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Ribonucleoside-diphosphate reductase 1 subunit beta (EC 1.17.4.1) (Protein B2) (Protein R2) (Ribonucleotide reductase 1)

 RIR2_ECOLI              Reviewed;         376 AA.
P69924; P00453;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
05-JUL-2017, entry version 122.
RecName: Full=Ribonucleoside-diphosphate reductase 1 subunit beta;
EC=1.17.4.1;
AltName: Full=Protein B2;
AltName: Full=Protein R2;
AltName: Full=Ribonucleotide reductase 1;
Name=nrdB; Synonyms=ftsB; OrderedLocusNames=b2235, JW2229;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=6087316; DOI=10.1073/pnas.81.14.4294;
Carlson J., Fuchs J.A., Messing J.;
"Primary structure of the Escherichia coli ribonucleoside diphosphate
reductase operon.";
Proc. Natl. Acad. Sci. U.S.A. 81:4294-4297(1984).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9205837; DOI=10.1093/dnares/4.2.91;
Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K.,
Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N.,
Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H.,
Oshima T., Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S.,
Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C.,
Yamagata S., Horiuchi T.;
"Construction of a contiguous 874-kb sequence of the Escherichia coli-
K12 genome corresponding to 50.0-68.8 min on the linkage map and
analysis of its sequence features.";
DNA Res. 4:91-113(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
PROTEIN SEQUENCE OF 2-21.
PubMed=3511029; DOI=10.1128/jb.165.2.363-366.1986;
Salowe S.P., Stubbe J.;
"Cloning, overproduction, and purification of the B2 subunit of
ribonucleoside-diphosphate reductase.";
J. Bacteriol. 165:363-366(1986).
[6]
ENZYME REGULATION, AND INDUCTION BY HYDROXYUREA.
STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
PubMed=20005847; DOI=10.1016/j.molcel.2009.11.024;
Davies B.W., Kohanski M.A., Simmons L.A., Winkler J.A., Collins J.J.,
Walker G.C.;
"Hydroxyurea induces hydroxyl radical-mediated cell death in
Escherichia coli.";
Mol. Cell 36:845-860(2009).
[7]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
PubMed=2190093; DOI=10.1038/345593a0;
Nordlund P., Sjoeberg B.-M., Eklund H.;
"Three-dimensional structure of the free radical protein of
ribonucleotide reductase.";
Nature 345:593-598(1990).
[8]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
PubMed=8331655; DOI=10.1006/jmbi.1993.1374;
Nordlund P., Eklund H.;
"Structure and function of the Escherichia coli ribonucleotide
reductase protein R2.";
J. Mol. Biol. 232:123-164(1993).
[9]
X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
PubMed=8805591; DOI=10.1016/S0969-2126(96)00112-8;
Logan D.T., Su X.-D., Aaberg A., Regnstroem K., Hajdu J., Eklund H.,
Nordlund P.;
"Crystal structure of reduced protein R2 of ribonucleotide reductase:
the structural basis for oxygen activation at a dinuclear iron site.";
Structure 4:1053-1064(1996).
[10]
X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
PubMed=9309223; DOI=10.1016/S0969-2126(97)00259-1;
Eriksson M., Uhlin U., Ramaswamy S., Ekberg M., Regnstroem K.,
Sjoeberg B.-M., Eklund H.;
"Binding of allosteric effectors to ribonucleotide reductase protein
R1: reduction of active-site cysteines promotes substrate binding.";
Structure 5:1077-1092(1997).
[11]
X-RAY CRYSTALLOGRAPHY (2.46 ANGSTROMS) OF MUTANT PHE-103.
PubMed=9558317; DOI=10.1021/bi9728811;
Tong W., Burdi D., Riggs-Gelasco P., Chen S., Edmondson D.,
Huynh B.H., Stubbe J., Han S., Arvai A., Tainer J.;
"Characterization of Y122F R2 of Escherichia coli ribonucleotide
reductase by time-resolved physical biochemical methods and X-ray
crystallography.";
Biochemistry 37:5840-5848(1998).
[12]
X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS).
PubMed=9692970; DOI=10.1021/bi9806403;
Logan D.T., DeMare F., Persson B.O., Slaby A., Sjoeberg B.-M.,
Nordlund P.;
"Crystal structures of two self-hydroxylating ribonucleotide reductase
protein R2 mutants: structural basis for the oxygen-insertion step of
hydroxylation reactions catalyzed by diiron proteins.";
Biochemistry 37:10798-10807(1998).
