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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: -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.

Activity 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: 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
Binding sitei161SubstrateBy similarity1
Sitei178Important for hydrogen atom transferBy similarity1
Sitei185Allosteric effector binding1
Binding sitei206Substrate; via amide nitrogenBy similarity1
Sitei215Allosteric effector binding1
Sitei222Allosteric effector binding1
Active sitei386Proton acceptorBy similarity1
Active sitei388Cysteine radical intermediateBy similarity1
Active sitei390Proton acceptorBy similarity1
Sitei415Important for hydrogen atom transferBy similarity1
Sitei692Important for electron transferBy similarity1
Sitei693Important for electron transferBy similarity1
Sitei709Interacts with thioredoxin/glutaredoxinBy similarity1
Sitei712Interacts with thioredoxin/glutaredoxinBy similarity1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: GO_Central

GO - Biological processi

Keywordsi

Molecular functionAllosteric enzyme, Oxidoreductase
Biological processDNA replication
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13835
SENT99287:G1FZD-2835-MONOMER
UniPathwayi
UPA00326

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Pathology & Biotechi

Chemistry databases

DrugBankiDB03222 2'-Deoxyadenosine 5'-Triphosphate
DB03258 2'-Deoxycytidine-5'-Triphosphate
DB02452 Thymidine-5'-Triphosphate

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001872252 – 714Ribonucleoside-diphosphate reductase 2 subunit alphaAdd BLAST713

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi178 ↔ 415Redox-active

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiQ08698
PRIDEiQ08698

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits.By similarity

Protein-protein interaction databases

STRINGi99287.STM2807

Structurei

Secondary structure

1714
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ08698
SMRiQ08698
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08698

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni177 – 178Substrate bindingBy similarity2
Regioni386 – 390Substrate bindingBy similarity5
Regioni588 – 592Substrate bindingBy similarity5

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105BZH Bacteria
COG0209 LUCA
HOGENOMiHOG000246165
KOiK00525
OMAiLEIWHID
PhylomeDBiQ08698

Family and domain databases

InterProiView protein in InterPro
IPR013346 NrdE_NrdA
IPR026459 RNR_1b_NrdE
IPR000788 RNR_lg_C
IPR013509 RNR_lsu_N
IPR013554 RNR_N
IPR008926 RNR_R1-su_N
IPR039718 Rrm1
PANTHERiPTHR11573 PTHR11573, 1 hit
PfamiView protein in Pfam
PF02867 Ribonuc_red_lgC, 1 hit
PF00317 Ribonuc_red_lgN, 1 hit
PF08343 RNR_N, 1 hit
PRINTSiPR01183 RIBORDTASEM1
SUPFAMiSSF48168 SSF48168, 1 hit
TIGRFAMsiTIGR02506 NrdE_NrdA, 1 hit
TIGR04170 RNR_1b_NrdE, 1 hit
PROSITEiView protein in PROSITE
PS00089 RIBORED_LARGE, 1 hit

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_003197.2
WP_000246626.1, NC_003197.2

Genome annotation databases

EnsemblBacteriaiAAL21692; AAL21692; STM2807
GeneIDi1254330
KEGGistm:STM2807
PATRICifig|99287.12.peg.2965

Similar proteinsi

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
PIRiS34271
RefSeqiNP_461733.1, NC_003197.2
WP_000246626.1, NC_003197.2

3D structure databases

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

Protein-protein interaction databases

STRINGi99287.STM2807

Chemistry databases

DrugBankiDB03222 2'-Deoxyadenosine 5'-Triphosphate
DB03258 2'-Deoxycytidine-5'-Triphosphate
DB02452 Thymidine-5'-Triphosphate

Proteomic databases

PaxDbiQ08698
PRIDEiQ08698

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL21692; AAL21692; STM2807
GeneIDi1254330
KEGGistm:STM2807
PATRICifig|99287.12.peg.2965

Phylogenomic databases

eggNOGiENOG4105BZH Bacteria
COG0209 LUCA
HOGENOMiHOG000246165
KOiK00525
OMAiLEIWHID
PhylomeDBiQ08698

Enzyme and pathway databases

UniPathwayi
UPA00326

BioCyciMetaCyc:MONOMER-13835
SENT99287:G1FZD-2835-MONOMER

Miscellaneous databases

EvolutionaryTraceiQ08698

Family and domain databases

InterProiView protein in InterPro
IPR013346 NrdE_NrdA
IPR026459 RNR_1b_NrdE
IPR000788 RNR_lg_C
IPR013509 RNR_lsu_N
IPR013554 RNR_N
IPR008926 RNR_R1-su_N
IPR039718 Rrm1
PANTHERiPTHR11573 PTHR11573, 1 hit
PfamiView protein in Pfam
PF02867 Ribonuc_red_lgC, 1 hit
PF00317 Ribonuc_red_lgN, 1 hit
PF08343 RNR_N, 1 hit
PRINTSiPR01183 RIBORDTASEM1
SUPFAMiSSF48168 SSF48168, 1 hit
TIGRFAMsiTIGR02506 NrdE_NrdA, 1 hit
TIGR04170 RNR_1b_NrdE, 1 hit
PROSITEiView protein in PROSITE
PS00089 RIBORED_LARGE, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRIR3_SALTY
AccessioniPrimary (citable) accession number: Q08698
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: January 23, 2007
Last modified: November 7, 2018
This is version 138 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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