RIR1_BACSU
ID RIR1_BACSU Reviewed; 700 AA.
AC P50620;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Ribonucleoside-diphosphate reductase subunit alpha;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase large subunit;
GN Name=nrdE {ECO:0000303|PubMed:8969495}; Synonyms=nrdA;
GN OrderedLocusNames=BSU17380;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], OPERON, DISRUPTION PHENOTYPE, AND
RP MUTAGENESIS OF HIS-255.
RC STRAIN=168;
RX PubMed=8969495; DOI=10.1099/13500872-142-11-2995;
RA Scotti C., Valbuzzi A., Perego M., Galizzi A., Albertini A.M.;
RT "The Bacillus subtilis genes for ribonucleotide reductase are similar to
RT the genes for the second class I NrdE/NrdF enzymes of Enterobacteriaceae.";
RL Microbiology 142:2995-3004(1996).
RN [2]
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).
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 -!- INDUCTION: Part of the probable nrdI(ymaA)-nrdE-nrdF-ymaB operon.
CC Expression is constitutive but low, dramatically induced by thymidine
CC starvation which requires recA. {ECO:0000269|PubMed:8969495}.
CC -!- DISRUPTION PHENOTYPE: Essential, at least the last 3 genes of the locus
CC cannot be deleted; could be due to polar effects on downstream ymaB.
CC {ECO:0000269|PubMed:8969495}.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase large
CC chain family. {ECO:0000305}.
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DR EMBL; Z68500; CAA92810.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13622.1; -; Genomic_DNA.
DR PIR; B69667; B69667.
DR RefSeq; NP_389620.1; NC_000964.3.
DR RefSeq; WP_003245700.1; NZ_JNCM01000035.1.
DR PDB; 6CGL; X-ray; 3.20 A; A/B=1-700.
DR PDB; 6CGM; X-ray; 2.00 A; A=1-700.
DR PDB; 6CGN; X-ray; 2.26 A; A=1-700.
DR PDB; 6MT9; X-ray; 2.50 A; A=1-700.
DR PDB; 6MV9; X-ray; 2.95 A; A/B=1-700.
DR PDB; 6MVE; X-ray; 2.55 A; A=1-700.
DR PDB; 6MW3; EM; 4.65 A; C/D=1-700.
DR PDB; 6MYX; EM; 6.00 A; C/D/I/J=1-700.
DR PDBsum; 6CGL; -.
DR PDBsum; 6CGM; -.
DR PDBsum; 6CGN; -.
DR PDBsum; 6MT9; -.
DR PDBsum; 6MV9; -.
DR PDBsum; 6MVE; -.
DR PDBsum; 6MW3; -.
DR PDBsum; 6MYX; -.
DR AlphaFoldDB; P50620; -.
DR SMR; P50620; -.
DR STRING; 224308.BSU17380; -.
DR jPOST; P50620; -.
DR PaxDb; P50620; -.
DR PRIDE; P50620; -.
DR EnsemblBacteria; CAB13622; CAB13622; BSU_17380.
DR GeneID; 940091; -.
DR KEGG; bsu:BSU17380; -.
DR PATRIC; fig|224308.179.peg.1884; -.
DR eggNOG; COG0209; Bacteria.
DR InParanoid; P50620; -.
DR OMA; RGSIQNI; -.
DR PhylomeDB; P50620; -.
DR BioCyc; BSUB:BSU17380-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:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IMP:CACAO.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IBA:GO_Central.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR InterPro; IPR013346; NrdE_NrdA.
DR InterPro; IPR026459; RNR_1b_NrdE.
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; PF02867; Ribonuc_red_lgC; 1.
DR Pfam; PF00317; Ribonuc_red_lgN; 1.
DR Pfam; PF08343; RNR_N; 1.
DR PRINTS; PR01183; RIBORDTASEM1.
DR SUPFAM; SSF48168; SSF48168; 1.
DR TIGRFAMs; TIGR02506; NrdE_NrdA; 1.
DR TIGRFAMs; TIGR04170; RNR_1b_NrdE; 1.
DR PROSITE; PS00089; RIBORED_LARGE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; ATP-binding;
KW Deoxyribonucleotide synthesis; Disulfide bond; Nucleotide-binding;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..700
FT /note="Ribonucleoside-diphosphate reductase subunit alpha"
FT /id="PRO_0000187209"
FT ACT_SITE 380
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 382
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 384
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 153
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 169..170
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 198
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 380..384
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 580..584
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 170
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 177
FT /note="Allosteric effector binding"
FT /evidence="ECO:0000250"
FT SITE 207
FT /note="Allosteric effector binding"
FT /evidence="ECO:0000250"
FT SITE 409
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 683
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 684
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 695
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 698
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT DISULFID 170..409
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT MUTAGEN 255
FT /note="H->Y: In ts-A 73; temperature-sensitive lethal
FT mutation."
