NRDEB_BACSU
ID NRDEB_BACSU Reviewed; 1084 AA.
AC O31875; Q7BVQ5;
DT 16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2003, sequence version 2.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Ribonucleoside-diphosphate reductase NrdEB subunit alpha;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase large subunit;
DE Contains:
DE RecName: Full=Bsu nrdEB intein;
GN Name=nrdEB; Synonyms=yojP, yosN; OrderedLocusNames=BSU20060;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP SEQUENCE REVISION TO C-TERMINUS.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 424-1084.
RC STRAIN=168;
RX PubMed=9679200; DOI=10.1093/dnares/5.2.121;
RA Ghim S.-Y., Choi S.-K., Shin B.-S., Park S.-H.;
RT "An 8 kb nucleotide sequence at the 3' flanking region of the sspC gene
RT (184 degrees) on the Bacillus subtilis 168 chromosome containing an intein
RT and an intron.";
RL DNA Res. 5:121-126(1998).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-
CC diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-
CC diphosphate; Xref=Rhea:RHEA:23252, Rhea:RHEA-COMP:10698, Rhea:RHEA-
CC COMP:10700, ChEBI:CHEBI:15377, ChEBI:CHEBI:29950, ChEBI:CHEBI:50058,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:73316; EC=1.17.4.1;
CC -!- ACTIVITY REGULATION: Under complex allosteric control mediated by
CC deoxynucleoside triphosphates and ATP binding. The type of nucleotide
CC bound at the specificity site determines substrate preference. It seems
CC probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP
CC reduction and dTTP favors GDP reduction (By similarity). {ECO:0000250}.
CC -!- PATHWAY: Genetic information processing; DNA replication.
CC -!- SUBUNIT: Tetramer of two alpha and two beta subunits. {ECO:0000250}.
CC -!- PTM: This protein undergoes protein self-splicing that involves post-
CC translational excision of the intervening region (intein) followed by
CC peptide ligation. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase large
CC chain family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL009126; CAB13898.2; -; Genomic_DNA.
DR EMBL; AF012906; AAB92484.1; -; Genomic_DNA.
DR PIR; H69926; H69926.
DR RefSeq; NP_389888.2; NC_000964.3.
DR RefSeq; WP_010886539.1; NC_000964.3.
DR AlphaFoldDB; O31875; -.
DR SMR; O31875; -.
DR STRING; 224308.BSU20060; -.
DR PaxDb; O31875; -.
DR PRIDE; O31875; -.
DR EnsemblBacteria; CAB13898; CAB13898; BSU_20060.
DR GeneID; 939475; -.
DR KEGG; bsu:BSU20060; -.
DR PATRIC; fig|224308.43.peg.2120; -.
DR eggNOG; COG0209; Bacteria.
DR eggNOG; COG1372; Bacteria.
DR InParanoid; O31875; -.
DR OMA; PLYPFES; -.
DR BioCyc; BSUB:BSU20060-MON; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IBA:GO_Central.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IBA:GO_Central.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR Gene3D; 3.10.28.10; -; 1.
DR InterPro; IPR003586; Hint_dom_C.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR027434; Homing_endonucl.
DR InterPro; IPR006142; INTEIN.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR004042; Intein_endonuc.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR004860; LAGLIDADG_2.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013509; RNR_lsu_N.
DR InterPro; IPR013554; RNR_N.
DR InterPro; IPR008926; RNR_R1-su_N.
DR InterPro; IPR039718; Rrm1.
DR PANTHER; PTHR11573; PTHR11573; 1.
DR Pfam; PF14528; LAGLIDADG_3; 1.
DR Pfam; PF02867; Ribonuc_red_lgC; 1.
DR Pfam; PF00317; Ribonuc_red_lgN; 1.
DR Pfam; PF08343; RNR_N; 1.
DR PRINTS; PR00379; INTEIN.
DR SMART; SM00305; HintC; 1.
DR SMART; SM00306; HintN; 1.
DR SUPFAM; SSF48168; SSF48168; 1.
DR SUPFAM; SSF51294; SSF51294; 1.
DR SUPFAM; SSF55608; SSF55608; 1.
