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Protein

Ribonucleoside-diphosphate reductase 2 subunit beta

Gene

nrdF

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. R2F contains the tyrosyl radical required for catalysis.

Catalytic activityi

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

Cofactori

Fe cationBy similarityNote: Binds 2 iron ions per subunit.By similarity

Pathway:iDNA 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi67 – 671Iron 1PROSITE-ProRule annotation
Metal bindingi98 – 981Iron 1PROSITE-ProRule annotation
Metal bindingi98 – 981Iron 2By similarity
Metal bindingi101 – 1011Iron 1PROSITE-ProRule annotation
Active sitei105 – 1051PROSITE-ProRule annotation
Metal bindingi158 – 1581Iron 2By similarity
Metal bindingi192 – 1921Iron 2
Metal bindingi195 – 1951Iron 2

GO - Molecular functioni

GO - Biological processi

  • deoxyribonucleoside diphosphate metabolic process Source: InterPro
  • deoxyribonucleotide biosynthetic process Source: EcoliWiki
  • DNA replication Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:NRDF-MONOMER.
ECOL316407:JW2651-MONOMER.
MetaCyc:NRDF-MONOMER.
BRENDAi1.17.4.1. 2026.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase 2 subunit beta (EC:1.17.4.1)
Alternative name(s):
R2F protein
Ribonucleotide reductase 2
Gene namesi
Name:nrdF
Synonyms:ygaD
Ordered Locus Names:b2676, JW2651
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12381. nrdF.

Subcellular locationi

GO - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 319319Ribonucleoside-diphosphate reductase 2 subunit betaPRO_0000190488Add
BLAST

Proteomic databases

PaxDbiP37146.
PRIDEiP37146.

Expressioni

Inductioni

Induced 2-fold by hydroxyurea.1 Publication

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits.By similarity

Protein-protein interaction databases

IntActiP37146. 9 interactions.
STRINGi511145.b2676.

Structurei

Secondary structure

1
319
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi17 – 2812Combined sources
Helixi33 – 353Combined sources
Helixi38 – 414Combined sources
Helixi42 – 454Combined sources
Helixi50 – 7223Combined sources
Helixi74 – 785Combined sources
Helixi79 – 813Combined sources
Helixi85 – 11228Combined sources
Helixi115 – 12713Combined sources
Helixi129 – 14315Combined sources
Helixi147 – 15913Combined sources
Turni160 – 1623Combined sources
Helixi163 – 17412Combined sources
Helixi179 – 20729Combined sources
Helixi212 – 24029Combined sources
Turni241 – 2433Combined sources
Helixi247 – 26418Combined sources
Helixi273 – 2753Combined sources
Helixi280 – 2867Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3N37X-ray1.65A1-319[»]
3N38X-ray1.90A1-319[»]
3N39X-ray2.50A/B1-319[»]
3N3AX-ray1.99A/B1-319[»]
3N3BX-ray2.36A/B1-319[»]
4M1FX-ray2.00A1-319[»]
ProteinModelPortaliP37146.
SMRiP37146. Positions 5-318.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP37146.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0208.
HOGENOMiHOG000246153.
InParanoidiP37146.
KOiK00526.
OMAiYYQADEP.
OrthoDBiEOG68DD19.
PhylomeDBiP37146.

