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P17424

- RIR4_SALTY

UniProt

P17424 - RIR4_SALTY

Protein

Ribonucleoside-diphosphate reductase 2 subunit beta

Gene

nrdF

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 125 (01 Oct 2014)
      Sequence version 2 (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. R2F contains the tyrosyl radical required for catalysis.

    Catalytic activityi

    2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.PROSITE-ProRule annotation

    Cofactori

    Binds 2 iron ions per subunit.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi67 – 671Iron 1
    Metal bindingi98 – 981Iron 1
    Metal bindingi98 – 981Iron 2
    Metal bindingi101 – 1011Iron 1
    Active sitei105 – 1051PROSITE-ProRule annotation
    Metal bindingi158 – 1581Iron 2
    Metal bindingi192 – 1921Iron 2
    Metal bindingi195 – 1951Iron 2

    GO - Molecular functioni

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

    GO - Biological processi

    1. deoxyribonucleoside diphosphate metabolic process Source: InterPro
    2. deoxyribonucleotide biosynthetic process Source: InterPro
    3. DNA replication Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13836.
    SENT99287:GCTI-2825-MONOMER.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase 2 subunit beta (EC:1.17.4.1)
    Alternative name(s):
    R2F protein
    Ribonucleotide reductase 2
    Gene namesi
    Name:nrdF
    Ordered Locus Names:STM2808
    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 – 319319Ribonucleoside-diphosphate reductase 2 subunit betaPRO_0000190489Add
    BLAST

    Proteomic databases

    PRIDEiP17424.

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta subunits.By similarity

    Protein-protein interaction databases

    STRINGi99287.STM2808.

    Structurei

    Secondary structure

    1
    319
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi17 – 2812
    Helixi33 – 353
    Helixi38 – 414
    Helixi42 – 465
    Helixi50 – 7223
    Helixi74 – 796
    Helixi85 – 11228
    Helixi115 – 12713
    Helixi129 – 14315
    Helixi147 – 15913
    Turni160 – 1623
    Helixi163 – 17412
    Helixi179 – 20830
    Helixi212 – 24029
    Turni241 – 2444
    Helixi247 – 26418
    Turni273 – 2753
    Helixi280 – 2867

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1R2FX-ray2.10A/B1-319[»]
    2BQ1X-ray4.00I/J1-319[»]
    2R2FX-ray2.25A/B1-319[»]
    ProteinModelPortaliP17424.
    SMRiP17424. Positions 4-318.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP17424.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0208.
    HOGENOMiHOG000246154.
    KOiK00526.
    OMAiNIKDFAF.
    OrthoDBiEOG68DD19.
    PhylomeDBiP17424.

    Family and domain databases

    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR026023. RNR_bsu_prok.
    IPR026494. RNR_NrdF.
    IPR000358. RNR_small.
    [Graphical view]
    PANTHERiPTHR23409. PTHR23409. 1 hit.
    PfamiPF00268. Ribonuc_red_sm. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000355. NrdB. 1 hit.
    SUPFAMiSSF47240. SSF47240. 1 hit.
    TIGRFAMsiTIGR04171. RNR_1b_NrdF. 1 hit.
    PROSITEiPS00368. RIBORED_SMALL. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P17424-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKLSRISAIN WNKIQDDKDL EVWNRLTSNF WLPEKVPLSN DIPAWQTLSA    50
    AEQQLTIRVF TGLTLLDTIQ NIAGAPSLMA DAITPHEEAV LSNISFMEAV 100
    HARSYSSIFS TLCQTKEVDA AYAWSEENPP LQRKAQIILA HYVSDEPLKK 150
    KIASVFLESF LFYSGFWLPM YFSSRGKLTN TADLIRLIIR DEAVHGYYIG 200
    YKYQIALQKL SAIEREELKL FALDLLMELY DNEIRYTEAL YAETGWVNDV 250
    KAFLCYNANK ALMNLGYEAL FPPEMADVNP AILAALSPNA DENHDFFSGS 300
    GSSYVMGKTV ETEDEDWNF 319
    Length:319
    Mass (Da):36,232
    Last modified:October 1, 1994 - v2
    Checksum:iAFBB6E02A57C959A
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti286 – 2861L → V in AAA88620. (PubMed:2548994)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X73226 Genomic DNA. Translation: CAA51695.1.
    AE006468 Genomic DNA. Translation: AAL21693.1.
    X52693 Genomic DNA. Translation: CAA36920.1.
    M26063 Genomic DNA. Translation: AAA88620.1.
    PIRiS34272.
    RefSeqiNP_461734.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL21693; AAL21693; STM2808.
    GeneIDi1254331.
    KEGGistm:STM2808.
    PATRICi32384298. VBISalEnt20916_2966.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X73226 Genomic DNA. Translation: CAA51695.1 .
    AE006468 Genomic DNA. Translation: AAL21693.1 .
    X52693 Genomic DNA. Translation: CAA36920.1 .
    M26063 Genomic DNA. Translation: AAA88620.1 .
    PIRi S34272.
    RefSeqi NP_461734.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1R2F X-ray 2.10 A/B 1-319 [» ]
    2BQ1 X-ray 4.00 I/J 1-319 [» ]
    2R2F X-ray 2.25 A/B 1-319 [» ]
    ProteinModelPortali P17424.
    SMRi P17424. Positions 4-318.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM2808.

    Proteomic databases

    PRIDEi P17424.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL21693 ; AAL21693 ; STM2808 .
    GeneIDi 1254331.
    KEGGi stm:STM2808.
    PATRICi 32384298. VBISalEnt20916_2966.

    Phylogenomic databases

    eggNOGi COG0208.
    HOGENOMi HOG000246154.
    KOi K00526.
    OMAi NIKDFAF.
    OrthoDBi EOG68DD19.
    PhylomeDBi P17424.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci MetaCyc:MONOMER-13836.
    SENT99287:GCTI-2825-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P17424.

    Family and domain databases

    Gene3Di 1.10.620.20. 1 hit.
    InterProi IPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR026023. RNR_bsu_prok.
    IPR026494. RNR_NrdF.
    IPR000358. RNR_small.
    [Graphical view ]
    PANTHERi PTHR23409. PTHR23409. 1 hit.
    Pfami PF00268. Ribonuc_red_sm. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000355. NrdB. 1 hit.
    SUPFAMi SSF47240. SSF47240. 1 hit.
    TIGRFAMsi TIGR04171. RNR_1b_NrdF. 1 hit.
    PROSITEi PS00368. RIBORED_SMALL. 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.
    3. "Molecular characterization of the proU loci of Salmonella typhimurium and Escherichia coli encoding osmoregulated glycine betaine transport systems."
      Stirling D.A., Hulton C.S.J., Waddell L., Park S.F., Stewart G.S.A.B., Booth I.R., Higgins C.F.
      Mol. Microbiol. 3:1025-1038(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 219-319.
      Strain: LT2.
    4. "Nucleotide sequence of the transcriptional control region of the osmotically regulated proU operon of Salmonella typhimurium and identification of the 5' endpoint of the proU mRNA."
      Overdier D.G., Olson E.R., Erickson B.D., Ederer M.M., Csonka L.N.
      J. Bacteriol. 171:4694-4706(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 219-319.
    5. "Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms."
      Eriksson M., Jordan A., Eklund H.
      Biochemistry 37:13359-13369(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

    Entry informationi

    Entry nameiRIR4_SALTY
    AccessioniPrimary (citable) accession number: P17424
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: October 1, 1994
    Last modified: October 1, 2014
    This is version 125 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, Complete proteome, 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