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P69924

- RIR2_ECOLI

UniProt

P69924 - RIR2_ECOLI

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Protein

Ribonucleoside-diphosphate reductase 1 subunit beta

Gene

nrdB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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 activityi

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.PROSITE-ProRule annotation

Cofactori

Fe cationNote: Binds 2 iron ions per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi85 – 851Iron 1
Metal bindingi116 – 1161Iron 1
Metal bindingi116 – 1161Iron 2
Metal bindingi119 – 1191Iron 1
Active sitei123 – 1231
Metal bindingi205 – 2051Iron 2
Metal bindingi239 – 2391Iron 2
Metal bindingi242 – 2421Iron 2

GO - Molecular functioni

  1. identical protein binding Source: IntAct
  2. iron ion binding Source: EcoCyc
  3. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. deoxyribonucleoside diphosphate metabolic process Source: InterPro
  2. deoxyribonucleotide biosynthetic process Source: EcoliWiki
  3. DNA replication Source: UniProtKB-UniPathway
  4. nucleobase-containing small molecule interconversion Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:NRDB-MONOMER.
ECOL316407:JW2229-MONOMER.
MetaCyc:NRDB-MONOMER.
SABIO-RKP69924.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase 1 subunit beta (EC:1.17.4.1)
Alternative name(s):
Protein B2
Protein R2
Ribonucleotide reductase 1
Gene namesi
Name:nrdB
Synonyms:ftsB
Ordered Locus Names:b2235, JW2229
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10661. nrdB.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: EcoliWiki
  2. cytosol Source: UniProtKB
  3. ribonucleoside-diphosphate reductase complex Source: EcoliWiki
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 376375Ribonucleoside-diphosphate reductase 1 subunit betaPRO_0000190476Add
BLAST

Proteomic databases

PaxDbiP69924.
PRIDEiP69924.

Expressioni

Gene expression databases

GenevestigatoriP69924.

Interactioni

Subunit structurei

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.

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-555196,EBI-555196

Protein-protein interaction databases

DIPiDIP-36213N.
IntActiP69924. 12 interactions.
MINTiMINT-1269534.
STRINGi511145.b2235.

Structurei

Secondary structure

1
376
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 153Combined sources
Beta strandi18 – 225Combined sources
Helixi35 – 4612Combined sources
Helixi51 – 533Combined sources
Helixi59 – 646Combined sources
Helixi68 – 9528Combined sources
Helixi97 – 993Combined sources
Helixi103 – 12826Combined sources
Helixi134 – 14310Combined sources
Helixi145 – 1517Combined sources
Helixi154 – 17118Combined sources
Beta strandi173 – 1786Combined sources
Beta strandi181 – 1855Combined sources
Helixi187 – 20620Combined sources
Helixi208 – 22114Combined sources
Helixi226 – 25530Combined sources
Beta strandi256 – 2583Combined sources
Helixi260 – 2689Combined sources
Helixi270 – 29122Combined sources
Turni292 – 2943Combined sources
Helixi302 – 31918Combined sources
Helixi334 – 3385Combined sources
Helixi368 – 3714Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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/B2-376[»]
1MXRX-ray1.42A/B2-376[»]
1PFRX-ray2.20A/B2-341[»]
1PIMX-ray2.00A/B2-376[»]
1PIUX-ray2.20A/B2-376[»]
1PIYX-ray1.68A/B2-376[»]
1PIZX-ray1.90A/B2-376[»]
1PJ0X-ray1.90A/B2-376[»]
1PJ1X-ray1.95A/B2-376[»]
1PM2X-ray1.80A/B2-340[»]
1R1RX-ray2.90D/E/F/P357-376[»]
1R65X-ray1.95A/B2-376[»]
1RIBX-ray2.20A/B2-376[»]
1RNRX-ray2.50A/B2-376[»]
1RSRX-ray2.00A/B2-376[»]
1RSVX-ray2.20A/B2-376[»]
1XIKX-ray1.70A/B2-376[»]
1YFDX-ray1.90A/B2-376[»]
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[»]
DisProtiDP00107.
ProteinModelPortaliP69924.
SMRiP69924. Positions 2-376.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69924.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0208.
HOGENOMiHOG000278087.
InParanoidiP69924.
KOiK00526.
OMAiWIETWAF.
OrthoDBiEOG6J48J7.
PhylomeDBiP69924.

