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P37146

- RIR4_ECOLI

UniProt

P37146 - RIR4_ECOLI

Protein

Ribonucleoside-diphosphate reductase 2 subunit beta

Gene

nrdF

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      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.By similarity

    Pathwayi

    Sites

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

    GO - Molecular functioni

    1. iron ion binding Source: EcoliWiki
    2. manganese ion binding Source: EcoCyc
    3. protein binding Source: EcoCyc
    4. 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: EcoliWiki
    3. DNA replication Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:NRDF-MONOMER.
    ECOL316407:JW2651-MONOMER.
    MetaCyc:NRDF-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
    Synonyms:ygaD
    Ordered Locus Names:b2676, JW2651
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG12381. nrdF.

    Subcellular locationi

    GO - Cellular componenti

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

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 319319Ribonucleoside-diphosphate reductase 2 subunit betaPRO_0000190488Add
    BLAST

    Proteomic databases

    PaxDbiP37146.
    PRIDEiP37146.

    Expressioni

    Gene expression databases

    GenevestigatoriP37146.

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta subunits.By similarity

    Protein-protein interaction databases

    DIPiDIP-374N.
    IntActiP37146. 9 interactions.
    STRINGi511145.b2676.

    Structurei

    Secondary structure

    1
    319
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi17 – 2812
    Helixi33 – 353
    Helixi38 – 414
    Helixi42 – 454
    Helixi50 – 7223
    Helixi74 – 785
    Helixi79 – 813
    Helixi85 – 11228
    Helixi115 – 12713
    Helixi129 – 14315
    Helixi147 – 15913
    Turni160 – 1623
    Helixi163 – 17412
    Helixi179 – 20729
    Helixi212 – 24029
    Turni241 – 2433
    Helixi247 – 26418
    Helixi273 – 2753
    Helixi280 – 2867

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3N37X-ray1.65A1-319[»]
    3N38X-ray1.90A1-319[»]
    3N39X-ray2.50A/B1-319[»]
    3N3AX-ray1.99A/B1-319[»]
    3N3BX-ray2.36A/B1-319[»]
    4M1FX-ray2.00A1-319[»]
    ProteinModelPortaliP37146.
    SMRiP37146. Positions 5-318.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP37146.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0208.
    HOGENOMiHOG000246153.
    KOiK00526.
    OMAiNIKDFAF.
    OrthoDBiEOG68DD19.
    PhylomeDBiP37146.

    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.

    P37146-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKLSRISAIN WNKISDDKDL EVWNRLTSNF WLPEKVPLSN DIPAWQTLTV    50
    VEQQLTMRVF TGLTLLDTLQ NVIGAPSLMP DALTPHEEAV LSNISFMEAV 100
    HARSYSSIFS TLCQTKDVDA AYAWSEENAP LQRKAQIIQQ HYRGDDPLKK 150
    KIASVFLESF LFYSGFWLPM YFSSRGKLTN TADLIRLIIR DEAVHGYYIG 200
    YKYQKNMEKI SLGQREELKS FAFDLLLELY DNELQYTDEL YAETPWADDV 250
    KAFLCYNANK ALMNLGYEPL FPAEMAEVNP AILAALSPNA DENHDFFSGS 300
    GSSYVMGKAV ETEDEDWNF 319
    Length:319
    Mass (Da):36,443
    Last modified:November 1, 1997 - v2
    Checksum:i0C95394CF150EEFB
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC75723.1.
    AP009048 Genomic DNA. Translation: BAA16541.1.
    M24856 Genomic DNA. No translation available.
    PIRiE65047.
    RefSeqiNP_417162.1. NC_000913.3.
    YP_490891.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75723; AAC75723; b2676.
    BAA16541; BAA16541; BAA16541.
    GeneIDi12933275.
    947149.
    KEGGiecj:Y75_p2619.
    eco:b2676.
    PATRICi32120742. VBIEscCol129921_2768.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC75723.1 .
    AP009048 Genomic DNA. Translation: BAA16541.1 .
    M24856 Genomic DNA. No translation available.
    PIRi E65047.
    RefSeqi NP_417162.1. NC_000913.3.
    YP_490891.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3N37 X-ray 1.65 A 1-319 [» ]
    3N38 X-ray 1.90 A 1-319 [» ]
    3N39 X-ray 2.50 A/B 1-319 [» ]
    3N3A X-ray 1.99 A/B 1-319 [» ]
    3N3B X-ray 2.36 A/B 1-319 [» ]
    4M1F X-ray 2.00 A 1-319 [» ]
    ProteinModelPortali P37146.
    SMRi P37146. Positions 5-318.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-374N.
    IntActi P37146. 9 interactions.
    STRINGi 511145.b2676.

    Proteomic databases

    PaxDbi P37146.
    PRIDEi P37146.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75723 ; AAC75723 ; b2676 .
    BAA16541 ; BAA16541 ; BAA16541 .
    GeneIDi 12933275.
    947149.
    KEGGi ecj:Y75_p2619.
    eco:b2676.
    PATRICi 32120742. VBIEscCol129921_2768.

    Organism-specific databases

    EchoBASEi EB2283.
    EcoGenei EG12381. nrdF.

    Phylogenomic databases

    eggNOGi COG0208.
    HOGENOMi HOG000246153.
    KOi K00526.
    OMAi NIKDFAF.
    OrthoDBi EOG68DD19.
    PhylomeDBi P37146.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci EcoCyc:NRDF-MONOMER.
    ECOL316407:JW2651-MONOMER.
    MetaCyc:NRDF-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P37146.
    PROi P37146.

    Gene expression databases

    Genevestigatori P37146.

    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. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Nucleotide sequence of the osmoregulatory proU operon of Escherichia coli."
      Gowrishankar J.
      J. Bacteriol. 171:1923-1931(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 210-319.
    5. Erratum
      Gowrishankar J.
      J. Bacteriol. 172:1165-1165(1990)
    6. "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: IDENTIFICATION.

    Entry informationi

    Entry nameiRIR4_ECOLI
    AccessioniPrimary (citable) accession number: P37146
    Secondary accession number(s): P78244
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 120 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3