[13]
X-RAY CRYSTALLOGRAPHY (1.61 ANGSTROMS).
PubMed=11315567; DOI=10.1007/s007750000205;
Hogbom M., Andersson M.E., Nordlund P.;
"Crystal structures of oxidized dinuclear manganese centres in Mn-
substituted class I ribonucleotide reductase from Escherichia coli:
carboxylate shifts with implications for O2 activation and radical
generation.";
J. Biol. Inorg. Chem. 6:315-323(2001).
-!- FUNCTION: Provides the precursors necessary for DNA synthesis.
Catalyzes the biosynthesis of deoxyribonucleotides from the
corresponding ribonucleotides. R2 contains the tyrosyl radical
required for catalysis.
-!- CATALYTIC ACTIVITY: 2'-deoxyribonucleoside diphosphate +
thioredoxin disulfide + H(2)O = ribonucleoside diphosphate +
thioredoxin. {ECO:0000255|PROSITE-ProRule:PRU10014}.
-!- COFACTOR:
Name=Fe cation; Xref=ChEBI:CHEBI:24875;
Note=Binds 2 iron ions per subunit.;
-!- ENZYME REGULATION: Inhibited by hydroxyurea, leads to dNTP
depletion, replication fork arrest and genomic instability.
{ECO:0000305|PubMed:20005847}.
-!- PATHWAY: Genetic information processing; DNA replication.
-!- SUBUNIT: Tetramer of two alpha (R1) and two beta (R2) subunits.
The B1 protein is a dimer of alpha subunits. A radical transfer
pathway occurs between Tyr-123 of R2 and R1.
-!- INTERACTION:
Self; NbExp=2; IntAct=EBI-555196, EBI-555196;
-!- INDUCTION: Induced 4.2-fold by hydroxyurea (at protein level).
{ECO:0000269|PubMed:20005847}.
-!- MISCELLANEOUS: E.coli produces two separate class I enzymes. This
one is the functional enzyme during growth.
-!- MISCELLANEOUS: A substrate-binding catalytic site, located on R1,
is formed only in the presence of the second subunit R2.
-!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase
small chain family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; K02672; AAA24224.1; -; Genomic_DNA.
EMBL; U00096; AAC75295.1; -; Genomic_DNA.
EMBL; AP009048; BAA16054.1; -; Genomic_DNA.
PIR; A00527; RDEC2R.
RefSeq; NP_416738.1; NC_000913.3.
RefSeq; WP_000332037.1; NZ_LN832404.1.
PDB; 1AV8; X-ray; 2.80 A; A/B=2-341.
PDB; 1BIQ; X-ray; 2.05 A; A/B=2-376.
PDB; 1JPR; X-ray; 1.88 A; A/B=2-376.
PDB; 1JQC; X-ray; 1.61 A; A/B=2-376.
PDB; 1MRR; X-ray; 2.50 A; A/B=2-376.
PDB; 1MXR; X-ray; 1.42 A; A/B=2-376.
PDB; 1PFR; X-ray; 2.20 A; A/B=2-341.
PDB; 1PIM; X-ray; 2.00 A; A/B=2-376.
PDB; 1PIU; X-ray; 2.20 A; A/B=2-376.
PDB; 1PIY; X-ray; 1.68 A; A/B=2-376.
PDB; 1PIZ; X-ray; 1.90 A; A/B=2-376.
PDB; 1PJ0; X-ray; 1.90 A; A/B=2-376.
PDB; 1PJ1; X-ray; 1.95 A; A/B=2-376.
PDB; 1PM2; X-ray; 1.80 A; A/B=2-340.
PDB; 1R1R; X-ray; 2.90 A; D/E/F/P=357-376.
PDB; 1R65; X-ray; 1.95 A; A/B=2-376.
PDB; 1RIB; X-ray; 2.20 A; A/B=2-376.
PDB; 1RNR; X-ray; 2.50 A; A/B=2-376.
PDB; 1RSR; X-ray; 2.00 A; A/B=2-376.
PDB; 1RSV; X-ray; 2.20 A; A/B=2-376.
PDB; 1XIK; X-ray; 1.70 A; A/B=2-376.
PDB; 1YFD; X-ray; 1.90 A; A/B=2-376.
