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P28903

- NRDD_ECOLI

UniProt

P28903 - NRDD_ECOLI

Protein

Anaerobic ribonucleoside-triphosphate reductase

Gene

nrdD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 124 (01 Oct 2014)
      Sequence version 2 (29 Aug 2003)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H2O = ribonucleoside triphosphate + thioredoxin.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi644 – 6441Zinc
    Metal bindingi647 – 6471Zinc
    Metal bindingi662 – 6621Zinc
    Metal bindingi665 – 6651Zinc

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. CTP reductase activity Source: EcoCyc
    3. ribonucleoside-triphosphate reductase activity Source: EcoCyc
    4. zinc ion binding Source: EcoCyc

    GO - Biological processi

    1. DNA replication Source: InterPro
    2. nucleobase-containing small molecule interconversion Source: EcoliWiki

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    ATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
    ECOL316407:JW4197-MONOMER.
    MetaCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
    SABIO-RKP28903.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Anaerobic ribonucleoside-triphosphate reductase (EC:1.17.4.2)
    Gene namesi
    Name:nrdD
    Ordered Locus Names:b4238, JW4197
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11417. nrdD.

    Subcellular locationi

    GO - Cellular componenti

    1. anaerobic ribonucleoside-triphosphate reductase complex Source: EcoliWiki

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 712712Anaerobic ribonucleoside-triphosphate reductasePRO_0000166683Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei681 – 6811Glycine radicalPROSITE-ProRule annotation

    Keywords - PTMi

    Organic radical

    Proteomic databases

    PaxDbiP28903.
    PRIDEiP28903.

    Expressioni

    Inductioni

    Probably by NrdD-activating enzyme under anaerobic conditions by generation of an organic free radical. Exposure of activated NrdD to oxygen may result in cleavage at the glycine residue harboring its organic radical with loss of the 31 C-terminal AA.

    Gene expression databases

    GenevestigatoriP28903.

    Interactioni

    Subunit structurei

    Tetramer consisting of 2 alpha (NrdD) and 2 beta (NrdG) subunits.

    Protein-protein interaction databases

    DIPiDIP-10358N.
    IntActiP28903. 6 interactions.
    STRINGi511145.b4238.

    Structurei

    3D structure databases

    ProteinModelPortaliP28903.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini3 – 9290ATP-conePROSITE-ProRule annotationAdd
    BLAST
    Domaini583 – 708126Glycine radicalPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation
    Contains 1 glycine radical domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG1328.
    HOGENOMiHOG000222474.
    KOiK00527.
    OMAiKRRVKHM.
    OrthoDBiEOG622PMK.
    PhylomeDBiP28903.

    Family and domain databases

    InterProiIPR005144. ATP-cone.
    IPR019777. Form_AcTrfase_GR_CS.
    IPR001150. Gly_radical.
    IPR012833. NrdD.
    [Graphical view]
    PfamiPF03477. ATP-cone. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR02487. NrdD. 1 hit.
    PROSITEiPS51161. ATP_CONE. 1 hit.
    PS00850. GLY_RADICAL_1. 1 hit.
    PS51149. GLY_RADICAL_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P28903-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTPHVMKRDG CKVPFKSERI KEAILRAAKA AEVDDADYCA TVAAVVSEQM    50
    QGRNQVDINE IQTAVENQLM SGPYKQLARA YIEYRHDRDI EREKRGRLNQ 100
    EIRGLVEQTN ASLLNENANK DSKVIPTQRD LLAGIVAKHY ARQHLLPRDV 150
    VQAHERGDIH YHDLDYSPFF PMFNCMLIDL KGMLTQGFKM GNAEIEPPKS 200
    ISTATAVTAQ IIAQVASHIY GGTTINRIDE VLAPFVTASY NKHRKTAEEW 250
    NIPDAEGYAN SRTIKECYDA FQSLEYEVNT LHTANGQTPF VTFGFGLGTS 300
    WESRLIQESI LRNRIAGLGK NRKTAVFPKL VFAIRDGLNH KKGDPNYDIK 350
    QLALECASKR MYPDILNYDQ VVKVTGSFKT PMGCRSFLGV WENENGEQIH 400
    DGRNNLGVIS LNLPRIALEA KGDEATFWKL LDERLVLARK ALMTRIARLE 450
    GVKARVAPIL YMEGACGVRL NADDDVSEIF KNGRASISLG YIGIHETINA 500
    LFGGEHVYDN EQLRAKGIAI VERLRQAVDQ WKEETGYGFS LYSTPSENLC 550
    DRFCRLDTAE FGVVPGVTDK GYYTNSFHLD VEKKVNPYDK IDFEAPYPPL 600
    ANGGFICYGE YPNIQHNLKA LEDVWDYSYQ HVPYYGTNTP IDECYECGFT 650
    GEFECTSKGF TCPKCGNHDA SRVSVTRRVC GYLGSPDARP FNAGKQEEVK 700
    RRVKHLGNGQ IG 712
    Length:712
    Mass (Da):80,023
    Last modified:August 29, 2003 - v2
    Checksum:i943589D653EB0C38
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti257 – 2571G → R in AAA24226. (PubMed:8421692)Curated
    Sequence conflicti420 – 4201A → P in AAA24226. (PubMed:8421692)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L06097 Genomic DNA. Translation: AAA24226.1.
    U14003 Genomic DNA. Translation: AAA97135.1.
    U00096 Genomic DNA. Translation: AAC77195.1.
    AP009048 Genomic DNA. Translation: BAE78237.1.
    U06195 Genomic DNA. Translation: AAC43383.1.
    Z46865 Genomic DNA. Translation: CAA86938.1.
    PIRiA47331.
    RefSeqiNP_418659.1. NC_000913.3.
    YP_492378.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77195; AAC77195; b4238.
    BAE78237; BAE78237; BAE78237.
    GeneIDi12930324.
    948755.
    KEGGiecj:Y75_p4123.
    eco:b4238.
    PATRICi32124049. VBIEscCol129921_4369.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L06097 Genomic DNA. Translation: AAA24226.1 .
    U14003 Genomic DNA. Translation: AAA97135.1 .
    U00096 Genomic DNA. Translation: AAC77195.1 .
    AP009048 Genomic DNA. Translation: BAE78237.1 .
    U06195 Genomic DNA. Translation: AAC43383.1 .
    Z46865 Genomic DNA. Translation: CAA86938.1 .
    PIRi A47331.
    RefSeqi NP_418659.1. NC_000913.3.
    YP_492378.1. NC_007779.1.

