NRDD_ECOLI
ID NRDD_ECOLI Reviewed; 712 AA.
AC P28903; Q2M669;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 29-AUG-2003, sequence version 2.
DT 03-AUG-2022, entry version 167.
DE RecName: Full=Anaerobic ribonucleoside-triphosphate reductase {ECO:0000305};
DE EC=1.1.98.6 {ECO:0000269|PubMed:1460049, ECO:0000269|PubMed:24827372, ECO:0000269|PubMed:7568012, ECO:0000269|PubMed:8381402, ECO:0000269|PubMed:9305874};
DE AltName: Full=Class III ribonucleoside-triphosphate reductase {ECO:0000305};
GN Name=nrdD {ECO:0000303|PubMed:8421692}; OrderedLocusNames=b4238, JW4197;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, AND ACTIVITY
RP REGULATION.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8421692; DOI=10.1073/pnas.90.2.577;
RA Sun X., Harder J., Krook M., Joernvall H., Sjoeberg B.-M., Reichard P.;
RT "A possible glycine radical in anaerobic ribonucleotide reductase from
RT Escherichia coli: nucleotide sequence of the cloned nrdD gene.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:577-581(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-229.
RC STRAIN=K12;
RX PubMed=8083158; DOI=10.1128/jb.176.18.5654-5664.1994;
RA Rimmele M., Boos W.;
RT "Trehalose-6-phosphate hydrolase of Escherichia coli.";
RL J. Bacteriol. 176:5654-5664(1994).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 703-712, AND ACTIVITY REGULATION.
RC STRAIN=K12;
RX PubMed=7852304; DOI=10.1074/jbc.270.6.2443;
RA Sun X., Eliasson R., Pontis E., Andersson J., Buist G., Sjoeberg B.-M.,
RA Reichard P.;
RT "Generation of the glycyl radical of the anaerobic Escherichia coli
RT ribonucleotide reductase requires a specific activating enzyme.";
RL J. Biol. Chem. 270:2443-2446(1995).
RN [7]
RP PROTEIN SEQUENCE OF 1-15, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=1460049; DOI=10.1016/s0021-9258(19)74074-5;
RA Eliasson R., Pontis E., Fontecave M., Gerez C., Harder J., Joernvall H.,
RA Krook M., Reichard P.;
RT "Characterization of components of the anaerobic ribonucleotide reductase
RT system from Escherichia coli.";
RL J. Biol. Chem. 267:25541-25547(1992).
RN [8]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=8381402; DOI=10.1016/s0021-9258(18)53772-8;
RA Mulliez E., Fontecave M., Gaillard J., Reichard P.;
RT "An iron-sulfur center and a free radical in the active anaerobic
RT ribonucleotide reductase of Escherichia coli.";
RL J. Biol. Chem. 268:2296-2299(1993).
RN [9]
RP ACTIVITY REGULATION, AND GLYCYL RADICAL AT GLY-681.
RX PubMed=7826394; DOI=10.1006/bbrc.1995.1103;
RA King D.S., Reichard P.;
RT "Mass spectrometric determination of the radical scission site in the
RT anaerobic ribonucleotide reductase of Escherichia coli.";
RL Biochem. Biophys. Res. Commun. 206:731-735(1995).
RN [10]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=7568012; DOI=10.1073/pnas.92.19.8759;
RA Mulliez E., Ollagnier S., Fontecave M., Eliasson R., Reichard P.;
RT "Formate is the hydrogen donor for the anaerobic ribonucleotide reductase
RT from Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:8759-8762(1995).
RN [11]
RP ACTIVITY REGULATION, GLYCYL RADICAL AT GLY-681, AND MUTAGENESIS OF CYS-680;
RP GLY-681 AND TYR-682.
RX PubMed=8636106; DOI=10.1074/jbc.271.12.6947;
RA Sun X., Ollagnier S., Schmidt P.P., Atta M., Mulliez E., Lepape L.,
RA Eliasson R., Graeslund A., Fontecave M., Reichard P., Sjoeberg B.M.;
RT "The free radical of the anaerobic ribonucleotide reductase from
RT Escherichia coli is at glycine 681.";
RL J. Biol. Chem. 271:6827-6831(1996).
RN [12]
RP SUBUNIT, AND INTERACTION WITH NRDG.
