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Protein

Ribonucleoside-diphosphate reductase nrdEB subunit alpha

Gene

bnrdE

Organism
Bacillus phage SPbeta (Bacillus phage SPBc2) (Bacteriophage SP-beta)
Status
Reviewed-Annotation score: 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).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 acceptorBy similarity
Active sitei381 – 3811Cysteine radical intermediateBy similarity
Active sitei768 – 7681Proton acceptorBy similarity
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
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

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:bnrdE
OrganismiBacillus phage SPbeta (Bacillus phage SPBc2) (Bacteriophage SP-beta)
Taxonomic identifieri66797 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesSiphoviridaeSpbetalikevirus
Virus hostiBacillus pumilus (Bacillus mesentericus) [TaxID: 1408]
Bacillus subtilis [TaxID: 1423]
ProteomesiUP000009091 Componenti: Genome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 380380Ribonucleoside-diphosphate reductase nrdEB subunit alpha, 1st partPRO_0000377533Add
BLAST
Chaini381 – 765385SPBc2 bnrdE inteinPRO_0000377534Add
BLAST
Chaini766 – 1084319Ribonucleoside-diphosphate reductase nrdEB subunit alpha, 2nd partPRO_0000377535Add
BLAST

Amino acid modifications

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

Post-translational modificationi

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

Keywords - PTMi

Autocatalytic cleavage, Disulfide bond, Protein splicing

Proteomic databases

PRIDEiO64173.

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits.By similarity

Structurei

3D structure databases

ProteinModelPortaliO64173.
SMRiO64173. 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

KOiK00525.

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.

O64173-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTNTIPNWIK LNNEIMIQKD GKYQFEKDKE AVHSYFVDYI NQNTVFFHDL
60 70 80 90 100
KEKLDYLIKN DYYEEEFLSK YTFEQIKSIY KIAYSYKFRF PSFMSAFKFY
110 120 130 140 150
NDYALKTNDK TKILERYEDR VSIVALYCAD GDYEKAVEEV HTMMKQEYQP
160 170 180 190 200
ATPTFLNAGR KRRGEMVSCF LLEVGDSLND ISRAIDISMQ LSKLGGGVAL
210 220 230 240 250
NLNKLRAKGE AIKDVENATK GVVGVMKLLD NAFRYADQMG QRQGSGAVYL
260 270 280 290 300
SVFHPDITDF LDTKKISADE DVRVKTLSIG VVVPDKFIEL AREDKDYYMF
310 320 330 340 350
YPHSVYKEYG QYLDELDINE MYDELVENPR VRKAKGNARK LLEQLAILRS
360 370 380 390 400
ESGYPYIMFA DNVNKVHPNE HISKVKFSNL CVTGETLLLT ENGYEKAADL
410 420 430 440 450
YKKQNDLKVV IDNRTKDFAV GSKGTTIVDA IPMQLTKKDA EIFKVKTKQG
460 470 480 490 500
YEIRATEWHK FYVKRDGEIQ KLQLNQLKTG DKLLVQSAEG AYGKIHEPDL
510 520 530 540 550
AYIMGIIAGD GTITEKTAKI YLYDNKKVLE QKVTDAVHRI IQKHKVDRAY
560 570 580 590 600
KHNTSLLPTF NMANPEKQDL LYMNSTVLFD ILKKFGMNKE TKTRVPEFIF
610 620 630 640 650
QANKETQAAY LSGLFQTDGC VNANHKAKAL TIELTSIHYE SLQDVQKLLL
660 670 680 690 700
NMGVYTTIYS NNKRSQELLP DGKGGSKLYN VKPTHKISIQ DRNSRELFMS
710 720 730 740 750
IVEMKEYDVY KFNLLTETLQ PKSRKPKHDF TAEIISIEED GVEDVYDTTQ
760 770 780 790 800
EDYHSLIFNG IVTGNCSEVL QSSQVSVYTD YDKEDEIGLD ISCNLGSMNI
810 820 830 840 850
VNVMSNQSIA STVRIAIDSL TTVTRKTNIV NAPAVARANT LMRSIGLGQM
860 870 880 890 900
NLHGFLAQNN IAYESEEAKD FANTYFMMVN FYSLQRSMEI ARETGETYYK
910 920 930 940 950
FDGSTYKSGE YFEKYVTNDY SPQYEKVKKL FGDQHIPNIQ DWMKLKEDVM
960 970 980 990 1000
KYGLYHSYRQ AIAPTGSISY VQSSTAGVMP IMERIEERTY GNSKTYYPMP
1010 1020 1030 1040 1050
GLSAQNWFFY KEAYDMDMFK VVDLIATIQQ HVDQGISFTL FLKDTMTTRD
1060 1070 1080
LNRIDLYAHH RGIKTLYYAR TKDTTQEGCL SCVV
Length:1,084
Mass (Da):124,621
Last modified:July 31, 1998 - v1
Checksum:iA89CFDF93218FC61
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF020713 Genomic DNA. Translation: AAC13134.1.
PIRiT12925.
RefSeqiNP_046713.1. NC_001884.1.

Genome annotation databases

GeneIDi1261459.
KEGGivg:1261459.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF020713 Genomic DNA. Translation: AAC13134.1.
PIRiT12925.
RefSeqiNP_046713.1. NC_001884.1.

3D structure databases

ProteinModelPortaliO64173.
SMRiO64173. Positions 374-466, 731-766.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiO64173.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1261459.
KEGGivg:1261459.

Phylogenomic databases

KOiK00525.

Enzyme and pathway databases

UniPathwayiUPA00326.

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]
ProtoNetiSearch...

Publicationsi

  1. "Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta."
    Lazarevic V., Soldo B., Duesterhoeft A., Hilbert H., Maueel C., Karamata D.
    Proc. Natl. Acad. Sci. U.S.A. 95:1692-1697(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].

Entry informationi

Entry nameiNRDEB_BPSPB
AccessioniPrimary (citable) accession number: O64173
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 15, 2009
Last sequence update: July 31, 1998
Last modified: March 31, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  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.