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P37426

- RIR1_SALTY

UniProt

P37426 - RIR1_SALTY

Protein

Ribonucleoside-diphosphate reductase 1 subunit alpha

Gene

nrdA

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 113 (01 Oct 2014)
      Sequence version 1 (01 Oct 1994)
      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.

    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

    BioCyciSENT99287:GCTI-2292-MONOMER.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase 1 subunit alpha (EC:1.17.4.1)
    Alternative name(s):
    Protein B1
    Ribonucleoside-diphosphate reductase 1 R1 subunit
    Ribonucleotide reductase 1
    Gene namesi
    Name:nrdA
    Ordered Locus Names:STM2277
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014: 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 1 subunit alphaPRO_0000187213Add
    BLAST

    Amino acid modifications

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

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiP37426.
    PRIDEiP37426.

    Interactioni

    Subunit structurei

    Tetramer of two alpha (R1) and two beta (R2) subunits. The B1 protein is a dimer of alpha subunits. A radical transfer pathway occurs between 'Tyr-122' of R2 and R1.

    Protein-protein interaction databases

    STRINGi99287.STM2277.

    Structurei

    3D structure databases

    ProteinModelPortaliP37426.
    SMRiP37426. 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.
    PhylomeDBiP37426.

    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.

    P37426-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNQSLLVTKR DGRTERINLD KIHRVLDWAA EGLNNVSVSQ VELRSHIQFY    50
    DGIKTSDIHE TIIKAAADLI SRDAPDYQYL AARLAIFHLR KKAFGQFEPP 100
    ALYHHVVKMV ELGKYDNHLL EDYTEEEFKQ MDSFIVHDRD MTFSYAAVKQ 150
    LEGKYLVQNR VTGEIYESAQ FLYILVAACL FSNYPRETRL DYVKRFYDAV 200
    STFKISLPTP IMSGVRTPTR QFSSCVLIEC GDSLDSINAT SSAIVKYVSQ 250
    RAGIGINAGR IRALGSPIRG GEAFHTGCIP FYKHFQTAVK SCSQGGVRGG 300
    AATLFYPMWH LEVESLLVLK NNRGVEGNRV RHMDYGVQIN KLMYTRLLKG 350
    GDITLFSPSD VPGLYDAFFA DQDEFERLYV KYEHDDSIRK QRVKAVELFS 400
    LMMQERASTG RIYIQNVDHC NTHSPFDPVV APVRQSNLCL EIALPTKPLN 450
    DVNDENGEIA LCTLSAFNLG AIKTLDELEE LAILAVRALD ALLDYQDYPI 500
    PAAKRGAMGR RTLGIGVINF AYWLAKNGKR YSDGSANNLT HKTFEAIQYY 550
    LLKASNELAK EQGACPWFNE TTYAKGILPI DTYKKDLDAI VNEPLHYDWE 600
    QLRESIKTHG LRNSTLSALM PSETSSQISN ATNGIEPPRG YVSIKASKDG 650
    ILRQVVPDYE HLKDAYELLW EMPNNDGYLQ LVGIMQKFID QSISANTNYD 700
    PSRFPSGKVP MQQLLKDLLT AYKFGVKTLY YQNTRDGAED AQDDLAPSIQ 750
    DDGCESGACK I 761
    Length:761
    Mass (Da):85,736
    Last modified:October 1, 1994 - v1
    Checksum:i0B3322D847CC58F9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X72948 Genomic DNA. Translation: CAA51452.1.
    AE006468 Genomic DNA. Translation: AAL21178.1.
    PIRiS32629.
    RefSeqiNP_461219.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL21178; AAL21178; STM2277.
    GeneIDi1253799.
    KEGGistm:STM2277.
    PATRICi32383161. VBISalEnt20916_2410.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X72948 Genomic DNA. Translation: CAA51452.1 .
    AE006468 Genomic DNA. Translation: AAL21178.1 .
    PIRi S32629.
    RefSeqi NP_461219.1. NC_003197.1.

    3D structure databases

    ProteinModelPortali P37426.
    SMRi P37426. Positions 5-737.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM2277.

    Proteomic databases

    PaxDbi P37426.
    PRIDEi P37426.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL21178 ; AAL21178 ; STM2277 .
    GeneIDi 1253799.
    KEGGi stm:STM2277.
    PATRICi 32383161. VBISalEnt20916_2410.

    Phylogenomic databases

    eggNOGi COG0209.
    HOGENOMi HOG000278076.
    KOi K00525.
    OMAi LLWQMPS.
    OrthoDBi EOG6J48HC.
    PhylomeDBi P37426.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci SENT99287:GCTI-2292-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. "Cloning and sequencing of the genes from Salmonella typhimurium encoding a new bacterial ribonucleotide reductase."
      Jordan A., Gibert I., Barbe J.
      J. Bacteriol. 176:3420-3427(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: LT2.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.

    Entry informationi

    Entry nameiRIR1_SALTY
    AccessioniPrimary (citable) accession number: P37426
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: October 1, 2014
    This is version 113 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    S.typhimurium produces two separate class I enzymes. This one is the functional enzyme during growth.

    Keywords - Technical termi

    Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3