RX PubMed=8621608; DOI=10.1074/jbc.271.16.9410;
RA Ollagnier S., Mulliez E., Gaillard J., Eliasson R., Fontecave M.,
RA Reichard P.;
RT "The anaerobic Escherichia coli ribonucleotide reductase. Subunit structure
RT and iron sulfur center.";
RL J. Biol. Chem. 271:9410-9416(1996).
RN [13]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND SUBUNIT.
RX PubMed=9305874; DOI=10.1074/jbc.272.39.24216;
RA Ollagnier S., Mulliez E., Schmidt P.P., Eliasson R., Gaillard J.,
RA Deronzier C., Bergman T., Graeslund A., Reichard P., Fontecave M.;
RT "Activation of the anaerobic ribonucleotide reductase from Escherichia
RT coli. The essential role of the iron-sulfur center for S-adenosylmethionine
RT reduction.";
RL J. Biol. Chem. 272:24216-24223(1997).
RN [14]
RP ZINC-BINDING, AND MUTAGENESIS OF CYS-644; CYS-647; CYS-662 AND CYS-665.
RX PubMed=12655046; DOI=10.1073/pnas.0736456100;
RA Logan D.T., Mulliez E., Larsson K.-M., Bodevin S., Atta M., Garnaud P.E.,
RA Sjoeberg B.-M., Fontecave M.;
RT "A metal-binding site in the catalytic subunit of anaerobic ribonucleotide
RT reductase.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:3826-3831(2003).
RN [15]
RP ZINC-BINDING, AND ACTIVITY REGULATION.
RX PubMed=19381696; DOI=10.1007/s00775-009-0505-9;
RA Luttringer F., Mulliez E., Dublet B., Lemaire D., Fontecave M.;
RT "The Zn center of the anaerobic ribonucleotide reductase from E. coli.";
RL J. Biol. Inorg. Chem. 14:923-933(2009).
RN [16]
RP INDUCTION BY HYDROXYUREA.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=20005847; DOI=10.1016/j.molcel.2009.11.024;
RA Davies B.W., Kohanski M.A., Simmons L.A., Winkler J.A., Collins J.J.,
RA Walker G.C.;
RT "Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia
RT coli.";
RL Mol. Cell 36:845-860(2009).
RN [17]
RP FUNCTION, CATALYTIC ACTIVITY, AND REACTION MECHANISM.
RX PubMed=24827372; DOI=10.1021/ja5030194;
RA Wei Y., Mathies G., Yokoyama K., Chen J., Griffin R.G., Stubbe J.;
RT "A chemically competent thiosulfuranyl radical on the Escherichia coli
RT class III ribonucleotide reductase.";
RL J. Am. Chem. Soc. 136:9001-9013(2014).
CC -!- FUNCTION: Catalyzes the conversion of ribonucleotides into
CC deoxyribonucleotides, which are required for DNA synthesis and repair.
CC {ECO:0000269|PubMed:1460049, ECO:0000269|PubMed:24827372,
CC ECO:0000269|PubMed:7568012, ECO:0000269|PubMed:8381402,
CC ECO:0000269|PubMed:9305874}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + formate + H(+) = a 2'-
CC deoxyribonucleoside 5'-triphosphate + CO2 + H2O;
CC Xref=Rhea:RHEA:51476, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:16526, ChEBI:CHEBI:61557,
CC ChEBI:CHEBI:61560; EC=1.1.98.6; Evidence={ECO:0000269|PubMed:1460049,
CC ECO:0000269|PubMed:24827372, ECO:0000269|PubMed:7568012,
CC ECO:0000269|PubMed:8381402, ECO:0000269|PubMed:9305874};
CC -!- ACTIVITY REGULATION: Activated under anaerobic conditions by NrdG, a
CC tightly associated activase (PubMed:1460049, PubMed:7852304,
CC PubMed:9305874). Activation involves the formation of a glycyl radical
CC at Gly-681 (PubMed:7852304, PubMed:8636106, PubMed:9305874). Exposure
CC of the activated reductase to oxygen leads to C-terminal truncation and
CC inactivation of the protein, by cleavage at the N-terminal side of Gly-
CC 681 (PubMed:8421692, PubMed:7826394). The presence of zinc protects the
CC protein from proteolysis and prevents the formation of disulfide
CC bridges within it (PubMed:19381696). {ECO:0000269|PubMed:1460049,
CC ECO:0000269|PubMed:19381696, ECO:0000269|PubMed:7826394,
CC ECO:0000269|PubMed:7852304, ECO:0000269|PubMed:8421692,
CC ECO:0000269|PubMed:8636106, ECO:0000269|PubMed:9305874}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.35 mM for CTP {ECO:0000269|PubMed:1460049};
CC -!- SUBUNIT: Homodimer (PubMed:1460049, PubMed:8621608). Forms a tetramer
CC composed of two NrdD and two NrdG subunits (PubMed:8621608,
CC PubMed:9305874). {ECO:0000269|PubMed:1460049,
CC ECO:0000269|PubMed:8621608, ECO:0000269|PubMed:9305874}.
