ID RIR2_ECOLI Reviewed; 376 AA. AC P69924; P00453; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 23-JAN-2007, sequence version 2. DT 27-MAR-2024, entry version 157. DE RecName: Full=Ribonucleoside-diphosphate reductase 1 subunit beta; DE EC=1.17.4.1; DE AltName: Full=Protein B2; DE AltName: Full=Protein R2; DE AltName: Full=Ribonucleotide reductase 1; GN Name=nrdB; Synonyms=ftsB; OrderedLocusNames=b2235, JW2229; OS Escherichia coli (strain K12). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=6087316; DOI=10.1073/pnas.81.14.4294; RA Carlson J., Fuchs J.A., Messing J.; RT "Primary structure of the Escherichia coli ribonucleoside diphosphate RT reductase operon."; RL Proc. Natl. Acad. Sci. U.S.A. 81:4294-4297(1984). RN [2] 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 [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 PROTEIN SEQUENCE OF 2-21. RX PubMed=3511029; DOI=10.1128/jb.165.2.363-366.1986; RA Salowe S.P., Stubbe J.; RT "Cloning, overproduction, and purification of the B2 subunit of RT ribonucleoside-diphosphate reductase."; RL J. Bacteriol. 165:363-366(1986). RN [6] RP ACTIVITY REGULATION, AND 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 [7] RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS). RX PubMed=2190093; DOI=10.1038/345593a0; RA Nordlund P., Sjoeberg B.-M., Eklund H.; RT "Three-dimensional structure of the free radical protein of ribonucleotide RT reductase."; RL Nature 345:593-598(1990). RN [8] RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS). RX PubMed=8331655; DOI=10.1006/jmbi.1993.1374; RA Nordlund P., Eklund H.; RT "Structure and function of the Escherichia coli ribonucleotide reductase RT protein R2."; RL J. Mol. Biol. 232:123-164(1993). RN [9] RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS). RX PubMed=8805591; DOI=10.1016/s0969-2126(96)00112-8; RA Logan D.T., Su X.-D., Aaberg A., Regnstroem K., Hajdu J., Eklund H., RA Nordlund P.; RT "Crystal structure of reduced protein R2 of ribonucleotide reductase: the RT structural basis for oxygen activation at a dinuclear iron site."; RL Structure 4:1053-1064(1996). RN [10] RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS). RX PubMed=9309223; DOI=10.1016/s0969-2126(97)00259-1; RA Eriksson M., Uhlin U., Ramaswamy S., Ekberg M., Regnstroem K., RA Sjoeberg B.-M., Eklund H.; RT "Binding of allosteric effectors to ribonucleotide reductase protein R1: RT reduction of active-site cysteines promotes substrate binding."; RL Structure 5:1077-1092(1997). RN [11] RP X-RAY CRYSTALLOGRAPHY (2.46 ANGSTROMS) OF MUTANT PHE-103. RX PubMed=9558317; DOI=10.1021/bi9728811; RA Tong W., Burdi D., Riggs-Gelasco P., Chen S., Edmondson D., Huynh B.H., RA Stubbe J., Han S., Arvai A., Tainer J.; RT "Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase RT by time-resolved physical biochemical methods and X-ray crystallography."; RL Biochemistry 37:5840-5848(1998). RN [12] RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS). RX PubMed=9692970; DOI=10.1021/bi9806403; RA Logan D.T., DeMare F., Persson B.O., Slaby A., Sjoeberg B.