Family and domain databases

Gene3Di1.10.620.20. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR026494. RNR_NrdF.
IPR000358. RNR_small.
IPR030475. RNR_small_AS.
[Graphical view]
PANTHERiPTHR23409. PTHR23409. 1 hit.
PfamiPF00268. Ribonuc_red_sm. 1 hit.
[Graphical view]
PIRSFiPIRSF000355. NrdB. 1 hit.
SUPFAMiSSF47240. SSF47240. 1 hit.
TIGRFAMsiTIGR04171. RNR_1b_NrdF. 1 hit.
PROSITEiPS00368. RIBORED_SMALL. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P37146-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLSRISAIN WNKISDDKDL EVWNRLTSNF WLPEKVPLSN DIPAWQTLTV
60 70 80 90 100
VEQQLTMRVF TGLTLLDTLQ NVIGAPSLMP DALTPHEEAV LSNISFMEAV
110 120 130 140 150
HARSYSSIFS TLCQTKDVDA AYAWSEENAP LQRKAQIIQQ HYRGDDPLKK
160 170 180 190 200
KIASVFLESF LFYSGFWLPM YFSSRGKLTN TADLIRLIIR DEAVHGYYIG
210 220 230 240 250
YKYQKNMEKI SLGQREELKS FAFDLLLELY DNELQYTDEL YAETPWADDV
260 270 280 290 300
KAFLCYNANK ALMNLGYEPL FPAEMAEVNP AILAALSPNA DENHDFFSGS
310
GSSYVMGKAV ETEDEDWNF
Length:319
Mass (Da):36,443
Last modified:November 1, 1997 - v2
Checksum:i0C95394CF150EEFB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75723.1.
AP009048 Genomic DNA. Translation: BAA16541.1.
M24856 Genomic DNA. No translation available.
PIRiE65047.
RefSeqiNP_417162.1. NC_000913.3.
WP_000777969.1. NZ_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC75723; AAC75723; b2676.
BAA16541; BAA16541; BAA16541.
GeneIDi947149.
KEGGieco:b2676.
PATRICi32120742. VBIEscCol129921_2768.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75723.1.
AP009048 Genomic DNA. Translation: BAA16541.1.
M24856 Genomic DNA. No translation available.
PIRiE65047.
RefSeqiNP_417162.1. NC_000913.3.
WP_000777969.1. NZ_CP010445.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3N37X-ray1.65A1-319[»]
3N38X-ray1.90A1-319[»]
3N39X-ray2.50A/B1-319[»]
3N3AX-ray1.99A/B1-319[»]
3N3BX-ray2.36A/B1-319[»]
4M1FX-ray2.00A1-319[»]
ProteinModelPortaliP37146.
SMRiP37146. Positions 5-318.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP37146. 9 interactions.
STRINGi511145.b2676.

Proteomic databases

PaxDbiP37146.
PRIDEiP37146.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75723; AAC75723; b2676.
BAA16541; BAA16541; BAA16541.
GeneIDi947149.
KEGGieco:b2676.
PATRICi32120742. VBIEscCol129921_2768.

Organism-specific databases

EchoBASEiEB2283.
EcoGeneiEG12381. nrdF.

Phylogenomic databases

eggNOGiCOG0208.
HOGENOMiHOG000246153.
InParanoidiP37146.
KOiK00526.
OMAiYYQADEP.
OrthoDBiEOG68DD19.
PhylomeDBiP37146.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciEcoCyc:NRDF-MONOMER.
ECOL316407:JW2651-MONOMER.
MetaCyc:NRDF-MONOMER.
BRENDAi1.17.4.1. 2026.

Miscellaneous databases

EvolutionaryTraceiP37146.
PROiP37146.

Family and domain databases

Gene3Di1.10.620.20. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR026494. RNR_NrdF.
IPR000358. RNR_small.
IPR030475. RNR_small_AS.
[Graphical view]
PANTHERiPTHR23409. PTHR23409. 1 hit.
PfamiPF00268. Ribonuc_red_sm. 1 hit.
[Graphical view]
PIRSFiPIRSF000355. NrdB. 1 hit.
SUPFAMiSSF47240. SSF47240. 1 hit.
TIGRFAMsiTIGR04171. RNR_1b_NrdF. 1 hit.
PROSITEiPS00368. RIBORED_SMALL. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "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.
  4. "Nucleotide sequence of the osmoregulatory proU operon of Escherichia coli."
    Gowrishankar J.
    J. Bacteriol. 171:1923-1931(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 210-319.
  5. Erratum
    Gowrishankar J.
    J. Bacteriol. 172:1165-1165(1990)
  6. "Cloning and sequencing of the genes from Salmonella typhimurium encoding a new bacterial ribonucleotide reductase."
    Jordan A., Gibert I., Barbe J.
    J. Bacteriol. 176:3420-3427(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  7. "Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli."
    Davies B.W., Kohanski M.A., Simmons L.A., Winkler J.A., Collins J.J., Walker G.C.
    Mol. Cell 36:845-860(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY HYDROXYUREA.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.

Entry informationi

Entry nameiRIR4_ECOLI
AccessioniPrimary (citable) accession number: P37146
Secondary accession number(s): P78244
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: November 1, 1997
Last modified: July 22, 2015
This is version 127 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, 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

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 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.