    3D structure databases

    ProteinModelPortali P28903.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10358N.
    IntActi P28903. 6 interactions.
    STRINGi 511145.b4238.

    Proteomic databases

    PaxDbi P28903.
    PRIDEi P28903.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC77195 ; AAC77195 ; b4238 .
    BAE78237 ; BAE78237 ; BAE78237 .
    GeneIDi 12930324.
    948755.
    KEGGi ecj:Y75_p4123.
    eco:b4238.
    PATRICi 32124049. VBIEscCol129921_4369.

    Organism-specific databases

    EchoBASEi EB1388.
    EcoGenei EG11417. nrdD.

    Phylogenomic databases

    eggNOGi COG1328.
    HOGENOMi HOG000222474.
    KOi K00527.
    OMAi KRRVKHM.
    OrthoDBi EOG622PMK.
    PhylomeDBi P28903.

    Enzyme and pathway databases

    BioCyci EcoCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
    ECOL316407:JW4197-MONOMER.
    MetaCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
    SABIO-RK P28903.

    Miscellaneous databases

    PROi P28903.

    Gene expression databases

    Genevestigatori P28903.

    Family and domain databases

    InterProi IPR005144. ATP-cone.
    IPR019777. Form_AcTrfase_GR_CS.
    IPR001150. Gly_radical.
    IPR012833. NrdD.
    [Graphical view ]
    Pfami PF03477. ATP-cone. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR02487. NrdD. 1 hit.
    PROSITEi PS51161. ATP_CONE. 1 hit.
    PS00850. GLY_RADICAL_1. 1 hit.
    PS51149. GLY_RADICAL_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene."
      Sun X., Harder J., Krook M., Joernvall H., Sjoeberg B.-M., Reichard P.
      Proc. Natl. Acad. Sci. U.S.A. 90:577-581(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
      Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    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. "Trehalose-6-phosphate hydrolase of Escherichia coli."
      Rimmele M., Boos W.
      J. Bacteriol. 176:5654-5664(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-229.
      Strain: K12.
    6. "Generation of the glycyl radical of the anaerobic Escherichia coli ribonucleotide reductase requires a specific activating enzyme."
      Sun X., Eliasson R., Pontis E., Andersson J., Buist G., Sjoeberg B.-M., Reichard P.
      J. Biol. Chem. 270:2443-2446(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 703-712.
      Strain: K12.
    7. "A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase."
      Logan D.T., Mulliez E., Larsson K.-M., Bodevin S., Atta M., Garnaud P.E., Sjoeberg B.-M., Fontecave M.
      Proc. Natl. Acad. Sci. U.S.A. 100:3826-3831(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF CYSTEINE RESIDUES, ENZYME ACTIVITY.

    Entry informationi

    Entry nameiNRDD_ECOLI
    AccessioniPrimary (citable) accession number: P28903
    Secondary accession number(s): Q2M669
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 1992
    Last sequence update: August 29, 2003
    Last modified: October 1, 2014
    This is version 124 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

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3