-M., Nordlund P.; RT "Crystal structures of two self-hydroxylating ribonucleotide reductase RT protein R2 mutants: structural basis for the oxygen-insertion step of RT hydroxylation reactions catalyzed by diiron proteins."; RL Biochemistry 37:10798-10807(1998). RN [13] RP X-RAY CRYSTALLOGRAPHY (1.61 ANGSTROMS). RX PubMed=11315567; DOI=10.1007/s007750000205; RA Hogbom M., Andersson M.E., Nordlund P.; RT "Crystal structures of oxidized dinuclear manganese centres in Mn- RT substituted class I ribonucleotide reductase from Escherichia coli: RT carboxylate shifts with implications for O2 activation and radical RT generation."; RL J. Biol. Inorg. Chem. 6:315-323(2001). CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis. CC Catalyzes the biosynthesis of deoxyribonucleotides from the CC corresponding ribonucleotides. R2 contains the tyrosyl radical required CC 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; CC Note=Binds 2 iron ions per subunit.; CC -!- ACTIVITY REGULATION: Inhibited by hydroxyurea, leads to dNTP depletion, CC replication fork arrest and genomic instability. CC {ECO:0000305|PubMed:20005847}. CC -!- SUBUNIT: Tetramer of two alpha (R1) and two beta (R2) subunits. The B1 CC protein is a dimer of alpha subunits. A radical transfer pathway occurs CC between Tyr-123 of R2 and R1. CC -!- INTERACTION: CC P69924; P0A6Y8: dnaK; NbExp=2; IntAct=EBI-555196, EBI-542092; CC P69924; P00452: nrdA; NbExp=11; IntAct=EBI-555196, EBI-370018; CC P69924; P69924: nrdB; NbExp=5; IntAct=EBI-555196, EBI-555196; CC -!- INDUCTION: Induced 4.2-fold by hydroxyurea (at protein level). CC {ECO:0000269|PubMed:20005847}. CC -!- MISCELLANEOUS: E.coli produces two separate class I enzymes. This one CC is the functional enzyme during growth. CC -!- MISCELLANEOUS: A substrate-binding catalytic site, located on R1, is CC formed only in the presence of the second subunit R2. CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase small CC chain family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; K02672; AAA24224.1; -; Genomic_DNA. DR EMBL; U00096; AAC75295.1; -; Genomic_DNA. DR EMBL; AP009048; BAA16054.1; -; Genomic_DNA. DR PIR; A00527; RDEC2R. DR RefSeq; NP_416738.1; NC_000913.3. DR RefSeq; WP_000332037.1; NZ_STEB01000002.1. DR PDB; 1AV8; X-ray; 2.80 A; A/B=2-341. DR PDB; 1BIQ; X-ray; 2.05 A; A/B=2-376. DR PDB; 1JPR; X-ray; 1.88 A; A/B=2-376. DR PDB; 1JQC; X-ray; 1.61 A; A/B=2-376. DR PDB; 1MRR; X-ray; 2.50 A; A/B=2-376. DR PDB; 1MXR; X-ray; 1.42 A; A/B=2-376. DR PDB; 1PFR; X-ray; 2.20 A; A/B=2-341. DR PDB; 1PIM; X-ray; 2.00 A; A/B=2-376. DR PDB; 1PIU; X-ray; 2.20 A; A/B=2-376. DR PDB; 1PIY; X-ray; 1.68 A; A/B=2-376. DR PDB; 1PIZ; X-ray; 1.90 A; A/B=2-376. DR PDB; 1PJ0; X-ray; 1.90 A; A/B=2-376. DR PDB; 1PJ1; X-ray; 1.95 A; A/B=2-376. DR PDB; 1PM2; X-ray; 1.80 A; A/B=2-340. DR PDB; 1R1R; X-ray; 2.90 A; D/E/F/P=357-376. DR PDB; 1R65; X-ray; 1.95 A; A/B=2-376. DR PDB; 1RIB; X-ray; 2.20 A; A/B=2-376. DR PDB; 1RNR; X-ray; 2.50 A; A/B=2-376. DR PDB; 1RSR; X-ray; 2.00 A; A/B=2-376. DR PDB; 1RSV; X-ray; 2.20 A; A/B=2-376. DR PDB; 1XIK; X-ray; 1.70 A; A/B=2-376. DR PDB; 1YFD; X-ray; 1.90 A; A/B=2-376. DR PDB; 2ALX; X-ray; 2.60 A; A=1-340. DR PDB; 2AV8; X-ray; 2.46 A; A/B=2-341. DR PDB; 2R1R; X-ray; 3.00 A; D/E/F/P=357-376. DR PDB; 2X0X; X-ray; 2.30 A; D/E/F/P=357-376. DR PDB; 2XAK; X-ray; 2.80 A; D/E/F/P=357-376. DR PDB; 2XAP; X-ray; 2.10 A; D/E/F/P=357-376. DR PDB; 2XAV; X-ray; 2.80 A; D/E/F/P=357-376. DR PDB; 2XAW; X-ray; 3.10 A; D/E/F/P=357-376. DR PDB; 2XAX; X-ray; 2.75 A; D/E/F/P=357-376. DR PDB; 2XAY; X-ray; 2.65 A; D/E/F/P=357-376. DR PDB; 2XAZ; X-ray; 2.60 A; D/E/F/P=357-376. DR