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P39452

- RIR3_ECOLI

UniProt

P39452 - RIR3_ECOLI

Protein

Ribonucleoside-diphosphate reductase 2 subunit alpha

Gene

nrdE

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
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    • History
      Entry version 125 (01 Oct 2014)
      Sequence version 3 (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 By similarity.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei161 – 1611SubstrateBy similarity
    Sitei178 – 1781Important for hydrogen atom transferBy similarity
    Sitei185 – 1851Allosteric effector bindingBy similarity
    Binding sitei206 – 2061Substrate; via amide nitrogenBy similarity
    Sitei215 – 2151Allosteric effector bindingBy similarity
    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. deoxyribonucleotide biosynthetic process Source: EcoliWiki
    2. DNA replication Source: UniProtKB-UniPathway
    3. nucleobase-containing small molecule interconversion Source: EcoliWiki

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:NRDE-MONOMER.
    ECOL316407:JW2650-MONOMER.
    MetaCyc:NRDE-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:b2675, JW2650
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG20257. nrdE.

    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
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 714713Ribonucleoside-diphosphate reductase 2 subunit alphaPRO_0000187224Add
    BLAST

    Amino acid modifications

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

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiP39452.
    PRIDEiP39452.

    Expressioni

    Gene expression databases

    GenevestigatoriP39452.

    Interactioni

    Subunit structurei

    Tetramer of two alpha and two beta subunits.By similarity

    Protein-protein interaction databases

    DIPiDIP-359N.
    IntActiP39452. 9 interactions.
    STRINGi511145.b2675.

    Structurei

    3D structure databases

    ProteinModelPortaliP39452.
    ModBaseiSearch...
    MobiDBiSearch...

    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.
    PhylomeDBiP39452.

    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.

    P39452-1 [UniParc]FASTAAdd to Basket

    « Hide

    MATTTAECLT QETMDYHALN AMLNLYDSAG RIQFDKDRQA VDAFIATHVR    50
    PNSVTFSSQQ QRLNWLVNEG YYDESVLNRY SRDFVITLFT HAHTSGFRFQ 100
    TFLGAWKFYT SYTLKTFDGK RYLEDFADRV TMVALTLAQG DETLALQLTD 150
    EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL LRIEDNMESI GRAVNSALQL 200
    SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED AFSYANQLGA 250
    RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFHLA 300
    KENAQMALFS PYDVERVYGK PFADVAISQH YDELVADERI RKKYLNARDF 350
    FQRLAEIQFE SGYPYIMYED TVNRANPIAG RINMSNLCSE ILQVNSASEY 400
    DENLDYTRTG HDISCNLGSL NIAHTMDSPD FARTVETAVR GLTAVSDMSH 450
    IRSVPSIEAG NAASHAIGLG QMNLHGYLAR EGIAYGSPEA LDFTNLYFYA 500
    ITWHALRTSM LLARERGETF AGFKQSRYAS GEYFSQYLQG NWQPKTAKVG 550
    ELFTRSGITL PTREMWAQLR DDVMRYGIYN QNLQAVPPTG SISYINHATS 600
    SIHPIVAKVE IRKEGKTGRV YYPAPFMTNE NLALYQDAYE IGAEKIIDTY 650
    AEATRHVDQG LSLTLFFPDT ATTRDINKAQ IYAWRKGIKT LYYIRLRQMA 700
    LEGTEIEGCV SCAL 714
    Length:714
    Mass (Da):80,479
    Last modified:January 23, 2007 - v3
    Checksum:i6DAD735BF78C1B77
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti545 – 5451K → P(PubMed:2158980)Curated
    Sequence conflicti548 – 5481K → H(PubMed:2158980)Curated
    Sequence conflicti551 – 5522EL → AP(PubMed:2158980)Curated
    Sequence conflicti556 – 5561S → R(PubMed:2158980)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC75722.1.
    AP009048 Genomic DNA. Translation: BAA16539.2.
    X79787 Genomic DNA. Translation: CAA56186.1.
    M31530 Genomic DNA. No translation available.
    PIRiD65047.
    RefSeqiNP_417161.1. NC_000913.3.
    YP_490890.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75722; AAC75722; b2675.
    BAA16539; BAA16539; BAA16539.
    GeneIDi12930227.
    947155.
    KEGGiecj:Y75_p2618.
    eco:b2675.
    PATRICi32120740. VBIEscCol129921_2767.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC75722.1 .
    AP009048 Genomic DNA. Translation: BAA16539.2 .
    X79787 Genomic DNA. Translation: CAA56186.1 .
    M31530 Genomic DNA. No translation available.
    PIRi D65047.
    RefSeqi NP_417161.1. NC_000913.3.
    YP_490890.1. NC_007779.1.

    3D structure databases

    ProteinModelPortali P39452.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-359N.
    IntActi P39452. 9 interactions.
    STRINGi 511145.b2675.

    Proteomic databases

    PaxDbi P39452.
    PRIDEi P39452.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75722 ; AAC75722 ; b2675 .
    BAA16539 ; BAA16539 ; BAA16539 .
    GeneIDi 12930227.
    947155.
    KEGGi ecj:Y75_p2618.
    eco:b2675.
    PATRICi 32120740. VBIEscCol129921_2767.

    Organism-specific databases

    EchoBASEi EB4158.
    EcoGenei EG20257. nrdE.

    Phylogenomic databases

    eggNOGi COG0209.
    HOGENOMi HOG000246165.
    KOi K00525.
    OMAi IYYIRIR.
    OrthoDBi EOG6J48HC.
    PhylomeDBi P39452.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci EcoCyc:NRDE-MONOMER.
    ECOL316407:JW2650-MONOMER.
    MetaCyc:NRDE-MONOMER.

    Miscellaneous databases

    PROi P39452.

    Gene expression databases

    Genevestigatori P39452.

    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. "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], SEQUENCE REVISION.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Promoter identification and expression analysis of Salmonella typhimurium and Escherichia coli nrdEF operons encoding one of two class I ribonucleotide reductases present in both bacteria."
      Jordan A., Aragall E., Gibert I., Barbe J.
      Mol. Microbiol. 19:777-790(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-103.
      Strain: K12.
    5. "Bacterial transposon Tn7 utilizes two different classes of target sites."
      Kubo K.M., Craig N.L.
      J. Bacteriol. 172:2774-2778(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 544-566.

    Entry informationi

    Entry nameiRIR3_ECOLI
    AccessioniPrimary (citable) accession number: P39452
    Secondary accession number(s): P78101
    , P78210, P78211, Q59417
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 125 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Allosteric enzyme, 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3