Family and domain databases

Gene3Di1.10.620.20. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR000358. RNR_small.
[Graphical view]
PANTHERiPTHR23409. PTHR23409. 1 hit.
PfamiPF00268. Ribonuc_red_sm. 2 hits.
[Graphical view]
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS00368. RIBORED_SMALL. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P69924-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR
60 70 80 90 100
PEEVDVSRDR IDYQALPEHE KHIFISNLKY QTLLDSIQGR SPNVALLPLI
110 120 130 140 150
SIPELETWVE TWAFSETIHS RSYTHIIRNI VNDPSVVFDD IVTNEQIQKR
160 170 180 190 200
AEGISSYYDE LIEMTSYWHL LGEGTHTVNG KTVTVSLREL KKKLYLCLMS
210 220 230 240 250
VNALEAIRFY VSFACSFAFA ERELMEGNAK IIRLIARDEA LHLTGTQHML
260 270 280 290 300
NLLRSGADDP EMAEIAEECK QECYDLFVQA AQQEKDWADY LFRDGSMIGL
310 320 330 340 350
NKDILCQYVE YITNIRMQAV GLDLPFQTRS NPIPWINTWL VSDNVQVAPQ
360 370
EVEVSSYLVG QIDSEVDTDD LSNFQL
Length:376
Mass (Da):43,517
Last modified:January 23, 2007 - v2
Checksum:iBF2D9A49B643E84A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02672 Genomic DNA. Translation: AAA24224.1.
U00096 Genomic DNA. Translation: AAC75295.1.
AP009048 Genomic DNA. Translation: BAA16054.1.
PIRiA00527. RDEC2R.
RefSeqiNP_416738.1. NC_000913.3.
YP_490474.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75295; AAC75295; b2235.
BAA16054; BAA16054; BAA16054.
GeneIDi12931498.
946732.
KEGGiecj:Y75_p2197.
eco:b2235.
PATRICi32119829. VBIEscCol129921_2324.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02672 Genomic DNA. Translation: AAA24224.1 .
U00096 Genomic DNA. Translation: AAC75295.1 .
AP009048 Genomic DNA. Translation: BAA16054.1 .
PIRi A00527. RDEC2R.
RefSeqi NP_416738.1. NC_000913.3.
YP_490474.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AV8 X-ray 2.80 A/B 2-341 [» ]
1BIQ X-ray 2.05 A/B 2-376 [» ]
1JPR X-ray 1.88 A/B 2-376 [» ]
1JQC X-ray 1.61 A/B 2-376 [» ]
1MRR X-ray 2.50 A/B 2-376 [» ]
1MXR X-ray 1.42 A/B 2-376 [» ]
1PFR X-ray 2.20 A/B 2-341 [» ]
1PIM X-ray 2.00 A/B 2-376 [» ]
1PIU X-ray 2.20 A/B 2-376 [» ]
1PIY X-ray 1.68 A/B 2-376 [» ]
1PIZ X-ray 1.90 A/B 2-376 [» ]
1PJ0 X-ray 1.90 A/B 2-376 [» ]
1PJ1 X-ray 1.95 A/B 2-376 [» ]
1PM2 X-ray 1.80 A/B 2-340 [» ]
1R1R X-ray 2.90 D/E/F/P 357-376 [» ]
1R65 X-ray 1.95 A/B 2-376 [» ]
1RIB X-ray 2.20 A/B 2-376 [» ]
1RNR X-ray 2.50 A/B 2-376 [» ]
1RSR X-ray 2.00 A/B 2-376 [» ]
1RSV X-ray 2.20 A/B 2-376 [» ]
1XIK X-ray 1.70 A/B 2-376 [» ]
1YFD X-ray 1.90 A/B 2-376 [» ]
2ALX X-ray 2.60 A 1-340 [» ]
2AV8 X-ray 2.46 A/B 2-341 [» ]
2R1R X-ray 3.00 D/E/F/P 357-376 [» ]
2X0X X-ray 2.30 D/E/F/P 357-376 [» ]
2XAK X-ray 2.80 D/E/F/P 357-376 [» ]
2XAP X-ray 2.10 D/E/F/P 357-376 [» ]
2XAV X-ray 2.80 D/E/F/P 357-376 [» ]
2XAW X-ray 3.10 D/E/F/P 357-376 [» ]
2XAX X-ray 2.75 D/E/F/P 357-376 [» ]
2XAY X-ray 2.65 D/E/F/P 357-376 [» ]
2XAZ X-ray 2.60 D/E/F/P 357-376 [» ]
2XO4 X-ray 2.50 D/E/F/P 357-376 [» ]
2XO5 X-ray 2.70 D/E/F/P 357-376 [» ]
2XOF X-ray 2.20 A/B 2-376 [» ]
3R1R X-ray 3.00 D/E/F/P 357-376 [» ]
3UUS X-ray 5.65 E/F/G/H 2-376 [» ]
4ERM X-ray 3.95 E/F/G/H 2-376 [» ]
4ERP X-ray 4.45 E/F/G/H 2-376 [» ]
4R1R X-ray 3.20 D/E/F/P 357-376 [» ]
5R1R X-ray 3.10 D/E/F/P 357-376 [» ]
6R1R X-ray 3.10 D/E/F/P 357-376 [» ]
7R1R X-ray 3.10 D/E/F/P 357-376 [» ]
DisProti DP00107.
ProteinModelPortali P69924.
SMRi P69924. Positions 2-376.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-36213N.
IntActi P69924. 12 interactions.
MINTi MINT-1269534.
STRINGi 511145.b2235.

Proteomic databases

PaxDbi P69924.
PRIDEi P69924.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75295 ; AAC75295 ; b2235 .
BAA16054 ; BAA16054 ; BAA16054 .
GeneIDi 12931498.
946732.
KEGGi ecj:Y75_p2197.
eco:b2235.
PATRICi 32119829. VBIEscCol129921_2324.

Organism-specific databases

EchoBASEi EB0655.
EcoGenei EG10661. nrdB.

Phylogenomic databases

eggNOGi COG0208.
HOGENOMi HOG000278087.
InParanoidi P69924.
KOi K00526.
OMAi WIETWAF.
OrthoDBi EOG6J48J7.
PhylomeDBi P69924.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci EcoCyc:NRDB-MONOMER.
ECOL316407:JW2229-MONOMER.
MetaCyc:NRDB-MONOMER.
SABIO-RK P69924.

Miscellaneous databases

EvolutionaryTracei P69924.
PROi P69924.

Gene expression databases

Genevestigatori P69924.

Family and domain databases

Gene3Di 1.10.620.20. 1 hit.
InterProi IPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR000358. RNR_small.
[Graphical view ]
PANTHERi PTHR23409. PTHR23409. 1 hit.
Pfami PF00268. Ribonuc_red_sm. 2 hits.
[Graphical view ]
SUPFAMi SSF47240. SSF47240. 1 hit.
PROSITEi PS00368. RIBORED_SMALL. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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).

Entry informationi

Entry nameiRIR2_ECOLI
AccessioniPrimary (citable) accession number: P69924
Secondary accession number(s): P00453
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 102 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3