PDB; 2XO4; X-ray; 2.50 A; D/E/F/P=357-376. DR PDB; 2XO5; X-ray; 2.70 A; D/E/F/P=357-376. DR PDB; 2XOF; X-ray; 2.20 A; A/B=2-376. DR PDB; 3R1R; X-ray; 3.00 A; D/E/F/P=357-376. DR PDB; 3UUS; X-ray; 5.65 A; E/F/G/H=2-376. DR PDB; 4ERM; X-ray; 3.95 A; E/F/G/H=2-376. DR PDB; 4ERP; X-ray; 4.45 A; E/F/G/H=2-376. DR PDB; 4R1R; X-ray; 3.20 A; D/E/F/P=357-376. DR PDB; 5CI2; X-ray; 2.25 A; A=2-376. DR PDB; 5CI3; X-ray; 2.40 A; A=2-376. DR PDB; 5CNS; X-ray; 2.98 A; E/F/G/H=2-376. DR PDB; 5CNT; X-ray; 3.25 A; E/F/G/H=2-376. DR PDB; 5CNU; X-ray; 3.40 A; E/F/G/H=2-376. DR PDB; 5CNV; X-ray; 3.20 A; E/F/G/H=2-376. DR PDB; 5R1R; X-ray; 3.10 A; D/E/F/P=357-376. DR PDB; 6R1R; X-ray; 3.10 A; D/E/F/P=357-376. DR PDB; 6W4X; EM; 3.60 A; C/D=1-376. DR PDB; 7AI8; X-ray; 2.10 A; A=1-376. DR PDB; 7AI9; X-ray; 2.00 A; A=1-376. DR PDB; 7BET; X-ray; 2.30 A; A=1-376. DR PDB; 7R1R; X-ray; 3.10 A; D/E/F/P=357-376. DR PDBsum; 1AV8; -. DR PDBsum; 1BIQ; -. DR PDBsum; 1JPR; -. DR PDBsum; 1JQC; -. DR PDBsum; 1MRR; -. DR PDBsum; 1MXR; -. DR PDBsum; 1PFR; -. DR PDBsum; 1PIM; -. DR PDBsum; 1PIU; -. DR PDBsum; 1PIY; -. DR PDBsum; 1PIZ; -. DR PDBsum; 1PJ0; -. DR PDBsum; 1PJ1; -. DR PDBsum; 1PM2; -. DR PDBsum; 1R1R; -. DR PDBsum; 1R65; -. DR PDBsum; 1RIB; -. DR PDBsum; 1RNR; -. DR PDBsum; 1RSR; -. DR PDBsum; 1RSV; -. DR PDBsum; 1XIK; -. DR PDBsum; 1YFD; -. DR PDBsum; 2ALX; -. DR PDBsum; 2AV8; -. DR PDBsum; 2R1R; -. DR PDBsum; 2X0X; -. DR PDBsum; 2XAK; -. DR PDBsum; 2XAP; -. DR PDBsum; 2XAV; -. DR PDBsum; 2XAW; -. DR PDBsum; 2XAX; -. DR PDBsum; 2XAY; -. DR PDBsum; 2XAZ; -. DR PDBsum; 2XO4; -. DR PDBsum; 2XO5; -. DR PDBsum; 2XOF; -. DR PDBsum; 3R1R; -. DR PDBsum; 3UUS; -. DR PDBsum; 4ERM; -. DR PDBsum; 4ERP; -. DR PDBsum; 4R1R; -. DR PDBsum; 5CI2; -. DR PDBsum; 5CI3; -. DR PDBsum; 5CNS; -. DR PDBsum; 5CNT; -. DR PDBsum; 5CNU; -. DR PDBsum; 5CNV; -. DR PDBsum; 5R1R; -. DR PDBsum; 6R1R; -. DR PDBsum; 6W4X; -. DR PDBsum; 7AI8; -. DR PDBsum; 7AI9; -. DR PDBsum; 7BET; -. DR PDBsum; 7R1R; -. DR AlphaFoldDB; P69924; -. DR EMDB; EMD-21540; -. DR SMR; P69924; -. DR BioGRID; 4260492; 56. DR ComplexPortal; CPX-1075; Ribonucleoside-diphosphate reductase 1 complex. DR DIP; DIP-36213N; -. DR IntAct; P69924; 13. DR STRING; 511145.b2235; -. DR DrugBank; DB09462; Glycerin. DR jPOST; P69924; -. DR PaxDb; 511145-b2235; -. DR EnsemblBacteria; AAC75295; AAC75295; b2235. DR GeneID; 75058011; -. DR GeneID; 946732; -. DR KEGG; ecj:JW2229; -. DR KEGG; eco:b2235; -. DR PATRIC; fig|511145.12.peg.2324; -. DR EchoBASE; EB0655; -. DR eggNOG; COG0208; Bacteria. DR HOGENOM; CLU_062403_0_0_6; -. DR InParanoid; P69924; -. DR OMA; LEPMFLG; -. DR OrthoDB; 9765051at2; -. DR PhylomeDB; P69924; -. DR BioCyc; EcoCyc:NRDB-MONOMER; -. DR BioCyc; MetaCyc:NRDB-MONOMER; -. DR BRENDA; 1.17.4.1; 2026. DR SABIO-RK; P69924; -. DR EvolutionaryTrace; P69924; -. DR PRO; PR:P69924; -. DR Proteomes; UP000000318; Chromosome. DR Proteomes; UP000000625; Chromosome. DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki. DR GO; GO:0005829; C:cytosol; IDA:EcoCyc. DR GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IDA:EcoliWiki. DR GO; GO:0042802; F:identical protein binding; IPI:IntAct. DR GO; GO:0005506; F:iron 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; IDA:ComplexPortal. DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IDA:EcoliWiki. DR GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IDA:EcoliWiki. DR GO; GO:0009185; P:ribonucleoside diphosphate metabolic process; IDA:ComplexPortal. DR CDD; cd01049; RNRR2; 1. DR DisProt; DP00107; -. DR Gene3D; 1.10.620.20; Ribonucleotide Reductase, subunit A; 1. DR InterPro; IPR009078; Ferritin-like_SF. DR InterPro; IPR012348; RNR-like. DR InterPro; IPR033909; RNR_small. DR InterPro; IPR030475; RNR_small_AS. DR InterPro; IPR000358; RNR_small_fam. 