CC -!- INTERACTION:
CC P28903; P0A9N8: nrdG; NbExp=3; IntAct=EBI-370011, EBI-1135026;
CC -!- INDUCTION: Induced 2-fold by hydroxyurea.
CC {ECO:0000269|PubMed:20005847}.
CC -!- MISCELLANEOUS: The glycyl radical is involved in generation of a
CC transient thiyl (sulfanyl) radical on a cysteine residue, which attacks
CC the substrate, forming a ribonucleotide 3'-radical, followed by water
CC loss to form a ketyl (alpha-oxoalkyl) radical. The ketyl radical gains
CC an electron from a cysteine residue and a proton from formic acid,
CC forming 3'-keto-deoxyribonucleotide and generating a thiosulfuranyl
CC radical bridge between methionine and cysteine residues. Oxidation of
CC formate by the thiosulfuranyl radical results in the release of CO(2)
CC and regeneration of the thiyl radical. {ECO:0000269|PubMed:24827372}.
CC -!- SIMILARITY: Belongs to the anaerobic ribonucleoside-triphosphate
CC reductase family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to contain an iron sulfur cluster
CC (PubMed:8381402). It was shown later that only NrdG contains an iron
CC sulfur center (PubMed:8621608). {ECO:0000269|PubMed:8621608,
CC ECO:0000303|PubMed:8381402}.
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DR EMBL; L06097; AAA24226.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97135.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77195.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78237.1; -; Genomic_DNA.
DR EMBL; U06195; AAC43383.1; -; Genomic_DNA.
DR EMBL; Z46865; CAA86938.1; -; Genomic_DNA.
DR PIR; A47331; A47331.
DR RefSeq; NP_418659.1; NC_000913.3.
DR RefSeq; WP_000187778.1; NZ_LN832404.1.
DR AlphaFoldDB; P28903; -.
DR SMR; P28903; -.
DR BioGRID; 4259318; 27.
DR BioGRID; 853044; 4.
DR ComplexPortal; CPX-3821; nrdDG class III anaerobic ribonucleotide reductase activation complex.
DR ComplexPortal; CPX-3822; nrdD class III anaerobic ribonucleotide reductase complex.
DR DIP; DIP-10358N; -.
DR IntAct; P28903; 9.
DR STRING; 511145.b4238; -.
DR jPOST; P28903; -.
DR PaxDb; P28903; -.
DR PRIDE; P28903; -.
DR EnsemblBacteria; AAC77195; AAC77195; b4238.
DR EnsemblBacteria; BAE78237; BAE78237; BAE78237.
DR GeneID; 66671845; -.
DR GeneID; 948755; -.
DR KEGG; ecj:JW4197; -.
DR KEGG; eco:b4238; -.
DR PATRIC; fig|1411691.4.peg.2464; -.
DR EchoBASE; EB1388; -.
DR eggNOG; COG1328; Bacteria.
DR HOGENOM; CLU_002707_2_0_6; -.
DR InParanoid; P28903; -.
DR OMA; YSYDRVP; -.
DR PhylomeDB; P28903; -.
DR BioCyc; EcoCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MON; -.
DR BioCyc; MetaCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MON; -.
DR BRENDA; 1.1.98.6; 2026.
DR SABIO-RK; P28903; -.
DR PRO; PR:P28903; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0031250; C:anaerobic ribonucleoside-triphosphate reductase complex; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IDA:EcoCyc.
DR GO; GO:0051065; F:CTP reductase activity; IDA:EcoCyc.
DR GO; GO:0032564; F:dATP binding; IDA:EcoCyc.
DR GO; GO:0032567; F:dGTP binding; IDA:EcoCyc.
DR GO; GO:0032556; F:pyrimidine deoxyribonucleotide binding; IDA:EcoCyc.
DR GO; GO:0008998; F:ribonucleoside-triphosphate reductase activity; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0009265; P:2'-deoxyribonucleotide biosynthetic process; IDA:EcoCyc.
