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Q08698

- RIR3_SALTY

UniProt

Q08698 - RIR3_SALTY

Protein

Ribonucleoside-diphosphate reductase 2 subunit alpha

Gene

nrdE

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1E 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. 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. Lacks the N-terminal activity site.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei161 – 1611SubstrateBy similarity
    Sitei178 – 1781Important for hydrogen atom transferBy similarity
    Sitei185 – 1851Allosteric effector binding
    Binding sitei206 – 2061Substrate; via amide nitrogenBy similarity
    Sitei215 – 2151Allosteric effector binding
    Sitei222 – 2221Allosteric effector binding
    Active sitei386 – 3861Proton acceptorBy similarity
    Active sitei388 – 3881Cysteine radical intermediateBy similarity
    Active sitei390 – 3901Proton acceptorBy similarity
    Sitei415 – 4151Important for hydrogen atom transferBy similarity
    Sitei692 – 6921Important for electron transferBy similarity
    Sitei693 – 6931Important for electron transferBy similarity
    Sitei709 – 7091Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei712 – 7121Interacts 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

    BioCyciMetaCyc:MONOMER-13835.
    SENT99287:GCTI-2824-MONOMER.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase 2 subunit alpha (EC:1.17.4.1)
    Alternative name(s):
    R1E protein
    Ribonucleotide reductase 2
    Gene namesi
    Name:nrdE
    Ordered Locus Names:STM2807
    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
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 714713Ribonucleoside-diphosphate reductase 2 subunit alphaPRO_0000187225Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi178 ↔ 415Redox-active

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PRIDEiQ08698.

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta subunits.By similarity

    Protein-protein interaction databases

    STRINGi99287.STM2807.

    Structurei

    Secondary structure

    1
    714
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi16 – 216
    Helixi22 – 243
    Helixi35 – 4713
    Helixi49 – 524
    Helixi59 – 6810
    Helixi74 – 774
    Helixi82 – 9413
    Helixi102 – 11110
    Beta strandi119 – 1224
    Helixi126 – 13813
    Helixi142 – 15312
    Beta strandi156 – 1594
    Helixi161 – 1666
    Beta strandi169 – 1713
    Beta strandi179 – 1813
    Helixi187 – 20115
    Turni202 – 2043
    Beta strandi206 – 2105
    Beta strandi224 – 2263
    Helixi232 – 24413
    Beta strandi254 – 2607
    Helixi266 – 2705
    Helixi271 – 2733
    Beta strandi279 – 2813
    Beta strandi287 – 2915
    Helixi295 – 3017
    Beta strandi305 – 3095
    Helixi311 – 3188
    Helixi322 – 3243
    Helixi327 – 33610
    Beta strandi342 – 3465
    Helixi347 – 36115
    Beta strandi365 – 3673
    Helixi369 – 3757
    Beta strandi378 – 3803
    Beta strandi406 – 4083
    Beta strandi416 – 4216
    Helixi422 – 4265
    Helixi431 – 44717
    Helixi455 – 46410
    Beta strandi467 – 4726
    Helixi474 – 4807
    Helixi488 – 51629
    Helixi523 – 5253
    Helixi527 – 5304
    Helixi532 – 5343
    Helixi535 – 5384
    Helixi547 – 55610
    Helixi563 – 57614
    Helixi592 – 5965
    Beta strandi600 – 6034
    Beta strandi608 – 6125
    Beta strandi615 – 6184
    Beta strandi620 – 6234
    Turni629 – 6313
    Helixi632 – 6343
    Helixi638 – 6414
    Helixi643 – 65412
    Beta strandi665 – 6673
    Helixi673 – 68614
    Beta strandi694 – 6963

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1PEMX-ray2.99A1-714[»]
    1PEOX-ray3.00A1-714[»]
    1PEQX-ray2.80A1-714[»]
    1PEUX-ray3.20A1-714[»]
    2BQ1X-ray3.99E/F2-714[»]
    ProteinModelPortaliQ08698.
    SMRiQ08698. Positions 8-699.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ08698.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni177 – 1782Substrate bindingBy similarity
    Regioni386 – 3905Substrate bindingBy similarity
    Regioni588 – 5925Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0209.
    HOGENOMiHOG000246165.
    KOiK00525.
    OMAiIYYIRIR.
    OrthoDBiEOG6J48HC.
    PhylomeDBiQ08698.

