RIR2_BACSU
ID RIR2_BACSU Reviewed; 329 AA.
AC P50621;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Ribonucleoside-diphosphate reductase subunit beta;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase small subunit;
GN Name=nrdF; OrderedLocusNames=BSU17390;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], OPERON, AND DISRUPTION PHENOTYPE.
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 Evidence={ECO:0000255|PROSITE-ProRule:PRU10014};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875; Evidence={ECO:0000250};
CC Note=Binds 2 iron ions per subunit. {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 small
CC chain family. {ECO:0000305}.
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DR EMBL; Z68500; CAA92811.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13623.1; -; Genomic_DNA.
DR PIR; C69667; C69667.
DR RefSeq; NP_389621.1; NC_000964.3.
DR RefSeq; WP_003231754.1; NZ_CP053102.1.
DR PDB; 4DR0; X-ray; 1.90 A; A/B=1-329.
DR PDBsum; 4DR0; -.
DR AlphaFoldDB; P50621; -.
DR SMR; P50621; -.
DR STRING; 224308.BSU17390; -.
DR jPOST; P50621; -.
DR PaxDb; P50621; -.
DR PRIDE; P50621; -.
DR EnsemblBacteria; CAB13623; CAB13623; BSU_17390.
DR GeneID; 940076; -.
DR KEGG; bsu:BSU17390; -.
DR PATRIC; fig|224308.179.peg.1885; -.
DR eggNOG; COG0208; Bacteria.
DR InParanoid; P50621; -.
DR OMA; LMESAMI; -.
DR PhylomeDB; P50621; -.
DR BioCyc; BSUB:BSU17390-MON; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:UniProtKB-EC.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IEA:InterPro.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR CDD; cd01049; RNRR2; 1.
DR Gene3D; 1.10.620.20; -; 1.
DR InterPro; IPR009078; Ferritin-like_SF.
DR InterPro; IPR012348; RNR-like.
DR InterPro; IPR026494; RNR_NrdF-like.
DR InterPro; IPR033909; RNR_small.
DR InterPro; IPR030475; RNR_small_AS.
DR InterPro; IPR000358; RNR_small_fam.
DR PANTHER; PTHR23409; PTHR23409; 1.
DR Pfam; PF00268; Ribonuc_red_sm; 1.
DR PIRSF; PIRSF000355; NrdB; 1.
DR SUPFAM; SSF47240; SSF47240; 1.
DR TIGRFAMs; TIGR04171; RNR_1b_NrdF; 1.
DR PROSITE; PS00368; RIBORED_SMALL; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Deoxyribonucleotide synthesis; Iron; Metal-binding;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..329
FT /note="Ribonucleoside-diphosphate reductase subunit beta"
FT /id="PRO_0000190469"
FT ACT_SITE 105
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 66
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 97
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 97
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 101
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 164
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 198
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 201
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT STRAND 10..12
FT /evidence="ECO:0007829|PDB:4DR0"
FT STRAND 14..17
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 18..27
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 32..34
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 38..40
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 41..45
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 49..71
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 73..80
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 84..99
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 101..112
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 115..127
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 129..143
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 150..165
FT /evidence="ECO:0007829|PDB:4DR0"
FT TURN 166..168
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 169..179
FT /evidence="ECO:0007829|PDB:4DR0"
FT TURN 180..182
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 185..213
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 218..247
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 248..250
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 253..270
FT /evidence="ECO:0007829|PDB:4DR0"
FT HELIX 284..288
FT /evidence="ECO:0007829|PDB:4DR0"
SQ SEQUENCE 329 AA; 38379 MW; 5080C014D2868EEB CRC64;
MTKIYDAANW SKHEDDFTQM FYNQNVKQFW LPEEIALNGD LLTWKYLGKN EQDTYMKVLA
GLTLLDTEQG NTGMPIVAEH VDGHQRKAVL NFMAMMENAV HAKSYSNIFM TLAPTETINE
VFEWVKQNKY LQKKAQMIVG LYKAIQKDDE ISLFKAMVAS VYLESFLFYS GFYYPLYFYG
QGKLMQSGEI INLILRDEAI HGVYVGLLAQ EIYNKQTEEK KAELREFAID LLNQLYENEL
EYTEDLYDQV GLSHDVKKFI RYNANKALMN LGFDPYFEEE DINPIVLNGL NTKTKSHDFF
SMKGNGYKKA TVEPLKDDDF YFEDEKEQI
