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Q08698

- RIR3_SALTY

UniProt

Q08698 - RIR3_SALTY

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Protein

Ribonucleoside-diphosphate reductase 2 subunit alpha

Gene

nrdE

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 – 1611SubstrateBy similarity
Sitei178 – 1781Important for hydrogen atom transferBy similarity
Sitei185 – 1851Allosteric effector binding
Binding sitei206 – 2061Substrate; via amide nitrogenBy similarity
Sitei215 – 2151Allosteric effector binding
Sitei222 – 2221Allosteric effector binding
Active sitei386 – 3861Proton acceptorBy similarity
Active sitei388 – 3881Cysteine radical intermediateBy similarity
Active sitei390 – 3901Proton acceptorBy similarity
Sitei415 – 4151Important for hydrogen atom transferBy similarity
Sitei692 – 6921Important for electron transferBy similarity
Sitei693 – 6931Important for electron transferBy similarity
Sitei709 – 7091Interacts with thioredoxin/glutaredoxinBy similarity
Sitei712 – 7121Interacts with thioredoxin/glutaredoxinBy 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

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

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ08698.

Family & Domainsi

Region

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

        10         20         30         40         50
MATTTPERVM QETMDYHALN AMLNLYDKAG HIQFDKDQQA IDAFFATHVR
60 70 80 90 100
PHSVTFASQH ERLGTLVREG YYDDAVLARY DRAFVLRLFE HAHASGFRFQ
110 120 130 140 150
TFLGAWKFYT SYTLKTFDGK RYLEHFEDRV TMVALTLAQG DETLATQLTD
160 170 180 190 200
EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL LRIEDNMESI GRAVNSALQL
210 220 230 240 250
SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED AFSYANQLGA
260 270 280 290 300
RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFRLA
310 320 330 340 350
KENAQMALFS PYDIQRRYGK PFGDIAISER YDELIADPHV RKTYINARDF
360 370 380 390 400
FQTLAEIQFE SGYPYIMFED TVNRANPIAG RINMSNLCSE ILQVNSASRY
410 420 430 440 450
DDNLDYTHIG HDISCNLGSL NIAHVMDSPD IGRTVETAIR GLTAVSDMSH
460 470 480 490 500
IRSVPSIAAG NAASHAIGLG QMNLHGYLAR EGIAYGSPEA LDFTNLYFYT
510 520 530 540 550
ITWHAVHTSM RLARERGKTF AGFAQSRYAS GDYFTQYLQD DWQPKTAKVR
560 570 580 590 600
ALFARSGITL PTREMWLKLR DDVMRYGIYN QNLQAVPPTG SISYINHATS
610 620 630 640 650
SIHPIVAKIE IRKEGKTGRV YYPAPFMTNE NLDMYQDAYD IGPEKIIDTY
660 670 680 690 700
AEATRHVDQG LSLTLFFPDT ATTRDINKAQ IYAWRKGIKS LYYIRLRQLA
710
LEGTEIEGCV SCAL
Length:714
Mass (Da):80,587
Last modified:January 23, 2007 - v2
Checksum:iB12F79B42B05000D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 121 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