    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q08698-1 [UniParc]FASTAAdd to Basket

    « Hide

    MATTTPERVM QETMDYHALN AMLNLYDKAG HIQFDKDQQA IDAFFATHVR    50
    PHSVTFASQH ERLGTLVREG YYDDAVLARY DRAFVLRLFE HAHASGFRFQ 100
    TFLGAWKFYT SYTLKTFDGK RYLEHFEDRV TMVALTLAQG DETLATQLTD 150
    EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL LRIEDNMESI GRAVNSALQL 200
    SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED AFSYANQLGA 250
    RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFRLA 300
    KENAQMALFS PYDIQRRYGK PFGDIAISER YDELIADPHV RKTYINARDF 350
    FQTLAEIQFE SGYPYIMFED TVNRANPIAG RINMSNLCSE ILQVNSASRY 400
    DDNLDYTHIG HDISCNLGSL NIAHVMDSPD IGRTVETAIR GLTAVSDMSH 450
    IRSVPSIAAG NAASHAIGLG QMNLHGYLAR EGIAYGSPEA LDFTNLYFYT 500
    ITWHAVHTSM RLARERGKTF AGFAQSRYAS GDYFTQYLQD DWQPKTAKVR 550
    ALFARSGITL PTREMWLKLR DDVMRYGIYN QNLQAVPPTG SISYINHATS 600
    SIHPIVAKIE IRKEGKTGRV YYPAPFMTNE NLDMYQDAYD IGPEKIIDTY 650
    AEATRHVDQG LSLTLFFPDT ATTRDINKAQ IYAWRKGIKS LYYIRLRQLA 700
    LEGTEIEGCV SCAL 714
    Length:714
    Mass (Da):80,587
    Last modified:January 23, 2007 - v2
    Checksum:iB12F79B42B05000D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X73226 Genomic DNA. Translation: CAA51699.1.
    AE006468 Genomic DNA. Translation: AAL21692.1.
    PIRiS34271.
    RefSeqiNP_461733.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL21692; AAL21692; STM2807.
    GeneIDi1254330.
    KEGGistm:STM2807.
    PATRICi32384296. VBISalEnt20916_2965.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X73226 Genomic DNA. Translation: CAA51699.1 .
    AE006468 Genomic DNA. Translation: AAL21692.1 .
    PIRi S34271.
    RefSeqi NP_461733.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1PEM X-ray 2.99 A 1-714 [» ]
    1PEO X-ray 3.00 A 1-714 [» ]
    1PEQ X-ray 2.80 A 1-714 [» ]
    1PEU X-ray 3.20 A 1-714 [» ]
    2BQ1 X-ray 3.99 E/F 2-714 [» ]
    ProteinModelPortali Q08698.
    SMRi Q08698. Positions 8-699.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM2807.

    Proteomic databases

    PRIDEi Q08698.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL21692 ; AAL21692 ; STM2807 .
    GeneIDi 1254330.
    KEGGi stm:STM2807.
    PATRICi 32384296. VBISalEnt20916_2965.

    Phylogenomic databases

    eggNOGi COG0209.
    HOGENOMi HOG000246165.
    KOi K00525.
    OMAi IYYIRIR.
    OrthoDBi EOG6J48HC.
    PhylomeDBi Q08698.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci MetaCyc:MONOMER-13835.
    SENT99287:GCTI-2824-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q08698.

    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. "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], PROTEIN SEQUENCE OF 2-15.
      Strain: LT2.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.
    3. "Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors."
      Uppsten M., Farnegardh M., Jordan A., Eliasson R., Eklund H., Uhlin U.
      J. Mol. Biol. 330:87-97(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEXES WITH ALLOSTERIC EFFECTORS.
    4. "The first holocomplex structure of ribonucleotide reductase gives new insight into its mechanism of action."
      Uppsten M., Farnegardh M., Domkin V., Uhlin U.
      J. Mol. Biol. 359:365-377(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 2-713.

    Entry informationi

    Entry nameiRIR3_SALTY
    AccessioniPrimary (citable) accession number: Q08698
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 119 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3