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P17424

- RIR4_SALTY

UniProt

P17424 - RIR4_SALTY

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Protein

Ribonucleoside-diphosphate reductase 2 subunit beta

Gene
nrdF, STM2808
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 4 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.

Cofactori

Binds 2 iron ions per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi67 – 671Iron 1
Metal bindingi98 – 981Iron 1
Metal bindingi98 – 981Iron 2
Metal bindingi101 – 1011Iron 1
Active sitei105 – 1051 By similarity
Metal bindingi158 – 1581Iron 2
Metal bindingi192 – 1921Iron 2
Metal bindingi195 – 1951Iron 2

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. 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: InterPro
  3. 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

BioCyciMetaCyc:MONOMER-13836.
SENT99287:GCTI-2825-MONOMER.
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
Ordered Locus Names:STM2808
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. ribonucleoside-diphosphate reductase complex Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 319319Ribonucleoside-diphosphate reductase 2 subunit betaPRO_0000190489Add
BLAST

Proteomic databases

PRIDEiP17424.

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits By similarity.

Protein-protein interaction databases

STRINGi99287.STM2808.

Structurei

Secondary structure

1
319
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi17 – 2812
Helixi33 – 353
Helixi38 – 414
Helixi42 – 465
Helixi50 – 7223
Helixi74 – 796
Helixi85 – 11228
Helixi115 – 12713
Helixi129 – 14315
Helixi147 – 15913
Turni160 – 1623
Helixi163 – 17412
Helixi179 – 20830
Helixi212 – 24029
Turni241 – 2444
Helixi247 – 26418
Turni273 – 2753
Helixi280 – 2867

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1R2FX-ray2.10A/B1-319[»]
2BQ1X-ray4.00I/J1-319[»]
2R2FX-ray2.25A/B1-319[»]
ProteinModelPortaliP17424.
SMRiP17424. Positions 4-318.

Miscellaneous databases

EvolutionaryTraceiP17424.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0208.
HOGENOMiHOG000246154.
KOiK00526.
OMAiNIKDFAF.
OrthoDBiEOG68DD19.
PhylomeDBiP17424.

Family and domain databases

Gene3Di1.10.620.20. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR026023. RNR_bsu_prok.
IPR026494. RNR_NrdF.
IPR000358. RNR_small.
[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.

P17424-1 [UniParc]FASTAAdd to Basket

« Hide

MKLSRISAIN WNKIQDDKDL EVWNRLTSNF WLPEKVPLSN DIPAWQTLSA    50
AEQQLTIRVF TGLTLLDTIQ NIAGAPSLMA DAITPHEEAV LSNISFMEAV 100
HARSYSSIFS TLCQTKEVDA AYAWSEENPP LQRKAQIILA HYVSDEPLKK 150
KIASVFLESF LFYSGFWLPM YFSSRGKLTN TADLIRLIIR DEAVHGYYIG 200
YKYQIALQKL SAIEREELKL FALDLLMELY DNEIRYTEAL YAETGWVNDV 250
KAFLCYNANK ALMNLGYEAL FPPEMADVNP AILAALSPNA DENHDFFSGS 300
GSSYVMGKTV ETEDEDWNF 319
Length:319
Mass (Da):36,232
Last modified:October 1, 1994 - v2
Checksum:iAFBB6E02A57C959A
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti286 – 2861L → V in AAA88620. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X73226 Genomic DNA. Translation: CAA51695.1.
AE006468 Genomic DNA. Translation: AAL21693.1.
X52693 Genomic DNA. Translation: CAA36920.1.
M26063 Genomic DNA. Translation: AAA88620.1.
PIRiS34272.
RefSeqiNP_461734.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL21693; AAL21693; STM2808.
GeneIDi1254331.
KEGGistm:STM2808.
PATRICi32384298. VBISalEnt20916_2966.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X73226 Genomic DNA. Translation: CAA51695.1 .
AE006468 Genomic DNA. Translation: AAL21693.1 .
X52693 Genomic DNA. Translation: CAA36920.1 .
M26063 Genomic DNA. Translation: AAA88620.1 .
PIRi S34272.
RefSeqi NP_461734.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1R2F X-ray 2.10 A/B 1-319 [» ]
2BQ1 X-ray 4.00 I/J 1-319 [» ]
2R2F X-ray 2.25 A/B 1-319 [» ]
ProteinModelPortali P17424.
SMRi P17424. Positions 4-318.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 99287.STM2808.

Proteomic databases

PRIDEi P17424.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL21693 ; AAL21693 ; STM2808 .
GeneIDi 1254331.
KEGGi stm:STM2808.
PATRICi 32384298. VBISalEnt20916_2966.

Phylogenomic databases

eggNOGi COG0208.
HOGENOMi HOG000246154.
KOi K00526.
OMAi NIKDFAF.
OrthoDBi EOG68DD19.
PhylomeDBi P17424.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci MetaCyc:MONOMER-13836.
SENT99287:GCTI-2825-MONOMER.

Miscellaneous databases

EvolutionaryTracei P17424.

Family and domain databases

Gene3Di 1.10.620.20. 1 hit.
InterProi IPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR026023. RNR_bsu_prok.
IPR026494. RNR_NrdF.
IPR000358. RNR_small.
[Graphical view ]
PANTHERi PTHR23409. PTHR23409. 1 hit.
Pfami PF00268. Ribonuc_red_sm. 1 hit.
[Graphical view ]
PIRSFi PIRSF000355. NrdB. 1 hit.
SUPFAMi SSF47240. SSF47240. 1 hit.
TIGRFAMsi TIGR04171. RNR_1b_NrdF. 1 hit.
PROSITEi PS00368. RIBORED_SMALL. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "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: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: LT2.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.
  3. "Molecular characterization of the proU loci of Salmonella typhimurium and Escherichia coli encoding osmoregulated glycine betaine transport systems."
    Stirling D.A., Hulton C.S.J., Waddell L., Park S.F., Stewart G.S.A.B., Booth I.R., Higgins C.F.
    Mol. Microbiol. 3:1025-1038(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 219-319.
    Strain: LT2.
  4. "Nucleotide sequence of the transcriptional control region of the osmotically regulated proU operon of Salmonella typhimurium and identification of the 5' endpoint of the proU mRNA."
    Overdier D.G., Olson E.R., Erickson B.D., Ederer M.M., Csonka L.N.
    J. Bacteriol. 171:4694-4706(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 219-319.
  5. "Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms."
    Eriksson M., Jordan A., Eklund H.
    Biochemistry 37:13359-13369(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

Entry informationi

Entry nameiRIR4_SALTY
AccessioniPrimary (citable) accession number: P17424
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: October 1, 1994
Last modified: September 3, 2014
This is version 124 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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