DR GO; GO:0006260; P:DNA replication; IEA:InterPro.
DR GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IMP:ComplexPortal.
DR CDD; cd01675; RNR_III; 1.
DR InterPro; IPR005144; ATP-cone_dom.
DR InterPro; IPR019777; Form_AcTrfase_GR_CS.
DR InterPro; IPR001150; Gly_radical.
DR InterPro; IPR012833; NrdD.
DR Pfam; PF03477; ATP-cone; 1.
DR Pfam; PF13597; NRDD; 1.
DR TIGRFAMs; TIGR02487; NrdD; 1.
DR PROSITE; PS51161; ATP_CONE; 1.
DR PROSITE; PS00850; GLY_RADICAL_1; 1.
DR PROSITE; PS51149; GLY_RADICAL_2; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Direct protein sequencing; Metal-binding; Nucleotide-binding;
KW Organic radical; Oxidoreductase; Reference proteome; Zinc.
FT CHAIN 1..712
FT /note="Anaerobic ribonucleoside-triphosphate reductase"
FT /id="PRO_0000166683"
FT DOMAIN 3..92
FT /note="ATP-cone"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00492"
FT DOMAIN 583..708
FT /note="Glycine radical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00493"
FT BINDING 644
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:12655046,
FT ECO:0000305|PubMed:19381696"
FT BINDING 647
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:12655046,
FT ECO:0000305|PubMed:19381696"
FT BINDING 662
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:12655046,
FT ECO:0000305|PubMed:19381696"
FT BINDING 665
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:12655046,
FT ECO:0000305|PubMed:19381696"
FT MOD_RES 681
FT /note="Glycine radical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00493,
FT ECO:0000269|PubMed:7826394, ECO:0000269|PubMed:8636106"
FT MUTAGEN 644
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12655046"
FT MUTAGEN 647
FT /note="C->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:12655046"
FT MUTAGEN 662
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12655046"
FT MUTAGEN 665
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12655046"
FT MUTAGEN 680
FT /note="C->S: Still retains some radical and some enzyme
FT activity."
FT /evidence="ECO:0000269|PubMed:8636106"
FT MUTAGEN 681
FT /note="G->A: Lacks both radical and enzyme activity."
FT /evidence="ECO:0000269|PubMed:8636106"
FT MUTAGEN 682
FT /note="Y->F: Still retains some radical and some enzyme
FT activity."
FT /evidence="ECO:0000269|PubMed:8636106"
FT CONFLICT 257
FT /note="G -> R (in Ref. 1; AAA24226)"
FT /evidence="ECO:0000305"
FT CONFLICT 420
FT /note="A -> P (in Ref. 1; AAA24226)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 712 AA; 80023 MW; 943589D653EB0C38 CRC64;
MTPHVMKRDG CKVPFKSERI KEAILRAAKA AEVDDADYCA TVAAVVSEQM QGRNQVDINE
IQTAVENQLM SGPYKQLARA YIEYRHDRDI EREKRGRLNQ EIRGLVEQTN ASLLNENANK
DSKVIPTQRD LLAGIVAKHY ARQHLLPRDV VQAHERGDIH YHDLDYSPFF PMFNCMLIDL
KGMLTQGFKM GNAEIEPPKS ISTATAVTAQ IIAQVASHIY GGTTINRIDE VLAPFVTASY
NKHRKTAEEW NIPDAEGYAN SRTIKECYDA FQSLEYEVNT LHTANGQTPF VTFGFGLGTS
WESRLIQESI LRNRIAGLGK NRKTAVFPKL VFAIRDGLNH KKGDPNYDIK QLALECASKR
MYPDILNYDQ VVKVTGSFKT PMGCRSFLGV WENENGEQIH DGRNNLGVIS LNLPRIALEA
KGDEATFWKL LDERLVLARK ALMTRIARLE GVKARVAPIL YMEGACGVRL NADDDVSEIF
KNGRASISLG YIGIHETINA LFGGEHVYDN EQLRAKGIAI VERLRQAVDQ WKEETGYGFS
LYSTPSENLC DRFCRLDTAE FGVVPGVTDK GYYTNSFHLD VEKKVNPYDK IDFEAPYPPL
ANGGFICYGE YPNIQHNLKA LEDVWDYSYQ HVPYYGTNTP IDECYECGFT GEFECTSKGF
TCPKCGNHDA SRVSVTRRVC GYLGSPDARP FNAGKQEEVK RRVKHLGNGQ IG