PDB; 2ALX; X-ray; 2.60 A; A=1-340.
PDB; 2AV8; X-ray; 2.46 A; A/B=2-341.
PDB; 2R1R; X-ray; 3.00 A; D/E/F/P=357-376.
PDB; 2X0X; X-ray; 2.30 A; D/E/F/P=357-376.
PDB; 2XAK; X-ray; 2.80 A; D/E/F/P=357-376.
PDB; 2XAP; X-ray; 2.10 A; D/E/F/P=357-376.
PDB; 2XAV; X-ray; 2.80 A; D/E/F/P=357-376.
PDB; 2XAW; X-ray; 3.10 A; D/E/F/P=357-376.
PDB; 2XAX; X-ray; 2.75 A; D/E/F/P=357-376.
PDB; 2XAY; X-ray; 2.65 A; D/E/F/P=357-376.
PDB; 2XAZ; X-ray; 2.60 A; D/E/F/P=357-376.
PDB; 2XO4; X-ray; 2.50 A; D/E/F/P=357-376.
PDB; 2XO5; X-ray; 2.70 A; D/E/F/P=357-376.
PDB; 2XOF; X-ray; 2.20 A; A/B=2-376.
PDB; 3R1R; X-ray; 3.00 A; D/E/F/P=357-376.
PDB; 3UUS; X-ray; 5.65 A; E/F/G/H=2-376.
PDB; 4ERM; X-ray; 3.95 A; E/F/G/H=2-376.
PDB; 4ERP; X-ray; 4.45 A; E/F/G/H=2-376.
PDB; 4R1R; X-ray; 3.20 A; D/E/F/P=357-376.
PDB; 5CI2; X-ray; 2.25 A; A=2-376.
PDB; 5CI3; X-ray; 2.40 A; A=2-376.
PDB; 5CNS; X-ray; 2.98 A; E/F/G/H=2-376.
PDB; 5CNT; X-ray; 3.25 A; E/F/G/H=2-376.
PDB; 5CNU; X-ray; 3.40 A; E/F/G/H=2-376.
PDB; 5CNV; X-ray; 3.20 A; E/F/G/H=2-376.
PDB; 5R1R; X-ray; 3.10 A; D/E/F/P=357-376.
PDB; 6R1R; X-ray; 3.10 A; D/E/F/P=357-376.
PDB; 7R1R; X-ray; 3.10 A; D/E/F/P=357-376.
PDBsum; 1AV8; -.
PDBsum; 1BIQ; -.
PDBsum; 1JPR; -.
PDBsum; 1JQC; -.
PDBsum; 1MRR; -.
PDBsum; 1MXR; -.
PDBsum; 1PFR; -.
PDBsum; 1PIM; -.
PDBsum; 1PIU; -.
PDBsum; 1PIY; -.
PDBsum; 1PIZ; -.
PDBsum; 1PJ0; -.
PDBsum; 1PJ1; -.
PDBsum; 1PM2; -.
PDBsum; 1R1R; -.
PDBsum; 1R65; -.
PDBsum; 1RIB; -.
PDBsum; 1RNR; -.
PDBsum; 1RSR; -.
PDBsum; 1RSV; -.
PDBsum; 1XIK; -.
PDBsum; 1YFD; -.
PDBsum; 2ALX; -.
PDBsum; 2AV8; -.
PDBsum; 2R1R; -.
PDBsum; 2X0X; -.
PDBsum; 2XAK; -.
PDBsum; 2XAP; -.
PDBsum; 2XAV; -.
PDBsum; 2XAW; -.
PDBsum; 2XAX; -.
PDBsum; 2XAY; -.
PDBsum; 2XAZ; -.
PDBsum; 2XO4; -.
PDBsum; 2XO5; -.
PDBsum; 2XOF; -.
PDBsum; 3R1R; -.
PDBsum; 3UUS; -.
PDBsum; 4ERM; -.
PDBsum; 4ERP; -.
PDBsum; 4R1R; -.
PDBsum; 5CI2; -.
PDBsum; 5CI3; -.
PDBsum; 5CNS; -.
PDBsum; 5CNT; -.
PDBsum; 5CNU; -.
PDBsum; 5CNV; -.
PDBsum; 5R1R; -.
PDBsum; 6R1R; -.
PDBsum; 7R1R; -.
DisProt; DP00107; -.
