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P69924

- RIR2_ECOLI

UniProt

P69924 - RIR2_ECOLI

Protein

Ribonucleoside-diphosphate reductase 1 subunit beta

Gene

nrdB

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 100 (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. R2 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 bindingi85 – 851Iron 1
    Metal bindingi116 – 1161Iron 1
    Metal bindingi116 – 1161Iron 2
    Metal bindingi119 – 1191Iron 1
    Active sitei123 – 1231
    Metal bindingi205 – 2051Iron 2
    Metal bindingi239 – 2391Iron 2
    Metal bindingi242 – 2421Iron 2

    GO - Molecular functioni

    1. identical protein binding Source: IntAct
    2. iron ion binding Source: EcoCyc
    3. 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
    4. nucleobase-containing small molecule interconversion Source: EcoliWiki

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:NRDB-MONOMER.
    ECOL316407:JW2229-MONOMER.
    MetaCyc:NRDB-MONOMER.
    SABIO-RKP69924.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase 1 subunit beta (EC:1.17.4.1)
    Alternative name(s):
    Protein B2
    Protein R2
    Ribonucleotide reductase 1
    Gene namesi
    Name:nrdB
    Synonyms:ftsB
    Ordered Locus Names:b2235, JW2229
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10661. nrdB.

    Subcellular locationi

    GO - Cellular componenti

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

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 376375Ribonucleoside-diphosphate reductase 1 subunit betaPRO_0000190476Add
    BLAST

    Proteomic databases

    PaxDbiP69924.
    PRIDEiP69924.

    Expressioni

    Gene expression databases

    GenevestigatoriP69924.

    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-123 of R2 and R1.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself2EBI-555196,EBI-555196

    Protein-protein interaction databases

    DIPiDIP-36213N.
    IntActiP69924. 12 interactions.
    MINTiMINT-1269534.
    STRINGi511145.b2235.

    Structurei

    Secondary structure

    1
    376
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi13 – 153
    Beta strandi18 – 225
    Helixi35 – 4612
    Helixi51 – 533
    Helixi59 – 646
    Helixi68 – 9528
    Helixi97 – 993
    Helixi103 – 12826
    Helixi134 – 14310
    Helixi145 – 1517
    Helixi154 – 17118
    Beta strandi173 – 1786
    Beta strandi181 – 1855
    Helixi187 – 20620
    Helixi208 – 22114
    Helixi226 – 25530
    Beta strandi256 – 2583
    Helixi260 – 2689
    Helixi270 – 29122
    Turni292 – 2943
    Helixi302 – 31918
    Helixi334 – 3385
    Helixi368 – 3714

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AV8X-ray2.80A/B2-341[»]
    1BIQX-ray2.05A/B2-376[»]
    1JPRX-ray1.88A/B2-376[»]
    1JQCX-ray1.61A/B2-376[»]
    1MRRX-ray2.50A/B2-376[»]
    1MXRX-ray1.42A/B2-376[»]
    1PFRX-ray2.20A/B2-341[»]
    1PIMX-ray2.00A/B2-376[»]
    1PIUX-ray2.20A/B2-376[»]
    1PIYX-ray1.68A/B2-376[»]
    1PIZX-ray1.90A/B2-376[»]
    1PJ0X-ray1.90A/B2-376[»]
    1PJ1X-ray1.95A/B2-376[»]
    1PM2X-ray1.80A/B2-340[»]
    1R1RX-ray2.90D/E/F/P357-376[»]
    1R65X-ray1.95A/B2-376[»]
    1RIBX-ray2.20A/B2-376[»]
    1RNRX-ray2.50A/B2-376[»]
    1RSRX-ray2.00A/B2-376[»]
    1RSVX-ray2.20A/B2-376[»]
    1XIKX-ray1.70A/B2-376[»]
    1YFDX-ray1.90A/B2-376[»]
    2ALXX-ray2.60A1-340[»]
    2AV8X-ray2.46A/B2-341[»]
    2R1RX-ray3.00D/E/F/P357-376[»]
    2X0XX-ray2.30D/E/F/P357-376[»]
    2XAKX-ray2.80D/E/F/P357-376[»]
    2XAPX-ray2.10D/E/F/P357-376[»]
    2XAVX-ray2.80D/E/F/P357-376[»]
    2XAWX-ray3.10D/E/F/P357-376[»]
    2XAXX-ray2.75D/E/F/P357-376[»]
    2XAYX-ray2.65D/E/F/P357-376[»]
    2XAZX-ray2.60D/E/F/P357-376[»]
    2XO4X-ray2.50D/E/F/P357-376[»]
    2XO5X-ray2.70D/E/F/P357-376[»]
    2XOFX-ray2.20A/B2-376[»]
    3R1RX-ray3.00D/E/F/P357-376[»]
    3UUSX-ray5.65E/F/G/H2-376[»]
    4ERMX-ray3.95E/F/G/H2-376[»]
    4ERPX-ray4.45E/F/G/H2-376[»]
    4R1RX-ray3.20D/E/F/P357-376[»]
    5R1RX-ray3.10D/E/F/P357-376[»]
    6R1RX-ray3.10D/E/F/P357-376[»]
    7R1RX-ray3.10D/E/F/P357-376[»]
    DisProtiDP00107.
    ProteinModelPortaliP69924.
    SMRiP69924. Positions 2-376.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP69924.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0208.
    HOGENOMiHOG000278087.
    KOiK00526.
    OMAiWIETWAF.
    OrthoDBiEOG6J48J7.
    PhylomeDBiP69924.

