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Q54Q71

- RIR1_DICDI

UniProt

Q54Q71 - RIR1_DICDI

Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

rnrA

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 72 (01 Oct 2014)
      Sequence version 1 (24 May 2005)
      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 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 sitei20 – 201Allosteric activatorBy similarity
    Binding sitei71 – 711Allosteric activatorBy similarity
    Binding sitei106 – 1061Allosteric activatorBy similarity
    Binding sitei220 – 2201SubstrateBy similarity
    Sitei236 – 2361Important for hydrogen atom transferBy similarity
    Sitei244 – 2441Allosteric effector binding, determines substrate specificityBy similarity
    Binding sitei265 – 2651Substrate; via amide nitrogenBy similarity
    Sitei274 – 2741Allosteric effector binding, determines substrate specificityBy similarity
    Active sitei446 – 4461Proton acceptorBy similarity
    Active sitei448 – 4481Cysteine radical intermediateBy similarity
    Active sitei450 – 4501Proton acceptorBy similarity
    Sitei463 – 4631Important for hydrogen atom transferBy similarity
    Sitei765 – 7651Important for electron transferBy similarity
    Sitei766 – 7661Important for electron transferBy similarity
    Sitei865 – 8651Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei868 – 8681Interacts with thioredoxin/glutaredoxinBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. deoxyribonucleoside diphosphate metabolic process Source: dictyBase
    2. deoxyribonucleotide biosynthetic process Source: UniProtKB
    3. DNA replication Source: dictyBase

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase large subunit (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase large subunit
    Gene namesi
    Name:rnrA
    ORF Names:DDB_G0284071
    OrganismiDictyostelium discoideum (Slime mold)
    Taxonomic identifieri44689 [NCBI]
    Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
    ProteomesiUP000002195: Chromosome 4, UP000002195: Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0284071. rnrA.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: dictyBase
    2. ribonucleoside-diphosphate reductase complex Source: dictyBase

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 870870Ribonucleoside-diphosphate reductase large subunitPRO_0000328498Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi236 ↔ 463Redox-activeBy similarity

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Subunit structurei

    Heterodimer of a large and a small subunit.By similarity

    Protein-protein interaction databases

    STRINGi44689.DDB_0230075.

    Structurei

    3D structure databases

    ProteinModelPortaliQ54Q71.
    SMRiQ54Q71. Positions 30-812.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini16 – 11095ATP-conePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni26 – 327Allosteric activator bindingBy similarity
    Regioni235 – 2362Substrate bindingBy similarity
    Regioni303 – 3064Allosteric effector binding, determines substrate specificityBy similarity
    Regioni446 – 4505Substrate bindingBy similarity
    Regioni631 – 6355Substrate bindingBy similarity

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi832 – 84413Poly-GlnAdd
    BLAST

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0209.
    KOiK10807.
    OMAiKECAMIS.
    PhylomeDBiQ54Q71.

    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.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q54Q71-1 [UniParc]FASTAAdd to Basket

    « Hide

    MISNSINVTP NKESKMYVVK RDGTKENVSF DKITSRISFL CEMEPKLNSD    50
    IVDPIEVAQK VVSGVFPGVK TTELDNLAAE TAAYMSTRHP DYGILAARIS 100
    VSNLHKQTSK SFVETVKKQY EFINPKSNLL APLVSKELYE IVMKHGERLE 150
    SVIDYYRDFD YDFFGFKTLE RSYLHRINGK IVERPQHMLM RVSIGIHGED 200
    LESAINTYKR LSEKLFTHAT PTLFNAGTPS PQMSSCFLVQ MKEDSIDGIY 250
    DTLKQCALIS KSAGGIGIAV HKIRAAQSYI RGTNGTSNGL VPMLRVFNDT 300
    ARYVDQGGGK RKGAFAVYLE PWHADVFEFI DLKKNTGKEE MRARDLFYAL 350
    WVSDIFMERV EQNGDWALFC PNEAPGLAET HSEEHRALYL KYEATPDLPR 400
    RVIKAQELWF AIMESQVETG TPFILYKDAC NAKSNQKNLG TISSSNLCTE 450
    IIQYTSPDEI AVCNLASIAL PKFVRQKVGS TDPKEKEFDH QFLFEITKLI 500
    TVNLNVIIDR NYYPVAEAKT SNLRHRPIGI GIQGLADVFI KMRMPFDSVA 550
    AAKLNVEIAE TIYFAALTAS HELAIRDGTY ESFKGSPASK GILQFDMWNV 600
    TPSSRWNWAE LKDNIVNKGG LRNSLLIAPM PTASTSQILG NNECFEPYTS 650
    NIYSRRVLAG EFTIVNKQLL EDLMELGIWS PEMKNQIVAA RGSIQSIGGI 700
    PDDLKELYKT VWEIRQRTLI DMAADRGAFI DQSQSFNVFI AEPTFAKLTS 750
    MHFYSWKKGL KTGMYYLRTR PAADAIQFTV DPIVSQTPKP VENNINSTTP 800
    LKTPTKTPNS SNRISTSPTN NLTSPIRFNI TQQQQQQQQQ QQQQNNNEDD 850
    LANYDGMTCR REEGCLVCGS 870
    Length:870
    Mass (Da):98,019
    Last modified:May 24, 2005 - v1
    Checksum:i41A13B6274074897
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AAFI02000063 Genomic DNA. Translation: EAL65376.1.
    RefSeqiXP_638726.1. XM_633634.1.

    Genome annotation databases

    EnsemblProtistsiDDB0230075; DDB0230075; DDB_G0284071.
    GeneIDi8624396.
    KEGGiddi:DDB_G0284071.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AAFI02000063 Genomic DNA. Translation: EAL65376.1 .
    RefSeqi XP_638726.1. XM_633634.1.

    3D structure databases

    ProteinModelPortali Q54Q71.
    SMRi Q54Q71. Positions 30-812.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 44689.DDB_0230075.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblProtistsi DDB0230075 ; DDB0230075 ; DDB_G0284071 .
    GeneIDi 8624396.
    KEGGi ddi:DDB_G0284071.

    Organism-specific databases

    dictyBasei DDB_G0284071. rnrA.

    Phylogenomic databases

    eggNOGi COG0209.
    KOi K10807.
    OMAi KECAMIS.
    PhylomeDBi Q54Q71.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .

    Miscellaneous databases

    PROi Q54Q71.

    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.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The genome of the social amoeba Dictyostelium discoideum."
      Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
      , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
      Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.

    Entry informationi

    Entry nameiRIR1_DICDI
    AccessioniPrimary (citable) accession number: Q54Q71
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 8, 2008
    Last sequence update: May 24, 2005
    Last modified: October 1, 2014
    This is version 72 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Keywords - Technical termi

    Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. Dictyostelium discoideum
      Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3