ID   RIR4_ECOLI              Reviewed;         319 AA.
AC   P37146; P78244;
DT   01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 2.
DT   27-MAR-2024, entry version 177.
DE   RecName: Full=Ribonucleoside-diphosphate reductase 2 subunit beta;
DE            EC=1.17.4.1;
DE   AltName: Full=R2F protein;
DE   AltName: Full=Ribonucleotide reductase 2;
GN   Name=nrdF; Synonyms=ygaD; OrderedLocusNames=b2676, JW2651;
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].
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 210-319.
RX   PubMed=2649479; DOI=10.1128/jb.171.4.1923-1931.1989;
RA   Gowrishankar J.;
RT   "Nucleotide sequence of the osmoregulatory proU operon of Escherichia
RT   coli.";
RL   J. Bacteriol. 171:1923-1931(1989).
RN   [5]
RP   ERRATUM OF PUBMED:2649479.
RA   Gowrishankar J.;
RL   J. Bacteriol. 172:1165-1165(1990).
RN   [6]
RP   IDENTIFICATION.
RX   PubMed=8195103; DOI=10.1128/jb.176.11.3420-3427.1994;
RA   Jordan A., Gibert I., Barbe J.;
RT   "Cloning and sequencing of the genes from Salmonella typhimurium encoding a
RT   new bacterial ribonucleotide reductase.";
RL   J. Bacteriol. 176:3420-3427(1994).
RN   [7]
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. R2F contains the tyrosyl radical
CC       required for catalysis.
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         Evidence={ECO:0000255|PROSITE-ProRule:PRU10014};
CC   -!- COFACTOR:
CC       Name=Fe cation; Xref=ChEBI:CHEBI:24875; Evidence={ECO:0000250};
CC       Note=Binds 2 iron ions per subunit. {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 small
CC       chain family. {ECO:0000305}.
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DR   EMBL; U00096; AAC75723.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA16541.1; -; Genomic_DNA.
DR   EMBL; M24856; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   PIR; E65047; E65047.
DR   RefSeq; NP_417162.1; NC_000913.3.
DR   RefSeq; WP_000777969.1; NZ_LN832404.1.
DR   PDB; 3N37; X-ray; 1.65 A; A=1-319.
DR   PDB; 3N38; X-ray; 1.90 A; A=1-319.
DR   PDB; 3N39; X-ray; 2.50 A; A/B=1-319.
DR   PDB; 3N3A; X-ray; 1.99 A; A/B=1-319.
DR   PDB; 3N3B; X-ray; 2.36 A; A/B=1-319.
DR   PDB; 4M1F; X-ray; 2.00 A; A=1-319.
DR   PDBsum; 3N37; -.
DR   PDBsum; 3N38; -.
DR   PDBsum; 3N39; -.
DR   PDBsum; 3N3A; -.
DR   PDBsum; 3N3B; -.
DR   PDBsum; 4M1F; -.
DR   AlphaFoldDB; P37146; -.
DR   SMR; P37146; -.
DR   BioGRID; 4262269; 135.
DR   BioGRID; 851481; 3.
DR   ComplexPortal; CPX-5157; Ribonucleoside-diphosphate reductase 2 complex.
DR   IntAct; P37146; 10.
DR   STRING; 511145.b2676; -.
DR   PaxDb; 511145-b2676; -.
DR   EnsemblBacteria; AAC75723; AAC75723; b2676.
DR   GeneID; 75205919; -.
DR   GeneID; 947149; -.
DR   KEGG; ecj:JW2651; -.
DR   KEGG; eco:b2676; -.
DR   PATRIC; fig|1411691.4.peg.4065; -.
DR   EchoBASE; EB2283; -.
DR   eggNOG; COG0208; Bacteria.
DR   HOGENOM; CLU_052495_0_0_6; -.
DR   InParanoid; P37146; -.
DR   OMA; LGYEAMF; -.
DR   OrthoDB; 9766544at2; -.
DR   PhylomeDB; P37146; -.
DR   BioCyc; EcoCyc:NRDF-MONOMER; -.
DR   BioCyc; MetaCyc:NRDF-MONOMER; -.
DR   BRENDA; 1.17.4.1; 2026.
DR   EvolutionaryTrace; P37146; -.
DR   PRO; PR:P37146; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IGI:EcoliWiki.
DR   GO; GO:0030145; F:manganese ion binding; IDA:EcoCyc.
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:0009185; P:ribonucleoside diphosphate metabolic process; ISS:ComplexPortal.
DR   CDD; cd01049; RNRR2; 1.
DR   Gene3D; 1.10.620.20; Ribonucleotide Reductase, subunit A; 1.
DR   InterPro; IPR009078; Ferritin-like_SF.
DR   InterPro; IPR012348; RNR-like.
DR   InterPro; IPR026494; RNR_NrdF-like.
DR   InterPro; IPR033909; RNR_small.
DR   InterPro; IPR030475; RNR_small_AS.
DR   InterPro; IPR000358; RNR_small_fam.
DR   NCBIfam; TIGR04171; RNR_1b_NrdF; 1.
DR   PANTHER; PTHR23409; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN; 1.
DR   PANTHER; PTHR23409:SF18; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2; 1.
DR   Pfam; PF00268; Ribonuc_red_sm; 1.
DR   PIRSF; PIRSF000355; NrdB; 1.
DR   SUPFAM; SSF47240; Ferritin-like; 1.
DR   PROSITE; PS00368; RIBORED_SMALL; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Deoxyribonucleotide synthesis; Iron; Metal-binding;
KW   Oxidoreductase; Reference proteome.
FT   CHAIN           1..319
FT                   /note="Ribonucleoside-diphosphate reductase 2 subunit beta"
FT                   /id="PRO_0000190488"
FT   ACT_SITE        105
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT   BINDING         67
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT   BINDING         98
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT   BINDING         98
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         101
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT   BINDING         158
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         192
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_label="2"
FT   BINDING         195
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_label="2"
FT   HELIX           17..28
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           33..35
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           38..41
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           42..45
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           50..72
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           74..78
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           79..81
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           85..112
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           115..127
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           129..143
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           147..159
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   TURN            160..162
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           163..174
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           179..207
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           212..240
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   TURN            241..243
FT                   /evidence="ECO:0007829|PDB:3N3B"
FT   HELIX           247..264
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           273..275
FT                   /evidence="ECO:0007829|PDB:3N37"
FT   HELIX           280..286
FT                   /evidence="ECO:0007829|PDB:3N37"
SQ   SEQUENCE   319 AA;  36443 MW;  0C95394CF150EEFB CRC64;
     MKLSRISAIN WNKISDDKDL EVWNRLTSNF WLPEKVPLSN DIPAWQTLTV VEQQLTMRVF
     TGLTLLDTLQ NVIGAPSLMP DALTPHEEAV LSNISFMEAV HARSYSSIFS TLCQTKDVDA
     AYAWSEENAP LQRKAQIIQQ HYRGDDPLKK KIASVFLESF LFYSGFWLPM YFSSRGKLTN
     TADLIRLIIR DEAVHGYYIG YKYQKNMEKI SLGQREELKS FAFDLLLELY DNELQYTDEL
     YAETPWADDV KAFLCYNANK ALMNLGYEPL FPAEMAEVNP AILAALSPNA DENHDFFSGS
     GSSYVMGKAV ETEDEDWNF
//