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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

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 bindingi67Iron 1PROSITE-ProRule annotation1
Metal bindingi98Iron 1PROSITE-ProRule annotation1
Metal bindingi98Iron 2By similarity1
Metal bindingi101Iron 1PROSITE-ProRule annotation1
Active sitei105PROSITE-ProRule annotation1
Metal bindingi158Iron 2By similarity1
Metal bindingi192Iron 21
Metal bindingi195Iron 21

GO - Molecular functioni

GO - Biological processi

  • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 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)DescriptionActionsGraphical viewLength
ChainiPRO_00001904881 – 319Ribonucleoside-diphosphate reductase 2 subunit betaAdd BLAST319

Proteomic databases

EPDiP37146.
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

BioGridi4262269. 135 interactors.
IntActiP37146. 9 interactors.
STRINGi511145.b2676.

Structurei

Secondary structure

1319
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi17 – 28Combined sources12
Helixi33 – 35Combined sources3
Helixi38 – 41Combined sources4
Helixi42 – 45Combined sources4
Helixi50 – 72Combined sources23
Helixi74 – 78Combined sources5
Helixi79 – 81Combined sources3
Helixi85 – 112Combined sources28
Helixi115 – 127Combined sources13
Helixi129 – 143Combined sources15
Helixi147 – 159Combined sources13
Turni160 – 162Combined sources3
Helixi163 – 174Combined sources12
Helixi179 – 207Combined sources29
Helixi212 – 240Combined sources29
Turni241 – 243Combined sources3
Helixi247 – 264Combined sources18
Helixi273 – 275Combined sources3
Helixi280 – 286Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP37146.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107R25. Bacteria.
COG0208. LUCA.
HOGENOMiHOG000246153.
InParanoidiP37146.
KOiK00526.
OMAiMNLGQEP.
PhylomeDBiP37146.

Family and domain databases

CDDicd01049. RNRR2. 1 hit.
Gene3Di1.10.620.20. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR026494. RNR_NrdF.
IPR033909. RNR_small.
IPR030475. RNR_small_AS.
IPR000358. RNR_small_fam.
[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_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75723; AAC75723; b2676.
BAA16541; BAA16541; BAA16541.
GeneIDi947149.
KEGGiecj:JW2651.
eco: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_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262269. 135 interactors.
IntActiP37146. 9 interactors.
STRINGi511145.b2676.

Proteomic databases

EPDiP37146.
PaxDbiP37146.
PRIDEiP37146.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75723; AAC75723; b2676.
BAA16541; BAA16541; BAA16541.
GeneIDi947149.
KEGGiecj:JW2651.
eco:b2676.
PATRICi32120742. VBIEscCol129921_2768.

Organism-specific databases

EchoBASEiEB2283.
EcoGeneiEG12381. nrdF.

Phylogenomic databases

eggNOGiENOG4107R25. Bacteria.
COG0208. LUCA.
HOGENOMiHOG000246153.
InParanoidiP37146.
KOiK00526.
OMAiMNLGQEP.
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

CDDicd01049. RNRR2. 1 hit.
Gene3Di1.10.620.20. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR026494. RNR_NrdF.
IPR033909. RNR_small.
IPR030475. RNR_small_AS.
IPR000358. RNR_small_fam.
[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...

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: November 30, 2016
This is version 138 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

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.