ID RIR3_ECOLI Reviewed; 714 AA.
AC P39452; P78101; P78210; P78211; Q59417;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 27-MAR-2024, entry version 174.
DE RecName: Full=Ribonucleoside-diphosphate reductase 2 subunit alpha;
DE EC=1.17.4.1;
DE AltName: Full=R1E protein;
DE AltName: Full=Ribonucleotide reductase 2;
GN Name=nrdE; OrderedLocusNames=b2675, JW2650;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION.
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-103.
RC STRAIN=K12;
RX PubMed=8820648; DOI=10.1046/j.1365-2958.1996.424950.x;
RA Jordan A., Aragall E., Gibert I., Barbe J.;
RT "Promoter identification and expression analysis of Salmonella typhimurium
RT and Escherichia coli nrdEF operons encoding one of two class I
RT ribonucleotide reductases present in both bacteria.";
RL Mol. Microbiol. 19:777-790(1996).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 544-566.
RX PubMed=2158980; DOI=10.1128/jb.172.5.2774-2778.1990;
RA Kubo K.M., Craig N.L.;
RT "Bacterial transposon Tn7 utilizes two different classes of target sites.";
RL J. Bacteriol. 172:2774-2778(1990).
RN [6]
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).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. R1E contains the binding sites for both
CC substrates and allosteric effectors and carries out the actual
CC reduction of the ribonucleotide.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-
CC diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-
CC diphosphate; Xref=Rhea:RHEA:23252, Rhea:RHEA-COMP:10698, Rhea:RHEA-
CC COMP:10700, ChEBI:CHEBI:15377, ChEBI:CHEBI:29950, ChEBI:CHEBI:50058,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:73316; EC=1.17.4.1;
CC -!- ACTIVITY REGULATION: Under complex allosteric control mediated by
CC deoxynucleoside triphosphates and ATP binding. The type of nucleotide
CC bound at the specificity site determines substrate preference. It seems
CC probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP
CC reduction and dTTP favors GDP reduction (By similarity). {ECO:0000250}.
CC -!- SUBUNIT: Tetramer of two alpha and two beta subunits. {ECO:0000250}.
CC -!- INDUCTION: Induced 2-fold by hydroxyurea.
CC {ECO:0000269|PubMed:20005847}.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase large
CC chain family. {ECO:0000305}.
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DR EMBL; U00096; AAC75722.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16539.2; -; Genomic_DNA.
DR EMBL; X79787; CAA56186.1; -; Genomic_DNA.
DR EMBL; M31530; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; D65047; D65047.
DR RefSeq; NP_417161.1; NC_000913.3.
DR RefSeq; WP_000246534.1; NZ_LN832404.1.
DR AlphaFoldDB; P39452; -.
DR SMR; P39452; -.
DR BioGRID; 4259221; 220.
DR BioGRID; 851487; 1.
DR ComplexPortal; CPX-5157; Ribonucleoside-diphosphate reductase 2 complex.
DR IntAct; P39452; 9.
DR STRING; 511145.b2675; -.
DR PaxDb; 511145-b2675; -.
DR EnsemblBacteria; AAC75722; AAC75722; b2675.
DR GeneID; 947155; -.
DR KEGG; ecj:JW2650; -.
DR KEGG; eco:b2675; -.
DR PATRIC; fig|1411691.4.peg.4066; -.
DR EchoBASE; EB4158; -.
DR eggNOG; COG0209; Bacteria.
DR HOGENOM; CLU_000404_4_1_6; -.
DR InParanoid; P39452; -.
DR OMA; TLFMTDK; -.
DR OrthoDB; 9762933at2; -.
DR PhylomeDB; P39452; -.
DR BioCyc; EcoCyc:NRDE-MONOMER; -.
DR BioCyc; MetaCyc:NRDE-MONOMER; -.
DR BRENDA; 1.17.4.1; 2026.
DR PRO; PR:P39452; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IGI:EcoliWiki.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:UniProtKB-EC.
DR GO; GO:0009265; P:2'-deoxyribonucleotide biosynthetic process; ISS:ComplexPortal.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IGI:EcoliWiki.
DR GO; GO:0006260; P:DNA replication; IEA:InterPro.
DR GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IGI:EcoliWiki.
DR GO; GO:0009185; P:ribonucleoside diphosphate metabolic process; ISS:ComplexPortal.
DR CDD; cd01679; RNR_I; 1.
DR Gene3D; 1.10.1650.20; -; 1.
DR Gene3D; 3.20.70.20; -; 1.
DR InterPro; IPR013346; NrdE_NrdA_C.
DR InterPro; IPR026459; RNR_1b_NrdE.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013509; RNR_lsu_N.
DR InterPro; IPR013554; RNR_N.
DR InterPro; IPR008926; RNR_R1-su_N.
DR InterPro; IPR039718; Rrm1.
DR NCBIfam; TIGR02506; NrdE_NrdA; 1.
DR NCBIfam; TIGR04170; RNR_1b_NrdE; 1.
DR PANTHER; PTHR11573; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN; 1.
DR PANTHER; PTHR11573:SF6; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE SUBUNIT; 1.
DR Pfam; PF02867; Ribonuc_red_lgC; 1.
DR Pfam; PF00317; Ribonuc_red_lgN; 1.
DR Pfam; PF08343; RNR_N; 1.
DR PRINTS; PR01183; RIBORDTASEM1.
DR SUPFAM; SSF51998; PFL-like glycyl radical enzymes; 1.
DR SUPFAM; SSF48168; R1 subunit of ribonucleotide reductase, N-terminal domain; 1.
DR PROSITE; PS00089; RIBORED_LARGE; 1.
PE 2: Evidence at transcript level;
KW Allosteric enzyme; ATP-binding; Deoxyribonucleotide synthesis;
KW Disulfide bond; Nucleotide-binding; Oxidoreductase; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250"
FT CHAIN 2..714
FT /note="Ribonucleoside-diphosphate reductase 2 subunit
FT alpha"
FT /id="PRO_0000187224"
FT ACT_SITE 386
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 388
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 390
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 161
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 177..178
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 206
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 386..390
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 588..592
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 178
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 185
FT /note="Allosteric effector binding"
FT /evidence="ECO:0000250"
FT SITE 215
FT /note="Allosteric effector binding"
FT /evidence="ECO:0000250"
FT SITE 415
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 692
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 693
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 709
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 712
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT DISULFID 178..415
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT CONFLICT 545
FT /note="K -> P (in Ref. 5; M31530)"
FT /evidence="ECO:0000305"
FT CONFLICT 548
FT /note="K -> H (in Ref. 5; M31530)"
FT /evidence="ECO:0000305"
FT CONFLICT 551..552
FT /note="EL -> AP (in Ref. 5; M31530)"
FT /evidence="ECO:0000305"
FT CONFLICT 556
FT /note="S -> R (in Ref. 5; M31530)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 714 AA; 80479 MW; 6DAD735BF78C1B77 CRC64;
MATTTAECLT QETMDYHALN AMLNLYDSAG RIQFDKDRQA VDAFIATHVR PNSVTFSSQQ
QRLNWLVNEG YYDESVLNRY SRDFVITLFT HAHTSGFRFQ TFLGAWKFYT SYTLKTFDGK
RYLEDFADRV TMVALTLAQG DETLALQLTD EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL
LRIEDNMESI GRAVNSALQL SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED
AFSYANQLGA RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFHLA
KENAQMALFS PYDVERVYGK PFADVAISQH YDELVADERI RKKYLNARDF FQRLAEIQFE
SGYPYIMYED TVNRANPIAG RINMSNLCSE ILQVNSASEY DENLDYTRTG HDISCNLGSL
NIAHTMDSPD FARTVETAVR GLTAVSDMSH IRSVPSIEAG NAASHAIGLG QMNLHGYLAR
EGIAYGSPEA LDFTNLYFYA ITWHALRTSM LLARERGETF AGFKQSRYAS GEYFSQYLQG
NWQPKTAKVG ELFTRSGITL PTREMWAQLR DDVMRYGIYN QNLQAVPPTG SISYINHATS
SIHPIVAKVE IRKEGKTGRV YYPAPFMTNE NLALYQDAYE IGAEKIIDTY AEATRHVDQG
LSLTLFFPDT ATTRDINKAQ IYAWRKGIKT LYYIRLRQMA LEGTEIEGCV SCAL
//