FT /evidence="ECO:0000269|PubMed:8969495"
FT HELIX 8..14
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 15..17
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 20..23
FT /evidence="ECO:0007829|PDB:6MT9"
FT HELIX 28..39
FT /evidence="ECO:0007829|PDB:6CGM"
FT TURN 40..44
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 51..60
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 67..70
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 74..86
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 94..103
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:6CGN"
FT HELIX 118..130
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 134..145
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 148..151
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 153..158
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:6CGN"
FT STRAND 170..174
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 179..193
FT /evidence="ECO:0007829|PDB:6CGM"
FT TURN 194..196
FT /evidence="ECO:0007829|PDB:6MV9"
FT STRAND 198..202
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 214..218
FT /evidence="ECO:0007829|PDB:6CGN"
FT HELIX 219..222
FT /evidence="ECO:0007829|PDB:6CGN"
FT HELIX 223..233
FT /evidence="ECO:0007829|PDB:6CGM"
FT TURN 239..241
FT /evidence="ECO:0007829|PDB:6MV9"
FT STRAND 246..252
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 258..263
FT /evidence="ECO:0007829|PDB:6CGM"
FT TURN 271..273
FT /evidence="ECO:0007829|PDB:6CGN"
FT STRAND 279..284
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 286..293
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 298..301
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 303..310
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 314..316
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 319..328
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 334..337
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 339..353
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 357..360
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 361..365
FT /evidence="ECO:0007829|PDB:6CGM"
FT TURN 369..373
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 397..399
FT /evidence="ECO:0007829|PDB:6MV9"
FT STRAND 407..415
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 416..422
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 425..442
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 449..458
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 461..466
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 468..474
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 482..510
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 517..519
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 521..524
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 526..528
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 529..533
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 541..546
FT /evidence="ECO:0007829|PDB:6CGM"
FT TURN 547..549
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 555..568
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 584..587
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 600..606
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 609..614
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 620..625
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 629..631
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 634..645
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 656..658
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 664..676
FT /evidence="ECO:0007829|PDB:6CGM"
FT STRAND 681..684
FT /evidence="ECO:0007829|PDB:6MT9"
FT STRAND 685..687
FT /evidence="ECO:0007829|PDB:6CGM"
FT HELIX 696..698
FT /evidence="ECO:0007829|PDB:6MT9"
SQ SEQUENCE 700 AA; 80689 MW; D2D4B914B97BBFA6 CRC64;
MSQNQVPKWI QLNNEIMIQK DGKFQFDKDK EAVHSYFVDY INQNTVFFHN LKEKLDYLVE
NQYYEEEFLS LYSFEDIKEV FKTAYAKKFR FPSFMSAFKF YNDYALKTND KKKILERYED
RISIVALFFA NGDTEKAKEY VNLMINQEYQ PSTPTFLNAG RKRRGELVSC FLLEVNDSLN
DISRAIDISM QLSKLGGGVS LNLSKLRAKG EAIKDVENAT KGVVGVMKLL DNAFRYADQM
GQRQGSGAAY LNIFHRDIND FLDTKKISAD EDVRVKTLSI GVVIPDKFVE LAREDKAAYV
FYPHTIYKEY GQHMDEMDMN EMYDKFVDNP RVKKEKINPR KLLEKLAMLR SESGYPYIMF
QDNVNKVHAN NHISKVKFSN LCSEVLQASQ VSSYTDYDEE DEIGLDISCN LGSLNILNVM
EHKSIEKTVK LATDSLTHVS ETTDIRNAPA VRRANKAMKS IGLGAMNLHG YLAQNGIAYE
SPEARDFANT FFMMVNFYSI QRSAEIAKEK GETFDQYEGS TYATGEYFDK YVSTDFSPKY
EKIANLFEGM HIPTTEDWKK LKAFVAEHGM YHSYRLCIAP TGSISYVQSS TASVMPIMER
IEERTYGNSK TYYPMPGLAS NNWFFYKEAY DMDMFKVVDM IATIQQHIDQ GISFTLFLKD
TMTTRDLNRI DLYAHHRGIK TIYYARTKDT GQDSCLSCVV