    Family and domain databases

    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR000358. RNR_small.
    [Graphical view]
    PANTHERiPTHR23409. PTHR23409. 1 hit.
    PfamiPF00268. Ribonuc_red_sm. 2 hits.
    [Graphical view]
    SUPFAMiSSF47240. SSF47240. 1 hit.
    PROSITEiPS00368. RIBORED_SMALL. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P69924-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR    50
    PEEVDVSRDR IDYQALPEHE KHIFISNLKY QTLLDSIQGR SPNVALLPLI 100
    SIPELETWVE TWAFSETIHS RSYTHIIRNI VNDPSVVFDD IVTNEQIQKR 150
    AEGISSYYDE LIEMTSYWHL LGEGTHTVNG KTVTVSLREL KKKLYLCLMS 200
    VNALEAIRFY VSFACSFAFA ERELMEGNAK IIRLIARDEA LHLTGTQHML 250
    NLLRSGADDP EMAEIAEECK QECYDLFVQA AQQEKDWADY LFRDGSMIGL 300
    NKDILCQYVE YITNIRMQAV GLDLPFQTRS NPIPWINTWL VSDNVQVAPQ 350
    EVEVSSYLVG QIDSEVDTDD LSNFQL 376
    Length:376
    Mass (Da):43,517
    Last modified:January 23, 2007 - v2
    Checksum:iBF2D9A49B643E84A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    K02672 Genomic DNA. Translation: AAA24224.1.
    U00096 Genomic DNA. Translation: AAC75295.1.
    AP009048 Genomic DNA. Translation: BAA16054.1.
    PIRiA00527. RDEC2R.
    RefSeqiNP_416738.1. NC_000913.3.
    YP_490474.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75295; AAC75295; b2235.
    BAA16054; BAA16054; BAA16054.
    GeneIDi12931498.
    946732.
    KEGGiecj:Y75_p2197.
    eco:b2235.
    PATRICi32119829. VBIEscCol129921_2324.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    K02672 Genomic DNA. Translation: AAA24224.1 .
    U00096 Genomic DNA. Translation: AAC75295.1 .
    AP009048 Genomic DNA. Translation: BAA16054.1 .
    PIRi A00527. RDEC2R.
    RefSeqi NP_416738.1. NC_000913.3.
    YP_490474.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AV8 X-ray 2.80 A/B 2-341 [» ]
    1BIQ X-ray 2.05 A/B 2-376 [» ]
    1JPR X-ray 1.88 A/B 2-376 [» ]
    1JQC X-ray 1.61 A/B 2-376 [» ]
    1MRR X-ray 2.50 A/B 2-376 [» ]
    1MXR X-ray 1.42 A/B 2-376 [» ]
    1PFR X-ray 2.20 A/B 2-341 [» ]
    1PIM X-ray 2.00 A/B 2-376 [» ]
    1PIU X-ray 2.20 A/B 2-376 [» ]
    1PIY X-ray 1.68 A/B 2-376 [» ]
    1PIZ X-ray 1.90 A/B 2-376 [» ]
    1PJ0 X-ray 1.90 A/B 2-376 [» ]
    1PJ1 X-ray 1.95 A/B 2-376 [» ]
    1PM2 X-ray 1.80 A/B 2-340 [» ]
    1R1R X-ray 2.90 D/E/F/P 357-376 [» ]
    1R65 X-ray 1.95 A/B 2-376 [» ]
    1RIB X-ray 2.20 A/B 2-376 [» ]
    1RNR X-ray 2.50 A/B 2-376 [» ]
    1RSR X-ray 2.00 A/B 2-376 [» ]
    1RSV X-ray 2.20 A/B 2-376 [» ]
    1XIK X-ray 1.70 A/B 2-376 [» ]
    1YFD X-ray 1.90 A/B 2-376 [» ]
    2ALX X-ray 2.60 A 1-340 [» ]
    2AV8 X-ray 2.46 A/B 2-341 [» ]
    2R1R X-ray 3.00 D/E/F/P 357-376 [» ]
    2X0X X-ray 2.30 D/E/F/P 357-376 [» ]
    2XAK X-ray 2.80 D/E/F/P 357-376 [» ]
    2XAP X-ray 2.10 D/E/F/P 357-376 [» ]
    2XAV X-ray 2.80 D/E/F/P 357-376 [» ]
    2XAW X-ray 3.10 D/E/F/P 357-376 [» ]
    2XAX X-ray 2.75 D/E/F/P 357-376 [» ]
    2XAY X-ray 2.65 D/E/F/P 357-376 [» ]
    2XAZ X-ray 2.60 D/E/F/P 357-376 [» ]
    2XO4 X-ray 2.50 D/E/F/P 357-376 [» ]
    2XO5 X-ray 2.70 D/E/F/P 357-376 [» ]
    2XOF X-ray 2.20 A/B 2-376 [» ]
    3R1R X-ray 3.00 D/E/F/P 357-376 [» ]
    3UUS X-ray 5.65 E/F/G/H 2-376 [» ]
    4ERM X-ray 3.95 E/F/G/H 2-376 [» ]
    4ERP X-ray 4.45 E/F/G/H 2-376 [» ]
    4R1R X-ray 3.20 D/E/F/P 357-376 [» ]
    5R1R X-ray 3.10 D/E/F/P 357-376 [» ]
    6R1R X-ray 3.10 D/E/F/P 357-376 [» ]
    7R1R X-ray 3.10 D/E/F/P 357-376 [» ]
    DisProti DP00107.
    ProteinModelPortali P69924.
    SMRi P69924. Positions 2-376.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-36213N.
    IntActi P69924. 12 interactions.
    MINTi MINT-1269534.
    STRINGi 511145.b2235.

