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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: 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: 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

GO - Biological processi

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.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi16 – 21Combined sources6
Helixi22 – 24Combined sources3
Helixi35 – 47Combined sources13
Helixi49 – 52Combined sources4
Helixi59 – 68Combined sources10
Helixi74 – 77Combined sources4
Helixi82 – 94Combined sources13
Helixi102 – 111Combined sources10
Beta strandi119 – 122Combined sources4
Helixi126 – 138Combined sources13
Helixi142 – 153Combined sources12
Beta strandi156 – 159Combined sources4
Helixi161 – 166Combined sources6
Beta strandi169 – 171Combined sources3
Beta strandi179 – 181Combined sources3
Helixi187 – 201Combined sources15
Turni202 – 204Combined sources3
Beta strandi206 – 210Combined sources5
Beta strandi224 – 226Combined sources3
Helixi232 – 244Combined sources13
Beta strandi254 – 260Combined sources7
Helixi266 – 270Combined sources5
Helixi271 – 273Combined sources3
Beta strandi279 – 281Combined sources3
Beta strandi287 – 291Combined sources5
Helixi295 – 301Combined sources7
Beta strandi305 – 309Combined sources5
Helixi311 – 318Combined sources8
Helixi322 – 324Combined sources3
Helixi327 – 336Combined sources10
Beta strandi342 – 346Combined sources5
Helixi347 – 361Combined sources15
Beta strandi365 – 367Combined sources3
Helixi369 – 375Combined sources7
Beta strandi378 – 380Combined sources3
Beta strandi406 – 408Combined sources3
Beta strandi416 – 421Combined sources6
Helixi422 – 426Combined sources5
Helixi431 – 447Combined sources17
Helixi455 – 464Combined sources10
Beta strandi467 – 472Combined sources6
Helixi474 – 480Combined sources7
Helixi488 – 516Combined sources29
Helixi523 – 525Combined sources3
Helixi527 – 530Combined sources4
Helixi532 – 534Combined sources3
Helixi535 – 538Combined sources4
Helixi547 – 556Combined sources10
Helixi563 – 576Combined sources14
Helixi592 – 596Combined sources5
Beta strandi600 – 603Combined sources4
Beta strandi608 – 612Combined sources5
Beta strandi615 – 618Combined sources4
Beta strandi620 – 623Combined sources4
Turni629 – 631Combined sources3
Helixi632 – 634Combined sources3
Helixi638 – 641Combined sources4
Helixi643 – 654Combined sources12
Beta strandi665 – 667Combined sources3
Helixi673 – 686Combined sources14
Beta strandi694 – 696Combined sources3

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...

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.
OMAiTLFMTDK.
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.
WP_000246626.1. 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.
PIRiS34271.
RefSeqiNP_461733.1. NC_003197.1.
WP_000246626.1. NC_003197.1.

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.

Proteomic databases

PaxDbiQ08698.
PRIDEiQ08698.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiENOG4105BZH. Bacteria.
COG0209. LUCA.
HOGENOMiHOG000246165.
KOiK00525.
OMAiTLFMTDK.
PhylomeDBiQ08698.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciMetaCyc:MONOMER-13835.

Miscellaneous databases

EvolutionaryTraceiQ08698.

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]
ProtoNetiSearch...

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 2, 2016
This is version 132 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

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.