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Protein

Ribonucleoside-diphosphate reductase subunit alpha

Gene

nrdE

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).By similarity

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 (By similarity).By similarity

Pathway: 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei153 – 1531SubstrateBy similarity
Sitei170 – 1701Important for hydrogen atom transferBy similarity
Sitei177 – 1771Allosteric effector bindingBy similarity
Binding sitei198 – 1981Substrate; via amide nitrogenBy similarity
Sitei207 – 2071Allosteric effector bindingBy similarity
Active sitei380 – 3801Proton acceptorBy similarity
Active sitei382 – 3821Cysteine radical intermediateBy similarity
Active sitei384 – 3841Proton acceptorBy similarity
Sitei409 – 4091Important for hydrogen atom transferBy similarity
Sitei683 – 6831Important for electron transferBy similarity
Sitei684 – 6841Important for electron transferBy similarity
Sitei695 – 6951Interacts with thioredoxin/glutaredoxinBy similarity
Sitei698 – 6981Interacts with thioredoxin/glutaredoxinBy similarity

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

BioCyciBSUB:BSU17380-MONOMER.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase subunit alpha (EC:1.17.4.1)
Alternative name(s):
Ribonucleotide reductase large subunit
Gene namesi
Name:nrdE
Synonyms:nrdA
Ordered Locus Names:BSU17380
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU17380. [Micado]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 700700Ribonucleoside-diphosphate reductase subunit alphaPRO_0000187209Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi170 ↔ 409Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP50620.
PRIDEiP50620.

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits.By similarity

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100009561.

Structurei

3D structure databases

ProteinModelPortaliP50620.
SMRiP50620. Positions 2-690.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni169 – 1702Substrate bindingBy similarity
Regioni380 – 3845Substrate bindingBy similarity
Regioni580 – 5845Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000246165.
InParanoidiP50620.
KOiK00525.
OMAiTCSAPRQ.
OrthoDBiEOG6J48HC.
PhylomeDBiP50620.

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.

P50620-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQNQVPKWI QLNNEIMIQK DGKFQFDKDK EAVHSYFVDY INQNTVFFHN
60 70 80 90 100
LKEKLDYLVE NQYYEEEFLS LYSFEDIKEV FKTAYAKKFR FPSFMSAFKF
110 120 130 140 150
YNDYALKTND KKKILERYED RISIVALFFA NGDTEKAKEY VNLMINQEYQ
160 170 180 190 200
PSTPTFLNAG RKRRGELVSC FLLEVNDSLN DISRAIDISM QLSKLGGGVS
210 220 230 240 250
LNLSKLRAKG EAIKDVENAT KGVVGVMKLL DNAFRYADQM GQRQGSGAAY
260 270 280 290 300
LNIFHRDIND FLDTKKISAD EDVRVKTLSI GVVIPDKFVE LAREDKAAYV
310 320 330 340 350
FYPHTIYKEY GQHMDEMDMN EMYDKFVDNP RVKKEKINPR KLLEKLAMLR
360 370 380 390 400
SESGYPYIMF QDNVNKVHAN NHISKVKFSN LCSEVLQASQ VSSYTDYDEE
410 420 430 440 450
DEIGLDISCN LGSLNILNVM EHKSIEKTVK LATDSLTHVS ETTDIRNAPA
460 470 480 490 500
VRRANKAMKS IGLGAMNLHG YLAQNGIAYE SPEARDFANT FFMMVNFYSI
510 520 530 540 550
QRSAEIAKEK GETFDQYEGS TYATGEYFDK YVSTDFSPKY EKIANLFEGM
560 570 580 590 600
HIPTTEDWKK LKAFVAEHGM YHSYRLCIAP TGSISYVQSS TASVMPIMER
610 620 630 640 650
IEERTYGNSK TYYPMPGLAS NNWFFYKEAY DMDMFKVVDM IATIQQHIDQ
660 670 680 690 700
GISFTLFLKD TMTTRDLNRI DLYAHHRGIK TIYYARTKDT GQDSCLSCVV
Length:700
Mass (Da):80,689
Last modified:October 1, 1996 - v1
Checksum:iD2D4B914B97BBFA6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z68500 Genomic DNA. Translation: CAA92810.1.
AL009126 Genomic DNA. Translation: CAB13622.1.
PIRiB69667.
RefSeqiNP_389620.1. NC_000964.3.
WP_003245700.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13622; CAB13622; BSU17380.
GeneIDi940091.
KEGGibsu:BSU17380.
PATRICi18975287. VBIBacSub10457_1835.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z68500 Genomic DNA. Translation: CAA92810.1.
AL009126 Genomic DNA. Translation: CAB13622.1.
PIRiB69667.
RefSeqiNP_389620.1. NC_000964.3.
WP_003245700.1. NZ_JNCM01000035.1.

3D structure databases

ProteinModelPortaliP50620.
SMRiP50620. Positions 2-690.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100009561.

Proteomic databases

PaxDbiP50620.
PRIDEiP50620.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13622; CAB13622; BSU17380.
GeneIDi940091.
KEGGibsu:BSU17380.
PATRICi18975287. VBIBacSub10457_1835.

Organism-specific databases

GenoListiBSU17380. [Micado]

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000246165.
InParanoidiP50620.
KOiK00525.
OMAiTCSAPRQ.
OrthoDBiEOG6J48HC.
PhylomeDBiP50620.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciBSUB:BSU17380-MONOMER.

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...

Publicationsi

« Hide 'large scale' publications
  1. "The Bacillus subtilis genes for ribonucleotide reductase are similar to the genes for the second class I NrdE/NrdF enzymes of Enterobacteriaceae."
    Scotti C., Valbuzzi A., Perego M., Galizzi A., Albertini A.M.
    Microbiology 142:2995-3004(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.

Entry informationi

Entry nameiRIR1_BACSU
AccessioniPrimary (citable) accession number: P50620
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: June 24, 2015
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.