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Protein

Ribonucleoside-diphosphate reductase 1 subunit beta

Gene

nrdB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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.

Enzyme regulationi

Inhibited by hydroxyurea, leads to dNTP depletion, replication fork arrest and genomic instability.1 Publication

Pathwayi: DNA replication

This protein is involved in the pathway DNA replication, which is part of Genetic information processing.
View all proteins of this organism that are known to be involved in the pathway DNA replication and in Genetic information processing.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi85Iron 11
Metal bindingi116Iron 11
Metal bindingi116Iron 21
Metal bindingi119Iron 11
Active sitei1231
Metal bindingi205Iron 21
Metal bindingi239Iron 21
Metal bindingi242Iron 21

GO - Molecular functioni

GO - Biological processi

  • deoxyribonucleotide biosynthetic process Source: EcoliWiki
  • DNA replication Source: UniProtKB-UniPathway
  • 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.
BRENDAi1.17.4.1. 2026.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10661. nrdB.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoliWiki
  • cytosol Source: UniProtKB
  • ribonucleoside-diphosphate reductase complex Source: EcoliWiki
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001904762 – 376Ribonucleoside-diphosphate reductase 1 subunit betaAdd BLAST375

Proteomic databases

PaxDbiP69924.
PRIDEiP69924.

Expressioni

Inductioni

Induced 4.2-fold by hydroxyurea (at protein level).1 Publication

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

BioGridi4260492. 50 interactors.
DIPiDIP-36213N.
IntActiP69924. 12 interactors.
MINTiMINT-1269534.
STRINGi511145.b2235.

Structurei

Secondary structure

1376
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi13 – 15Combined sources3
Beta strandi18 – 22Combined sources5
Helixi35 – 46Combined sources12
Helixi51 – 53Combined sources3
Helixi59 – 64Combined sources6
Helixi68 – 95Combined sources28
Helixi97 – 99Combined sources3
Helixi103 – 128Combined sources26
Helixi134 – 143Combined sources10
Helixi145 – 151Combined sources7
Helixi154 – 171Combined sources18
Beta strandi173 – 178Combined sources6
Beta strandi181 – 185Combined sources5
Helixi187 – 206Combined sources20
Helixi208 – 221Combined sources14
Helixi226 – 255Combined sources30
Beta strandi256 – 258Combined sources3
Helixi260 – 268Combined sources9
Helixi270 – 291Combined sources22
Turni292 – 294Combined sources3
Helixi302 – 319Combined sources18
Helixi334 – 338Combined sources5
Helixi368 – 371Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5CI2X-ray2.25A2-376[»]
5CI3X-ray2.40A2-376[»]
5CNSX-ray2.98E/F/G/H2-376[»]
5CNTX-ray3.25E/F/G/H2-376[»]
5CNUX-ray3.40E/F/G/H2-376[»]
5CNVX-ray3.20E/F/G/H2-376[»]
5R1RX-ray3.10D/E/F/P357-376[»]
6R1RX-ray3.10D/E/F/P357-376[»]
7R1RX-ray3.10D/E/F/P357-376[»]
DisProtiDP00107.
ProteinModelPortaliP69924.
SMRiP69924.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69924.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105E05. Bacteria.
COG0208. LUCA.
HOGENOMiHOG000278087.
InParanoidiP69924.
KOiK00526.
OMAiLEPMFLG.
PhylomeDBiP69924.

Family and domain databases

CDDicd01049. RNRR2. 1 hit.
Gene3Di1.10.620.20. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR033909. RNR_small.
IPR030475. RNR_small_AS.
IPR000358. RNR_small_fam.
[Graphical view]
PANTHERiPTHR23409. PTHR23409. 2 hits.
PfamiPF00268. Ribonuc_red_sm. 1 hit.
[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.
WP_000332037.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75295; AAC75295; b2235.
BAA16054; BAA16054; BAA16054.
GeneIDi946732.
KEGGiecj:JW2229.
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.
PIRiA00527. RDEC2R.
RefSeqiNP_416738.1. NC_000913.3.
WP_000332037.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5CI2X-ray2.25A2-376[»]
5CI3X-ray2.40A2-376[»]
5CNSX-ray2.98E/F/G/H2-376[»]
5CNTX-ray3.25E/F/G/H2-376[»]
5CNUX-ray3.40E/F/G/H2-376[»]
5CNVX-ray3.20E/F/G/H2-376[»]
5R1RX-ray3.10D/E/F/P357-376[»]
6R1RX-ray3.10D/E/F/P357-376[»]
7R1RX-ray3.10D/E/F/P357-376[»]
DisProtiDP00107.
ProteinModelPortaliP69924.
SMRiP69924.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260492. 50 interactors.
DIPiDIP-36213N.
IntActiP69924. 12 interactors.
MINTiMINT-1269534.
STRINGi511145.b2235.

Proteomic databases

PaxDbiP69924.
PRIDEiP69924.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75295; AAC75295; b2235.
BAA16054; BAA16054; BAA16054.
GeneIDi946732.
KEGGiecj:JW2229.
eco:b2235.
PATRICi32119829. VBIEscCol129921_2324.

Organism-specific databases

EchoBASEiEB0655.
EcoGeneiEG10661. nrdB.

Phylogenomic databases

eggNOGiENOG4105E05. Bacteria.
COG0208. LUCA.
HOGENOMiHOG000278087.
InParanoidiP69924.
KOiK00526.
OMAiLEPMFLG.
PhylomeDBiP69924.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciEcoCyc:NRDB-MONOMER.
ECOL316407:JW2229-MONOMER.
MetaCyc:NRDB-MONOMER.
BRENDAi1.17.4.1. 2026.
SABIO-RKP69924.

Miscellaneous databases

EvolutionaryTraceiP69924.
PROiP69924.

Family and domain databases

CDDicd01049. RNRR2. 1 hit.
Gene3Di1.10.620.20. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR033909. RNR_small.
IPR030475. RNR_small_AS.
IPR000358. RNR_small_fam.
[Graphical view]
PANTHERiPTHR23409. PTHR23409. 2 hits.
PfamiPF00268. Ribonuc_red_sm. 1 hit.
[Graphical view]
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS00368. RIBORED_SMALL. 1 hit.
[Graphical view]
ProtoNetiSearch...

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 30, 2016
This is version 116 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.