    Proteomic databases

    PaxDbi P69924.
    PRIDEi P69924.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75295 ; AAC75295 ; b2235 .
    BAA16054 ; BAA16054 ; BAA16054 .
    GeneIDi 12931498.
    946732.
    KEGGi ecj:Y75_p2197.
    eco:b2235.
    PATRICi 32119829. VBIEscCol129921_2324.

    Organism-specific databases

    EchoBASEi EB0655.
    EcoGenei EG10661. nrdB.

    Phylogenomic databases

    eggNOGi COG0208.
    HOGENOMi HOG000278087.
    KOi K00526.
    OMAi WIETWAF.
    OrthoDBi EOG6J48J7.
    PhylomeDBi P69924.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci EcoCyc:NRDB-MONOMER.
    ECOL316407:JW2229-MONOMER.
    MetaCyc:NRDB-MONOMER.
    SABIO-RK P69924.

    Miscellaneous databases

    EvolutionaryTracei P69924.
    PROi P69924.

    Gene expression databases

    Genevestigatori P69924.

    Family and domain databases

    Gene3Di 1.10.620.20. 1 hit.
    InterProi IPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR000358. RNR_small.
    [Graphical view ]
    PANTHERi PTHR23409. PTHR23409. 1 hit.
    Pfami PF00268. Ribonuc_red_sm. 2 hits.
    [Graphical view ]
    SUPFAMi SSF47240. SSF47240. 1 hit.
    PROSITEi PS00368. RIBORED_SMALL. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Primary structure of the Escherichia coli ribonucleoside diphosphate reductase operon."
      Carlson J., Fuchs J.A., Messing J.
      Proc. Natl. Acad. Sci. U.S.A. 81:4294-4297(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "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.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "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.
    5. "Cloning, overproduction, and purification of the B2 subunit of ribonucleoside-diphosphate reductase."
      Salowe S.P., Stubbe J.
      J. Bacteriol. 165:363-366(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-21.
    6. "Three-dimensional structure of the free radical protein of ribonucleotide reductase."
      Nordlund P., Sjoeberg B.-M., Eklund H.
      Nature 345:593-598(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
    7. "Structure and function of the Escherichia coli ribonucleotide reductase protein R2."
      Nordlund P., Eklund H.
      J. Mol. Biol. 232:123-164(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
    8. "Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site."
      Logan D.T., Su X.-D., Aaberg A., Regnstroem K., Hajdu J., Eklund H., Nordlund P.
      Structure 4:1053-1064(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
    9. "Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding."
      Eriksson M., Uhlin U., Ramaswamy S., Ekberg M., Regnstroem K., Sjoeberg B.-M., Eklund H.
      Structure 5:1077-1092(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
    10. "Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-ray crystallography."
      Tong W., Burdi D., Riggs-Gelasco P., Chen S., Edmondson D., Huynh B.H., Stubbe J., Han S., Arvai A., Tainer J.
      Biochemistry 37:5840-5848(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.46 ANGSTROMS) OF MUTANT PHE-103.
    11. "Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins."
      Logan D.T., DeMare F., Persson B.O., Slaby A., Sjoeberg B.-M., Nordlund P.
      Biochemistry 37:10798-10807(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS).
    12. "Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation."
      Hogbom M., Andersson M.E., Nordlund P.
      J. Biol. Inorg. Chem. 6:315-323(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.61 ANGSTROMS).

    Entry informationi

    Entry nameiRIR2_ECOLI
    AccessioniPrimary (citable) accession number: P69924
    Secondary accession number(s): P00453
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 100 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    E.coli produces two separate class I enzymes. This one is the functional enzyme during growth.
    A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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