RIR4_ECOLI
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 03-AUG-2022, entry version 168.
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; Proteobacteria; 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 -!- PATHWAY: Genetic information processing; DNA replication.
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; P37146; -.
DR PRIDE; P37146; -.
DR EnsemblBacteria; AAC75723; AAC75723; b2676.
DR EnsemblBacteria; BAA16541; BAA16541; BAA16541.
DR GeneID; 66673454; -.
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; IGYKYQR; -.
DR PhylomeDB; P37146; -.
DR BioCyc; EcoCyc:NRDF-MON; -.
DR BioCyc; MetaCyc:NRDF-MON; -.
DR BRENDA; 1.17.4.1; 2026.
DR UniPathway; UPA00326; -.
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:0009263; P:deoxyribonucleotide biosynthetic process; IGI:EcoliWiki.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR CDD; cd01049; RNRR2; 1.
DR Gene3D; 1.10.620.20; -; 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 PANTHER; PTHR23409; PTHR23409; 1.
DR Pfam; PF00268; Ribonuc_red_sm; 1.
DR PIRSF; PIRSF000355; NrdB; 1.
DR SUPFAM; SSF47240; SSF47240; 1.
DR TIGRFAMs; TIGR04171; RNR_1b_NrdF; 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