ProteinModelPortal; P69924; -.
SMR; P69924; -.
BioGrid; 4260492; 50.
DIP; DIP-36213N; -.
IntAct; P69924; 12.
MINT; MINT-1269534; -.
STRING; 316385.ECDH10B_2394; -.
DrugBank; DB04077; Glycerol.
PaxDb; P69924; -.
PRIDE; P69924; -.
EnsemblBacteria; AAC75295; AAC75295; b2235.
EnsemblBacteria; BAA16054; BAA16054; BAA16054.
GeneID; 946732; -.
KEGG; ecj:JW2229; -.
KEGG; eco:b2235; -.
PATRIC; fig|511145.12.peg.2324; -.
EchoBASE; EB0655; -.
EcoGene; EG10661; nrdB.
eggNOG; ENOG4105E05; Bacteria.
eggNOG; COG0208; LUCA.
HOGENOM; HOG000278087; -.
InParanoid; P69924; -.
KO; K00526; -.
PhylomeDB; P69924; -.
BioCyc; EcoCyc:NRDB-MONOMER; -.
BioCyc; MetaCyc:NRDB-MONOMER; -.
BRENDA; 1.17.4.1; 2026.
SABIO-RK; P69924; -.
UniPathway; UPA00326; -.
EvolutionaryTrace; P69924; -.
PRO; PR:P69924; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
GO; GO:0005829; C:cytosol; IDA:UniProtKB.
GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IDA:EcoliWiki.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0005506; F:iron ion binding; IDA:EcoCyc.
GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:UniProtKB-EC.
GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IDA:EcoliWiki.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IDA:EcoliWiki.
CDD; cd01049; RNRR2; 1.
InterPro; IPR009078; Ferritin-like_SF.
InterPro; IPR033909; RNR_small.
InterPro; IPR030475; RNR_small_AS.
InterPro; IPR000358; RNR_small_fam.
PANTHER; PTHR23409; PTHR23409; 1.
Pfam; PF00268; Ribonuc_red_sm; 1.
SUPFAM; SSF47240; SSF47240; 1.
PROSITE; PS00368; RIBORED_SMALL; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Direct protein sequencing;
DNA replication; Iron; Metal-binding; Oxidoreductase;
Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:3511029}.
CHAIN 2 376 Ribonucleoside-diphosphate reductase 1
subunit beta.
/FTId=PRO_0000190476.
ACT_SITE 123 123
METAL 85 85 Iron 1.
METAL 116 116 Iron 1.
METAL 116 116 Iron 2.
METAL 119 119 Iron 1.
METAL 205 205 Iron 2.
METAL 239 239 Iron 2.
METAL 242 242 Iron 2.
HELIX 13 15 {ECO:0000244|PDB:1JQC}.
STRAND 18 22 {ECO:0000244|PDB:1MXR}.
HELIX 35 46 {ECO:0000244|PDB:1MXR}.
HELIX 51 53 {ECO:0000244|PDB:1MXR}.
HELIX 59 64 {ECO:0000244|PDB:1MXR}.
HELIX 68 95 {ECO:0000244|PDB:1MXR}.
HELIX 97 99 {ECO:0000244|PDB:1MXR}.
HELIX 103 128 {ECO:0000244|PDB:1MXR}.
HELIX 134 143 {ECO:0000244|PDB:1MXR}.
HELIX 145 151 {ECO:0000244|PDB:1MXR}.
HELIX 154 171 {ECO:0000244|PDB:1MXR}.
STRAND 173 178 {ECO:0000244|PDB:1MXR}.
STRAND 181 185 {ECO:0000244|PDB:1MXR}.
HELIX 187 206 {ECO:0000244|PDB:1MXR}.
HELIX 208 221 {ECO:0000244|PDB:1MXR}.
HELIX 226 255 {ECO:0000244|PDB:1MXR}.
STRAND 256 258 {ECO:0000244|PDB:1PJ1}.
HELIX 260 268 {ECO:0000244|PDB:1MXR}.
HELIX 270 291 {ECO:0000244|PDB:1MXR}.
TURN 292 294 {ECO:0000244|PDB:1MXR}.
HELIX 302 319 {ECO:0000244|PDB:1MXR}.
HELIX 334 338 {ECO:0000244|PDB:1MXR}.
HELIX 368 371 {ECO:0000244|PDB:2XAP}.
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


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