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O31875 (NRDEB_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 98. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribonucleoside-diphosphate reductase NrdEB subunit alpha

EC=1.17.4.1
Alternative name(s):
Ribonucleotide reductase large subunit

Cleaved into the following chain:

  1. Bsu nrdEB intein
Gene names
Name:nrdEB
Synonyms:yojP, yosN
Ordered Locus Names:BSU20060
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length1084 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

General annotation (Comments)

Function

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

Catalytic activity

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

Enzyme regulation

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.

Pathway

Genetic information processing; DNA replication.

Subunit structure

Tetramer of two alpha and two beta subunits By similarity.

Post-translational modification

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

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase large chain family.

Contains 1 DOD-type homing endonuclease domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 380380Ribonucleoside-diphosphate reductase NrdEB subunit alpha, 1st part
PRO_0000377530
Chain381 – 765385Bsu nrdEB intein
PRO_0000377531
Chain766 – 1084319Ribonucleoside-diphosphate reductase NrdEB subunit alpha, 2nd part
PRO_0000377532

Regions

Domain503 – 654152DOD-type homing endonuclease
Region168 – 1692Substrate binding By similarity
Region964 – 9685Substrate binding By similarity

Sites

Active site3791Proton acceptor Potential
Active site3811Cysteine radical intermediate Potential
Active site7681Proton acceptor Potential
Binding site1521Substrate By similarity
Binding site1971Substrate; via amide nitrogen By similarity
Site1691Important for hydrogen atom transfer By similarity
Site1761Allosteric effector binding By similarity
Site2061Allosteric effector binding By similarity
Site7931Important for hydrogen atom transfer By similarity
Site10671Important for electron transfer By similarity
Site10681Important for electron transfer By similarity
Site10791Interacts with thioredoxin/glutaredoxin By similarity
Site10821Interacts with thioredoxin/glutaredoxin By similarity

Amino acid modifications

Disulfide bond169 ↔ 793Redox-active By similarity

Sequences

Sequence LengthMass (Da)Tools
O31875 [UniParc].

Last modified October 1, 2003. Version 2.
Checksum: A89CFDF93218FC61

FASTA1,084124,621
        10         20         30         40         50         60 
MTNTIPNWIK LNNEIMIQKD GKYQFEKDKE AVHSYFVDYI NQNTVFFHDL KEKLDYLIKN 

        70         80         90        100        110        120 
DYYEEEFLSK YTFEQIKSIY KIAYSYKFRF PSFMSAFKFY NDYALKTNDK TKILERYEDR 

       130        140        150        160        170        180 
VSIVALYCAD GDYEKAVEEV HTMMKQEYQP ATPTFLNAGR KRRGEMVSCF LLEVGDSLND 

       190        200        210        220        230        240 
ISRAIDISMQ LSKLGGGVAL NLNKLRAKGE AIKDVENATK GVVGVMKLLD NAFRYADQMG 

       250        260        270        280        290        300 
QRQGSGAVYL SVFHPDITDF LDTKKISADE DVRVKTLSIG VVVPDKFIEL AREDKDYYMF 

       310        320        330        340        350        360 
YPHSVYKEYG QYLDELDINE MYDELVENPR VRKAKGNARK LLEQLAILRS ESGYPYIMFA 

       370        380        390        400        410        420 
DNVNKVHPNE HISKVKFSNL CVTGETLLLT ENGYEKAADL YKKQNDLKVV IDNRTKDFAV 

       430        440        450        460        470        480 
GSKGTTIVDA IPMQLTKKDA EIFKVKTKQG YEIRATEWHK FYVKRDGEIQ KLQLNQLKTG 

       490        500        510        520        530        540 
DKLLVQSAEG AYGKIHEPDL AYIMGIIAGD GTITEKTAKI YLYDNKKVLE QKVTDAVHRI 

       550        560        570        580        590        600 
IQKHKVDRAY KHNTSLLPTF NMANPEKQDL LYMNSTVLFD ILKKFGMNKE TKTRVPEFIF 

       610        620        630        640        650        660 
QANKETQAAY LSGLFQTDGC VNANHKAKAL TIELTSIHYE SLQDVQKLLL NMGVYTTIYS 

       670        680        690        700        710        720 
NNKRSQELLP DGKGGSKLYN VKPTHKISIQ DRNSRELFMS IVEMKEYDVY KFNLLTETLQ 

       730        740        750        760        770        780 
PKSRKPKHDF TAEIISIEED GVEDVYDTTQ EDYHSLIFNG IVTGNCSEVL QSSQVSVYTD 

       790        800        810        820        830        840 
YDKEDEIGLD ISCNLGSMNI VNVMSNQSIA STVRIAIDSL TTVTRKTNIV NAPAVARANT 

       850        860        870        880        890        900 
LMRSIGLGQM NLHGFLAQNN IAYESEEAKD FANTYFMMVN FYSLQRSMEI ARETGETYYK 

       910        920        930        940        950        960 
FDGSTYKSGE YFEKYVTNDY SPQYEKVKKL FGDQHIPNIQ DWMKLKEDVM KYGLYHSYRQ 

       970        980        990       1000       1010       1020 
AIAPTGSISY VQSSTAGVMP IMERIEERTY GNSKTYYPMP GLSAQNWFFY KEAYDMDMFK 

      1030       1040       1050       1060       1070       1080 
VVDLIATIQQ HVDQGISFTL FLKDTMTTRD LNRIDLYAHH RGIKTLYYAR TKDTTQEGCL 


SCVV 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AL009126 Genomic DNA. Translation: CAB13898.2.
AF012906 Genomic DNA. Translation: AAB92484.1.
PIRH69926.
RefSeqNP_389888.2. NC_000964.3.

3D structure databases

ProteinModelPortalO31875.
SMRO31875. Positions 374-466, 731-766.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU20060.

Proteomic databases

PaxDbO31875.
PRIDEO31875.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB13898; CAB13898; BSU20060.
GeneID939475.
KEGGbsu:BSU20060.
PATRIC18975859. VBIBacSub10457_2120.

Organism-specific databases

GenoListBSU20060. [Micado]

Phylogenomic databases

eggNOGCOG0209.
HOGENOMHOG000113851.
KOK00525.
OMATVVYHAL.
OrthoDBEOG6NKQVV.

Enzyme and pathway databases

BioCycBSUB:BSU20060-MONOMER.
UniPathwayUPA00326.

Family and domain databases

Gene3D2.170.16.10. 2 hits.
3.10.28.10. 1 hit.
InterProIPR028992. 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]
PfamPF14528. LAGLIDADG_3. 1 hit.
PF02867. Ribonuc_red_lgC. 2 hits.
PF00317. Ribonuc_red_lgN. 1 hit.
PF08343. RNR_N. 1 hit.
[Graphical view]
PRINTSPR00379. INTEIN.
SMARTSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMSSF48168. SSF48168. 1 hit.
SSF51294. SSF51294. 2 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameNRDEB_BACSU
AccessionPrimary (citable) accession number: O31875
Secondary accession number(s): Q7BVQ5
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

Intein-containing proteins

List of intein-containing protein entries

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList