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Protein

Anaerobic ribonucleoside-triphosphate reductase

Gene

nrdD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of ribonucleotides into deoxyribonucleotides, which are required for DNA synthesis and repair.5 Publications

Miscellaneous

The glycyl radical is involved in generation of a transient thiyl (sulfanyl) radical on a cysteine residue, which attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl (alpha-oxoalkyl) radical. The ketyl radical gains an electron from a cysteine residue and a proton from formic acid, forming 3'-keto-deoxyribonucleotide and generating a thiosulfuranyl radical bridge between methionine and cysteine residues. Oxidation of formate by the thiosulfuranyl radical results in the release of CO2 and regeneration of the thiyl radical.1 Publication

Catalytic activityi

Ribonucleoside 5'-triphosphate + formate = 2'-deoxyribonucleoside 5'-triphosphate + CO2 + H2O.5 Publications

Enzyme regulationi

Activated under anaerobic conditions by NrdG, a tightly associated activase (PubMed:1460049, PubMed:7852304, PubMed:9305874). Activation involves the formation of a glycyl radical at Gly-681 (PubMed:7852304, PubMed:8636106, PubMed:9305874). Exposure of the activated reductase to oxygen leads to C-terminal truncation and inactivation of the protein, by cleavage at the N-terminal side of Gly-681 (PubMed:8421692, PubMed:7826394). The presence of zinc protects the protein from proteolysis and prevents the formation of disulfide bridges within it (PubMed:19381696).7 Publications

Kineticsi

  1. KM=0.35 mM for CTP1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi644Zinc2 Publications1
    Metal bindingi647Zinc2 Publications1
    Metal bindingi662Zinc2 Publications1
    Metal bindingi665Zinc2 Publications1

    GO - Molecular functioni

    • ATP binding Source: EcoCyc
    • CTP reductase activity Source: EcoCyc
    • dATP binding Source: EcoCyc
    • dGTP binding Source: EcoCyc
    • pyrimidine deoxyribonucleotide binding Source: EcoCyc
    • ribonucleoside-triphosphate reductase activity Source: EcoCyc
    • zinc ion binding Source: EcoCyc

    GO - Biological processi

    • 2'-deoxyribonucleotide biosynthetic process Source: EcoCyc
    • DNA replication Source: InterPro
    • nucleobase-containing small molecule interconversion Source: EcoliWiki

    Keywordsi

    Molecular functionOxidoreductase
    LigandATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
    MetaCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER.
    SABIO-RKiP28903.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Anaerobic ribonucleoside-triphosphate reductaseCurated (EC:1.1.98.65 Publications)
    Alternative name(s):
    Class III ribonucleoside-triphosphate reductaseCurated
    Gene namesi
    Name:nrdD1 Publication
    Ordered Locus Names:b4238, JW4197
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11417. nrdD.

    Subcellular locationi

    GO - Cellular componenti

    • anaerobic ribonucleoside-triphosphate reductase complex Source: EcoCyc

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi644C → A: Loss of activity. 1 Publication1
    Mutagenesisi647C → A: Almost loss of activity. 1 Publication1
    Mutagenesisi662C → A: Loss of activity. 1 Publication1
    Mutagenesisi665C → A: Loss of activity. 1 Publication1
    Mutagenesisi680C → S: Still retains some radical and some enzyme activity. 1 Publication1
    Mutagenesisi681G → A: Lacks both radical and enzyme activity. 1 Publication1
    Mutagenesisi682Y → F: Still retains some radical and some enzyme activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001666831 – 712Anaerobic ribonucleoside-triphosphate reductaseAdd BLAST712

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei681Glycine radicalPROSITE-ProRule annotation2 Publications1

    Keywords - PTMi

    Organic radical

    Proteomic databases

    PaxDbiP28903.
    PRIDEiP28903.

    Expressioni

    Inductioni

    Induced 2-fold by hydroxyurea.1 Publication

    Interactioni

    Subunit structurei

    Homodimer (PubMed:1460049, PubMed:8621608). Forms a tetramer composed of two NrdD and two NrdG subunits (PubMed:8621608, PubMed:9305874).3 Publications

    Protein-protein interaction databases

    BioGridi4259318. 3 interactors.
    DIPiDIP-10358N.
    IntActiP28903. 6 interactors.
    STRINGi316385.ECDH10B_4433.

