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Q08698

- RIR3_SALTY

UniProt

Q08698 - RIR3_SALTY

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Protein

Ribonucleoside-diphosphate reductase 2 subunit alpha

Gene
nrdE, STM2807
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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. R1E contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide.

Catalytic activityi

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

Enzyme regulationi

Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Lacks the N-terminal activity site.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei161 – 1611Substrate By similarity
Sitei178 – 1781Important for hydrogen atom transfer By similarity
Sitei185 – 1851Allosteric effector binding
Binding sitei206 – 2061Substrate; via amide nitrogen By similarity
Sitei215 – 2151Allosteric effector binding
Sitei222 – 2221Allosteric effector binding
Active sitei386 – 3861Proton acceptor By similarity
Active sitei388 – 3881Cysteine radical intermediate By similarity
Active sitei390 – 3901Proton acceptor By similarity
Sitei415 – 4151Important for hydrogen atom transfer By similarity
Sitei692 – 6921Important for electron transfer By similarity
Sitei693 – 6931Important for electron transfer By similarity
Sitei709 – 7091Interacts with thioredoxin/glutaredoxin By similarity
Sitei712 – 7121Interacts with thioredoxin/glutaredoxin By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. DNA replication Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13835.
SENT99287:GCTI-2824-MONOMER.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase 2 subunit alpha (EC:1.17.4.1)
Alternative name(s):
R1E protein
Ribonucleotide reductase 2
Gene namesi
Name:nrdE
Ordered Locus Names:STM2807
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
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 714713Ribonucleoside-diphosphate reductase 2 subunit alphaPRO_0000187225Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi178 ↔ 415Redox-active

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiQ08698.

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits By similarity.

Protein-protein interaction databases

STRINGi99287.STM2807.

Structurei

Secondary structure

1
714
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi16 – 216
Helixi22 – 243
Helixi35 – 4713
Helixi49 – 524
Helixi59 – 6810
Helixi74 – 774
Helixi82 – 9413
Helixi102 – 11110
Beta strandi119 – 1224
Helixi126 – 13813
Helixi142 – 15312
Beta strandi156 – 1594
Helixi161 – 1666
Beta strandi169 – 1713
Beta strandi179 – 1813
Helixi187 – 20115
Turni202 – 2043
Beta strandi206 – 2105
Beta strandi224 – 2263
Helixi232 – 24413
Beta strandi254 – 2607
Helixi266 – 2705
Helixi271 – 2733
Beta strandi279 – 2813
Beta strandi287 – 2915
Helixi295 – 3017
Beta strandi305 – 3095
Helixi311 – 3188
Helixi322 – 3243
Helixi327 – 33610
Beta strandi342 – 3465
Helixi347 – 36115
Beta strandi365 – 3673
Helixi369 – 3757
Beta strandi378 – 3803
Beta strandi406 – 4083
Beta strandi416 – 4216
Helixi422 – 4265
Helixi431 – 44717
Helixi455 – 46410
Beta strandi467 – 4726
Helixi474 – 4807
Helixi488 – 51629
Helixi523 – 5253
Helixi527 – 5304
Helixi532 – 5343
Helixi535 – 5384
Helixi547 – 55610
Helixi563 – 57614
Helixi592 – 5965
Beta strandi600 – 6034
Beta strandi608 – 6125
Beta strandi615 – 6184
Beta strandi620 – 6234
Turni629 – 6313
Helixi632 – 6343
Helixi638 – 6414
Helixi643 – 65412
Beta strandi665 – 6673
Helixi673 – 68614
Beta strandi694 – 6963

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PEMX-ray2.99A1-714[»]
1PEOX-ray3.00A1-714[»]
1PEQX-ray2.80A1-714[»]
1PEUX-ray3.20A1-714[»]
2BQ1X-ray3.99E/F2-714[»]
ProteinModelPortaliQ08698.
SMRiQ08698. Positions 8-699.

Miscellaneous databases

EvolutionaryTraceiQ08698.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni177 – 1782Substrate binding By similarity
Regioni386 – 3905Substrate binding By similarity
Regioni588 – 5925Substrate binding By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000246165.
KOiK00525.
OMAiIYYIRIR.
OrthoDBiEOG6J48HC.
PhylomeDBiQ08698.