DR TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
DR PROSITE; PS00089; RIBORED_LARGE; 1.
PE 3: Inferred from homology;
KW Allosteric enzyme; ATP-binding; Autocatalytic cleavage;
KW Deoxyribonucleotide synthesis; Disulfide bond; Nucleotide-binding;
KW Oxidoreductase; Protein splicing; Reference proteome.
FT CHAIN 1..380
FT /note="Ribonucleoside-diphosphate reductase NrdEB subunit
FT alpha, 1st part"
FT /id="PRO_0000377530"
FT CHAIN 381..765
FT /note="Bsu nrdEB intein"
FT /id="PRO_0000377531"
FT CHAIN 766..1084
FT /note="Ribonucleoside-diphosphate reductase NrdEB subunit
FT alpha, 2nd part"
FT /id="PRO_0000377532"
FT DOMAIN 503..654
FT /note="DOD-type homing endonuclease"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273"
FT ACT_SITE 379
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT ACT_SITE 381
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000255"
FT ACT_SITE 768
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT BINDING 152
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 168..169
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 197
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 964..968
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 169
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 176
FT /note="Allosteric effector binding"
FT /evidence="ECO:0000250"
FT SITE 206
FT /note="Allosteric effector binding"
FT /evidence="ECO:0000250"
FT SITE 793
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 1067
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 1068
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 1079
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 1082
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT DISULFID 169..793
FT /note="Redox-active"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1084 AA; 124621 MW; A89CFDF93218FC61 CRC64;
MTNTIPNWIK LNNEIMIQKD GKYQFEKDKE AVHSYFVDYI NQNTVFFHDL KEKLDYLIKN
DYYEEEFLSK YTFEQIKSIY KIAYSYKFRF PSFMSAFKFY NDYALKTNDK TKILERYEDR
VSIVALYCAD GDYEKAVEEV HTMMKQEYQP ATPTFLNAGR KRRGEMVSCF LLEVGDSLND
ISRAIDISMQ LSKLGGGVAL NLNKLRAKGE AIKDVENATK GVVGVMKLLD NAFRYADQMG
QRQGSGAVYL SVFHPDITDF LDTKKISADE DVRVKTLSIG VVVPDKFIEL AREDKDYYMF
YPHSVYKEYG QYLDELDINE MYDELVENPR VRKAKGNARK LLEQLAILRS ESGYPYIMFA
DNVNKVHPNE HISKVKFSNL CVTGETLLLT ENGYEKAADL YKKQNDLKVV IDNRTKDFAV
GSKGTTIVDA IPMQLTKKDA EIFKVKTKQG YEIRATEWHK FYVKRDGEIQ KLQLNQLKTG
DKLLVQSAEG AYGKIHEPDL AYIMGIIAGD GTITEKTAKI YLYDNKKVLE QKVTDAVHRI
IQKHKVDRAY KHNTSLLPTF NMANPEKQDL LYMNSTVLFD ILKKFGMNKE TKTRVPEFIF
QANKETQAAY LSGLFQTDGC VNANHKAKAL TIELTSIHYE SLQDVQKLLL NMGVYTTIYS
NNKRSQELLP DGKGGSKLYN VKPTHKISIQ DRNSRELFMS IVEMKEYDVY KFNLLTETLQ
PKSRKPKHDF TAEIISIEED GVEDVYDTTQ EDYHSLIFNG IVTGNCSEVL QSSQVSVYTD
YDKEDEIGLD ISCNLGSMNI VNVMSNQSIA STVRIAIDSL TTVTRKTNIV NAPAVARANT
LMRSIGLGQM NLHGFLAQNN IAYESEEAKD FANTYFMMVN FYSLQRSMEI ARETGETYYK
FDGSTYKSGE YFEKYVTNDY SPQYEKVKKL FGDQHIPNIQ DWMKLKEDVM KYGLYHSYRQ
AIAPTGSISY VQSSTAGVMP IMERIEERTY GNSKTYYPMP GLSAQNWFFY KEAYDMDMFK
VVDLIATIQQ HVDQGISFTL FLKDTMTTRD LNRIDLYAHH RGIKTLYYAR TKDTTQEGCL
SCVV