    Structurei

    3D structure databases

    ProteinModelPortaliP28903.
    SMRiP28903.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini3 – 92ATP-conePROSITE-ProRule annotationAdd BLAST90
    Domaini583 – 708Glycine radicalPROSITE-ProRule annotationAdd BLAST126

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CJD. Bacteria.
    COG1328. LUCA.
    HOGENOMiHOG000222474.
    InParanoidiP28903.
    KOiK21636.
    PhylomeDBiP28903.

    Family and domain databases

    CDDicd01675. RNR_III. 1 hit.
    InterProiView protein in InterPro
    IPR005144. ATP-cone_dom.
    IPR019777. Form_AcTrfase_GR_CS.
    IPR001150. Gly_radical.
    IPR012833. NrdD.
    PfamiView protein in Pfam
    PF03477. ATP-cone. 1 hit.
    PF13597. NRDD. 1 hit.
    TIGRFAMsiTIGR02487. NrdD. 1 hit.
    PROSITEiView protein in PROSITE
    PS51161. ATP_CONE. 1 hit.
    PS00850. GLY_RADICAL_1. 1 hit.
    PS51149. GLY_RADICAL_2. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P28903-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTPHVMKRDG CKVPFKSERI KEAILRAAKA AEVDDADYCA TVAAVVSEQM
    60 70 80 90 100
    QGRNQVDINE IQTAVENQLM SGPYKQLARA YIEYRHDRDI EREKRGRLNQ
    110 120 130 140 150
    EIRGLVEQTN ASLLNENANK DSKVIPTQRD LLAGIVAKHY ARQHLLPRDV
    160 170 180 190 200
    VQAHERGDIH YHDLDYSPFF PMFNCMLIDL KGMLTQGFKM GNAEIEPPKS
    210 220 230 240 250
    ISTATAVTAQ IIAQVASHIY GGTTINRIDE VLAPFVTASY NKHRKTAEEW
    260 270 280 290 300
    NIPDAEGYAN SRTIKECYDA FQSLEYEVNT LHTANGQTPF VTFGFGLGTS
    310 320 330 340 350
    WESRLIQESI LRNRIAGLGK NRKTAVFPKL VFAIRDGLNH KKGDPNYDIK
    360 370 380 390 400
    QLALECASKR MYPDILNYDQ VVKVTGSFKT PMGCRSFLGV WENENGEQIH
    410 420 430 440 450
    DGRNNLGVIS LNLPRIALEA KGDEATFWKL LDERLVLARK ALMTRIARLE
    460 470 480 490 500
    GVKARVAPIL YMEGACGVRL NADDDVSEIF KNGRASISLG YIGIHETINA
    510 520 530 540 550
    LFGGEHVYDN EQLRAKGIAI VERLRQAVDQ WKEETGYGFS LYSTPSENLC
    560 570 580 590 600
    DRFCRLDTAE FGVVPGVTDK GYYTNSFHLD VEKKVNPYDK IDFEAPYPPL
    610 620 630 640 650
    ANGGFICYGE YPNIQHNLKA LEDVWDYSYQ HVPYYGTNTP IDECYECGFT
    660 670 680 690 700
    GEFECTSKGF TCPKCGNHDA SRVSVTRRVC GYLGSPDARP FNAGKQEEVK
    710
    RRVKHLGNGQ IG
    Length:712
    Mass (Da):80,023
    Last modified:August 29, 2003 - v2
    Checksum:i943589D653EB0C38
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti257G → R in AAA24226 (PubMed:8421692).Curated1
    Sequence conflicti420A → P in AAA24226 (PubMed:8421692).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.
    WP_000187778.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77195; AAC77195; b4238.
    BAE78237; BAE78237; BAE78237.
    GeneIDi948755.
    KEGGiecj:JW4197.
    eco:b4238.
    PATRICifig|1411691.4.peg.2464.

    Similar proteinsi

    Entry informationi

    Entry nameiNRDD_ECOLI
    AccessioniPrimary (citable) accession number: P28903
    Secondary accession number(s): Q2M669
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 1992
    Last sequence update: August 29, 2003
    Last modified: September 27, 2017
    This is version 143 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally thought to contain an iron sulfur cluster (PubMed:8381402). It was shown later that only NrdG contains an iron sulfur center (PubMed:8621608).1 Publication1 Publication

    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