Family and domain databases

InterProiIPR013346. NrdE_NrdA.
IPR026459. RNR_1b_NrdE.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR013554. RNR_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
TIGR04170. RNR_1b_NrdE. 1 hit.
PROSITEiPS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q08698-1 [UniParc]FASTAAdd to Basket

« Hide

MATTTPERVM QETMDYHALN AMLNLYDKAG HIQFDKDQQA IDAFFATHVR    50
PHSVTFASQH ERLGTLVREG YYDDAVLARY DRAFVLRLFE HAHASGFRFQ 100
TFLGAWKFYT SYTLKTFDGK RYLEHFEDRV TMVALTLAQG DETLATQLTD 150
EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL LRIEDNMESI GRAVNSALQL 200
SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED AFSYANQLGA 250
RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFRLA 300
KENAQMALFS PYDIQRRYGK PFGDIAISER YDELIADPHV RKTYINARDF 350
FQTLAEIQFE SGYPYIMFED TVNRANPIAG RINMSNLCSE ILQVNSASRY 400
DDNLDYTHIG HDISCNLGSL NIAHVMDSPD IGRTVETAIR GLTAVSDMSH 450
IRSVPSIAAG NAASHAIGLG QMNLHGYLAR EGIAYGSPEA LDFTNLYFYT 500
ITWHAVHTSM RLARERGKTF AGFAQSRYAS GDYFTQYLQD DWQPKTAKVR 550
ALFARSGITL PTREMWLKLR DDVMRYGIYN QNLQAVPPTG SISYINHATS 600
SIHPIVAKIE IRKEGKTGRV YYPAPFMTNE NLDMYQDAYD IGPEKIIDTY 650
AEATRHVDQG LSLTLFFPDT ATTRDINKAQ IYAWRKGIKS LYYIRLRQLA 700
LEGTEIEGCV SCAL 714
Length:714
Mass (Da):80,587
Last modified:January 23, 2007 - v2
Checksum:iB12F79B42B05000D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X73226 Genomic DNA. Translation: CAA51699.1.
AE006468 Genomic DNA. Translation: AAL21692.1.
PIRiS34271.
RefSeqiNP_461733.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL21692; AAL21692; STM2807.
GeneIDi1254330.
KEGGistm:STM2807.
PATRICi32384296. VBISalEnt20916_2965.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X73226 Genomic DNA. Translation: CAA51699.1 .
AE006468 Genomic DNA. Translation: AAL21692.1 .
PIRi S34271.
RefSeqi NP_461733.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1PEM X-ray 2.99 A 1-714 [» ]
1PEO X-ray 3.00 A 1-714 [» ]
1PEQ X-ray 2.80 A 1-714 [» ]
1PEU X-ray 3.20 A 1-714 [» ]
2BQ1 X-ray 3.99 E/F 2-714 [» ]
ProteinModelPortali Q08698.
SMRi Q08698. Positions 8-699.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 99287.STM2807.

Proteomic databases

PRIDEi Q08698.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL21692 ; AAL21692 ; STM2807 .
GeneIDi 1254330.
KEGGi stm:STM2807.
PATRICi 32384296. VBISalEnt20916_2965.

Phylogenomic databases

eggNOGi COG0209.
HOGENOMi HOG000246165.
KOi K00525.
OMAi IYYIRIR.
OrthoDBi EOG6J48HC.
PhylomeDBi Q08698.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci MetaCyc:MONOMER-13835.
SENT99287:GCTI-2824-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q08698.

Family and domain databases

InterProi IPR013346. NrdE_NrdA.
IPR026459. RNR_1b_NrdE.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR013554. RNR_N.
IPR008926. RNR_R1-su_N.
[Graphical view ]
Pfami PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view ]
PRINTSi PR01183. RIBORDTASEM1.
SUPFAMi SSF48168. SSF48168. 1 hit.
TIGRFAMsi TIGR02506. NrdE_NrdA. 1 hit.
TIGR04170. RNR_1b_NrdE. 1 hit.
PROSITEi PS00089. RIBORED_LARGE. 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], PROTEIN SEQUENCE OF 2-15.
    Strain: LT2.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.
  3. "Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors."
    Uppsten M., Farnegardh M., Jordan A., Eliasson R., Eklund H., Uhlin U.
    J. Mol. Biol. 330:87-97(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEXES WITH ALLOSTERIC EFFECTORS.
  4. "The first holocomplex structure of ribonucleotide reductase gives new insight into its mechanism of action."
    Uppsten M., Farnegardh M., Domkin V., Uhlin U.
    J. Mol. Biol. 359:365-377(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 2-713.

Entry informationi

Entry nameiRIR3_SALTY
AccessioniPrimary (citable) accession number: Q08698
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 118 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, Allosteric enzyme, Complete proteome, Direct protein sequencing, 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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