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P69924 (RIR2_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 96. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribonucleoside-diphosphate reductase 1 subunit beta

EC=1.17.4.1
Alternative name(s):
Protein B2
Protein R2
Ribonucleotide reductase 1
Gene names
Name:nrdB
Synonyms:ftsB
Ordered Locus Names:b2235, JW2229
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length376 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

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 + H2O = ribonucleoside diphosphate + thioredoxin.

Cofactor

Binds 2 iron ions per subunit.

Pathway

Genetic information processing; DNA replication.

Subunit structure

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.

Miscellaneous

E.coli produces two separate class I enzymes. This one is the functional enzyme during growth.

A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2.

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase small chain family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

itself2EBI-555196,EBI-555196

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.5
Chain2 – 376375Ribonucleoside-diphosphate reductase 1 subunit beta
PRO_0000190476

Sites

Active site1231
Metal binding851Iron 1
Metal binding1161Iron 1
Metal binding1161Iron 2
Metal binding1191Iron 1
Metal binding2051Iron 2
Metal binding2391Iron 2
Metal binding2421Iron 2

Secondary structure

............................................. 376
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P69924 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: BF2D9A49B643E84A

FASTA37643,517
        10         20         30         40         50         60 
MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR PEEVDVSRDR 

        70         80         90        100        110        120 
IDYQALPEHE KHIFISNLKY QTLLDSIQGR SPNVALLPLI SIPELETWVE TWAFSETIHS 

       130        140        150        160        170        180 
RSYTHIIRNI VNDPSVVFDD IVTNEQIQKR AEGISSYYDE LIEMTSYWHL LGEGTHTVNG 

       190        200        210        220        230        240 
KTVTVSLREL KKKLYLCLMS VNALEAIRFY VSFACSFAFA ERELMEGNAK IIRLIARDEA 

       250        260        270        280        290        300 
LHLTGTQHML NLLRSGADDP EMAEIAEECK QECYDLFVQA AQQEKDWADY LFRDGSMIGL 

       310        320        330        340        350        360 
NKDILCQYVE YITNIRMQAV GLDLPFQTRS NPIPWINTWL VSDNVQVAPQ EVEVSSYLVG 

