Two distinct regulatory sites have been defined: one controls substrate specificity and the other regulates the overall catalytic activity. A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2.

    Keywords - Technical termi

    Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: 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