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O31875

- NRDEB_BACSU

UniProt

O31875 - NRDEB_BACSU

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Protein
Ribonucleoside-diphosphate reductase NrdEB subunit alpha
Gene
nrdEB, yojP, yosN, BSU20060
Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 4 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.

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.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei152 – 1521Substrate By similarity
Sitei169 – 1691Important for hydrogen atom transfer By similarity
Sitei176 – 1761Allosteric effector binding By similarity
Binding sitei197 – 1971Substrate; via amide nitrogen By similarity
Sitei206 – 2061Allosteric effector binding By similarity
Active sitei379 – 3791Proton acceptor Reviewed prediction
Active sitei381 – 3811Cysteine radical intermediate Reviewed prediction
Active sitei768 – 7681Proton acceptor Reviewed prediction
Sitei793 – 7931Important for hydrogen atom transfer By similarity
Sitei1067 – 10671Important for electron transfer By similarity
Sitei1068 – 10681Important for electron transfer By similarity
Sitei1079 – 10791Interacts with thioredoxin/glutaredoxin By similarity
Sitei1082 – 10821Interacts with thioredoxin/glutaredoxin By similarity

GO - Molecular functioni

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

GO - Biological processi

  1. DNA replication Source: UniProtKB-UniPathway
  2. intein-mediated protein splicing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU20060-MONOMER.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase NrdEB subunit alpha (EC:1.17.4.1)
Alternative name(s):
Ribonucleotide reductase large subunit
Cleaved into the following chain:
Gene namesi
Name:nrdEB
Synonyms:yojP, yosN
Ordered Locus Names:BSU20060
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570: Chromosome

Organism-specific databases

GenoListiBSU20060. [Micado]

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
Chaini1 – 380380Ribonucleoside-diphosphate reductase NrdEB subunit alpha, 1st part
PRO_0000377530Add
BLAST
Chaini381 – 765385Bsu nrdEB intein
PRO_0000377531Add
BLAST
Chaini766 – 1084319Ribonucleoside-diphosphate reductase NrdEB subunit alpha, 2nd part
PRO_0000377532Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi169 ↔ 793Redox-active By similarity

Post-translational modificationi

This protein undergoes protein self-splicing that involves post-translational excision of the intervening region (intein) followed by peptide ligation Inferred.

Keywords - PTMi

Autocatalytic cleavage, Disulfide bond, Protein splicing

Proteomic databases

PaxDbiO31875.
PRIDEiO31875.

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits By similarity.

Protein-protein interaction databases

STRINGi224308.BSU20060.

Structurei

3D structure databases

ProteinModelPortaliO31875.
SMRiO31875. Positions 374-466, 731-766.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini503 – 654152DOD-type homing endonuclease
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni168 – 1692Substrate binding By similarity
Regioni964 – 9685Substrate binding By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000113851.
KOiK00525.
OMAiTVVYHAL.
OrthoDBiEOG6NKQVV.

Family and domain databases

Gene3Di2.170.16.10. 2 hits.
3.10.28.10. 1 hit.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR013554. RNR_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF14528. LAGLIDADG_3. 1 hit.
PF02867. Ribonuc_red_lgC. 2 hits.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF48168. SSF48168. 1 hit.
SSF51294. SSF51294. 2 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O31875-1 [UniParc]FASTAAdd to Basket

