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O31875

- NRDEB_BACSU

UniProt

O31875 - NRDEB_BACSU

Protein

Ribonucleoside-diphosphate reductase NrdEB subunit alpha

Gene

nrdEB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 99 (01 Oct 2014)
      Sequence version 2 (01 Oct 2003)
      Previous versions | rss
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    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

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei152 – 1521SubstrateBy similarity
    Sitei169 – 1691Important for hydrogen atom transferBy similarity
    Sitei176 – 1761Allosteric effector bindingBy similarity
    Binding sitei197 – 1971Substrate; via amide nitrogenBy similarity
    Sitei206 – 2061Allosteric effector bindingBy similarity
    Active sitei379 – 3791Proton acceptorSequence Analysis
    Active sitei381 – 3811Cysteine radical intermediateSequence Analysis
    Active sitei768 – 7681Proton acceptorSequence Analysis
    Sitei793 – 7931Important for hydrogen atom transferBy similarity
    Sitei1067 – 10671Important for electron transferBy similarity
    Sitei1068 – 10681Important for electron transferBy similarity
    Sitei1079 – 10791Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei1082 – 10821Interacts with thioredoxin/glutaredoxinBy 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

    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

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 380380Ribonucleoside-diphosphate reductase NrdEB subunit alpha, 1st partPRO_0000377530Add
    BLAST
    Chaini381 – 765385Bsu nrdEB inteinPRO_0000377531Add
    BLAST
    Chaini766 – 1084319Ribonucleoside-diphosphate reductase NrdEB subunit alpha, 2nd partPRO_0000377532Add
    BLAST

    Amino acid modifications

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

    Post-translational modificationi

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

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini503 – 654152DOD-type homing endonucleasePROSITE-ProRule annotationAdd
    BLAST

    Region

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

    Sequence similaritiesi

    Contains 1 DOD-type homing endonuclease domain.PROSITE-ProRule annotation

    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

    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: October 1, 2014
    This is version 99 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