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 SUPFAM; SSF47240; Ferritin-like; 1. DR PROSITE; PS00368; RIBORED_SMALL; 1. PE 1: Evidence at protein level; KW 3D-structure; Deoxyribonucleotide synthesis; Direct protein sequencing; KW Iron; Metal-binding; Oxidoreductase; Reference proteome. FT INIT_MET 1 FT /note="Removed" FT /evidence="ECO:0000269|PubMed:3511029" FT CHAIN 2..376 FT /note="Ribonucleoside-diphosphate reductase 1 subunit beta" FT /id="PRO_0000190476" FT ACT_SITE 123 FT BINDING 85 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_label="1" FT BINDING 116 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_label="1" FT BINDING 116 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_label="2" FT BINDING 119 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_label="1" FT BINDING 205 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_label="2" FT BINDING 239 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_label="2" FT BINDING 242 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_label="2" FT HELIX 13..15 FT /evidence="ECO:0007829|PDB:1JQC" FT STRAND 18..22 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 35..46 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 51..53 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 59..64 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 68..95 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 97..99 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 103..128 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 134..143 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 145..151 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 154..171 FT /evidence="ECO:0007829|PDB:1MXR" FT STRAND 173..178 FT /evidence="ECO:0007829|PDB:1MXR" FT STRAND 181..185 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 187..206 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 208..221 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 226..255 FT /evidence="ECO:0007829|PDB:1MXR" FT STRAND 256..258 FT /evidence="ECO:0007829|PDB:1PJ1" FT HELIX 260..268 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 270..291 FT /evidence="ECO:0007829|PDB:1MXR" FT TURN 292..294 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 302..319 FT /evidence="ECO:0007829|PDB:1MXR" FT HELIX 334..338 FT /evidence="ECO:0007829|PDB:1MXR" FT STRAND 343..345 FT /evidence="ECO:0007829|PDB:5CI2" FT HELIX 368..371 FT /evidence="ECO:0007829|PDB:2XAP" SQ SEQUENCE 376 AA; 43517 MW; BF2D9A49B643E84A CRC64; MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR PEEVDVSRDR IDYQALPEHE KHIFISNLKY QTLLDSIQGR SPNVALLPLI SIPELETWVE TWAFSETIHS RSYTHIIRNI VNDPSVVFDD IVTNEQIQKR AEGISSYYDE LIEMTSYWHL LGEGTHTVNG KTVTVSLREL KKKLYLCLMS VNALEAIRFY VSFACSFAFA ERELMEGNAK IIRLIARDEA LHLTGTQHML NLLRSGADDP EMAEIAEECK QECYDLFVQA AQQEKDWADY LFRDGSMIGL NKDILCQYVE YITNIRMQAV GLDLPFQTRS NPIPWINTWL VSDNVQVAPQ EVEVSSYLVG QIDSEVDTDD LSNFQL //