« Hide

MTNTIPNWIK LNNEIMIQKD GKYQFEKDKE AVHSYFVDYI NQNTVFFHDL     50
KEKLDYLIKN DYYEEEFLSK YTFEQIKSIY KIAYSYKFRF PSFMSAFKFY 100
NDYALKTNDK TKILERYEDR VSIVALYCAD GDYEKAVEEV HTMMKQEYQP 150
ATPTFLNAGR KRRGEMVSCF LLEVGDSLND ISRAIDISMQ LSKLGGGVAL 200
NLNKLRAKGE AIKDVENATK GVVGVMKLLD NAFRYADQMG QRQGSGAVYL 250
SVFHPDITDF LDTKKISADE DVRVKTLSIG VVVPDKFIEL AREDKDYYMF 300
YPHSVYKEYG QYLDELDINE MYDELVENPR VRKAKGNARK LLEQLAILRS 350
ESGYPYIMFA DNVNKVHPNE HISKVKFSNL CVTGETLLLT ENGYEKAADL 400
YKKQNDLKVV IDNRTKDFAV GSKGTTIVDA IPMQLTKKDA EIFKVKTKQG 450
YEIRATEWHK FYVKRDGEIQ KLQLNQLKTG DKLLVQSAEG AYGKIHEPDL 500
AYIMGIIAGD GTITEKTAKI YLYDNKKVLE QKVTDAVHRI IQKHKVDRAY 550
KHNTSLLPTF NMANPEKQDL LYMNSTVLFD ILKKFGMNKE TKTRVPEFIF 600
QANKETQAAY LSGLFQTDGC VNANHKAKAL TIELTSIHYE SLQDVQKLLL 650
NMGVYTTIYS NNKRSQELLP DGKGGSKLYN VKPTHKISIQ DRNSRELFMS 700
IVEMKEYDVY KFNLLTETLQ PKSRKPKHDF TAEIISIEED GVEDVYDTTQ 750
EDYHSLIFNG IVTGNCSEVL QSSQVSVYTD YDKEDEIGLD ISCNLGSMNI 800
VNVMSNQSIA STVRIAIDSL TTVTRKTNIV NAPAVARANT LMRSIGLGQM 850
NLHGFLAQNN IAYESEEAKD FANTYFMMVN FYSLQRSMEI ARETGETYYK 900
FDGSTYKSGE YFEKYVTNDY SPQYEKVKKL FGDQHIPNIQ DWMKLKEDVM 950
KYGLYHSYRQ AIAPTGSISY VQSSTAGVMP IMERIEERTY GNSKTYYPMP 1000
GLSAQNWFFY KEAYDMDMFK VVDLIATIQQ HVDQGISFTL FLKDTMTTRD 1050
LNRIDLYAHH RGIKTLYYAR TKDTTQEGCL SCVV 1084
Length:1,084
Mass (Da):124,621
Last modified:October 1, 2003 - v2
Checksum:iA89CFDF93218FC61
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL009126 Genomic DNA. Translation: CAB13898.2.
AF012906 Genomic DNA. Translation: AAB92484.1.
PIRiH69926.
RefSeqiNP_389888.2. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB13898; CAB13898; BSU20060.
GeneIDi939475.
KEGGibsu:BSU20060.
PATRICi18975859. VBIBacSub10457_2120.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL009126 Genomic DNA. Translation: CAB13898.2 .
AF012906 Genomic DNA. Translation: AAB92484.1 .
PIRi H69926.
RefSeqi NP_389888.2. NC_000964.3.

3D structure databases

ProteinModelPortali O31875.
SMRi O31875. Positions 374-466, 731-766.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 224308.BSU20060.

Proteomic databases

PaxDbi O31875.
PRIDEi O31875.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAB13898 ; CAB13898 ; BSU20060 .
GeneIDi 939475.
KEGGi bsu:BSU20060.
PATRICi 18975859. VBIBacSub10457_2120.

Organism-specific databases

GenoListi BSU20060. [Micado ]

Phylogenomic databases

eggNOGi COG0209.
HOGENOMi HOG000113851.
KOi K00525.
OMAi TVVYHAL.
OrthoDBi EOG6NKQVV.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci BSUB:BSU20060-MONOMER.

Family and domain databases

Gene3Di 2.170.16.10. 2 hits.
3.10.28.10. 1 hit.
InterProi IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR013554. RNR_N.
IPR008926. RNR_R1-su_N.
[Graphical view ]
Pfami PF14528. LAGLIDADG_3. 1 hit.
PF02867. Ribonuc_red_lgC. 2 hits.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view ]
PRINTSi PR00379. INTEIN.
SMARTi SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view ]
SUPFAMi SSF48168. SSF48168. 1 hit.
SSF51294. SSF51294. 2 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsi TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEi PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "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.
  2. "From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later."
    Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.
    Microbiology 155:1758-1775(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION TO C-TERMINUS.
  3. "An 8 kb nucleotide sequence at the 3' flanking region of the sspC gene (184 degrees) on the Bacillus subtilis 168 chromosome containing an intein and an intron."
    Ghim S.-Y., Choi S.-K., Shin B.-S., Park S.-H.
    DNA Res. 5:121-126(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 424-1084.
    Strain: 168.

Entry informationi

Entry nameiNRDEB_BACSU
AccessioniPrimary (citable) accession number: O31875
Secondary accession number(s): Q7BVQ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 16, 2009
Last sequence update: October 1, 2003
Last modified: June 11, 2014
This is version 98 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

Allosteric enzyme, Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3

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