       370 
QIDSEVDTDD LSNFQL 

« Hide

References

« Hide 'large scale' references
[1]"Primary structure of the Escherichia coli ribonucleoside diphosphate reductase operon."
Carlson J., Fuchs J.A., Messing J.
Proc. Natl. Acad. Sci. U.S.A. 81:4294-4297(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"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."
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. expand/collapse author list , 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.
DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
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.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Cloning, overproduction, and purification of the B2 subunit of ribonucleoside-diphosphate reductase."
Salowe S.P., Stubbe J.
J. Bacteriol. 165:363-366(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-21.
[6]"Three-dimensional structure of the free radical protein of ribonucleotide reductase."
Nordlund P., Sjoeberg B.-M., Eklund H.
Nature 345:593-598(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[7]"Structure and function of the Escherichia coli ribonucleotide reductase protein R2."
Nordlund P., Eklund H.
J. Mol. Biol. 232:123-164(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[8]"Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site."
Logan D.T., Su X.-D., Aaberg A., Regnstroem K., Hajdu J., Eklund H., Nordlund P.
Structure 4:1053-1064(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
[9]"Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding."
Eriksson M., Uhlin U., Ramaswamy S., Ekberg M., Regnstroem K., Sjoeberg B.-M., Eklund H.
Structure 5:1077-1092(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
[10]"Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-ray crystallography."
Tong W., Burdi D., Riggs-Gelasco P., Chen S., Edmondson D., Huynh B.H., Stubbe J., Han S., Arvai A., Tainer J.
Biochemistry 37:5840-5848(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.46 ANGSTROMS) OF MUTANT PHE-103.
[11]"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."
Logan D.T., DeMare F., Persson B.O., Slaby A., Sjoeberg B.-M., Nordlund P.
Biochemistry 37:10798-10807(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS).
[12]"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."
Hogbom M., Andersson M.E., Nordlund P.
J. Biol. Inorg. Chem. 6:315-323(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.61 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
K02672 Genomic DNA. Translation: AAA24224.1.
U00096 Genomic DNA. Translation: AAC75295.1.
AP009048 Genomic DNA. Translation: BAA16054.1.
PIRRDEC2R. A00527.
RefSeqNP_416738.1. NC_000913.3.
YP_490474.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AV8X-ray2.80A/B2-341[»]
1BIQX-ray2.05A/B2-376[»]
1JPRX-ray1.88A/B2-376[»]
1JQCX-ray1.61A/B2-376[»]
1MRRX-ray2.50A/B2-375[»]
1MXRX-ray1.42A/B2-375[»]
1PFRX-ray2.20A/B2-341[»]
1PIMX-ray2.00A/B2-375[»]
1PIUX-ray2.20A/B2-375[»]
1PIYX-ray1.68A/B2-375[»]
1PIZX-ray1.90A/B2-375[»]
1PJ0X-ray1.90A/B2-375[»]
1PJ1X-ray1.95A/B2-375[»]
1PM2X-ray1.80A/B2-339[»]
1R1RX-ray2.90D/E/F/P357-376[»]
1R65X-ray1.95A/B2-375[»]
1RIBX-ray2.20A/B2-376[»]
1RNRX-ray2.50A/B2-375[»]
1RSRX-ray2.00A/B2-375[»]
1RSVX-ray2.20A/B2-375[»]
1XIKX-ray1.70A/B2-376[»]
1YFDX-ray1.90A/B2-375[»]
2ALXX-ray2.60A1-340[»]
2AV8X-ray2.46A/B2-341[»]
2R1RX-ray3.00D/E/F/P357-376[»]
2X0XX-ray2.30D/E/F/P357-376[»]
2XAKX-ray2.80D/E/F/P357-376[»]
2XAPX-ray2.10D/E/F/P357-376[»]
2XAVX-ray2.80D/E/F/P357-376[»]
2XAWX-ray3.10D/E/F/P357-376[»]
2XAXX-ray2.75D/E/F/P357-376[»]
2XAYX-ray2.65D/E/F/P357-376[»]
2XAZX-ray2.60D/E/F/P357-376[»]
2XO4X-ray2.50D/E/F/P357-376[»]
2XO5X-ray2.70D/E/F/P357-376[»]
2XOFX-ray2.20A/B2-376[»]
3R1RX-ray3.00D/E/F/P357-376[»]
3UUSX-ray5.65E/F/G/H2-376[»]
4ERMX-ray3.95E/F/G/H2-376[»]
4ERPX-ray4.45E/F/G/H2-376[»]
4R1RX-ray3.20D/E/F/P357-376[»]
5R1RX-ray3.10D/E/F/P357-376[»]
6R1RX-ray3.10D/E/F/P357-376[»]
7R1RX-ray3.10D/E/F/P357-376[»]
DisProtDP00107.
ProteinModelPortalP69924.
SMRP69924. Positions 2-376.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36213N.
IntActP69924. 12 interactions.
MINTMINT-1269534.
STRING511145.b2235.

Proteomic databases

PaxDbP69924.
PRIDEP69924.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75295; AAC75295; b2235.
BAA16054; BAA16054; BAA16054.
GeneID12931498.
946732.
KEGGecj:Y75_p2197.
eco:b2235.
PATRIC32119829. VBIEscCol129921_2324.

Organism-specific databases

EchoBASEEB0655.
EcoGeneEG10661. nrdB.

Phylogenomic databases

eggNOGCOG0208.
HOGENOMHOG000278087.
KOK00526.
OMAWIETWAF.
OrthoDBEOG6J48J7.
ProtClustDBPRK09101.

Enzyme and pathway databases

BioCycEcoCyc:NRDB-MONOMER.
ECOL316407:JW2229-MONOMER.
MetaCyc:NRDB-MONOMER.
SABIO-RKP69924.
UniPathwayUPA00326.

Gene expression databases

GenevestigatorP69924.

Family and domain databases

Gene3D1.10.620.20. 1 hit.
InterProIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR000358. RNR_small.
[Graphical view]
PANTHERPTHR23409. PTHR23409. 1 hit.
PfamPF00268. Ribonuc_red_sm. 2 hits.
[Graphical view]
SUPFAMSSF47240. SSF47240. 1 hit.
PROSITEPS00368. RIBORED_SMALL. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP69924.
PROP69924.

Entry information

Entry nameRIR2_ECOLI
AccessionPrimary (citable) accession number: P69924
Secondary accession number(s): P00453
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: March 19, 2014
This is version 96 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene