RIR4_SALTY
ID RIR4_SALTY Reviewed; 319 AA.
AC P17424;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 2.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Ribonucleoside-diphosphate reductase 2 subunit beta;
DE EC=1.17.4.1;
DE AltName: Full=R2F protein;
DE AltName: Full=Ribonucleotide reductase 2;
GN Name=nrdF; OrderedLocusNames=STM2808;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=LT2;
RX PubMed=8195103; DOI=10.1128/jb.176.11.3420-3427.1994;
RA Jordan A., Gibert I., Barbe J.;
RT "Cloning and sequencing of the genes from Salmonella typhimurium encoding a
RT new bacterial ribonucleotide reductase.";
RL J. Bacteriol. 176:3420-3427(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 219-319.
RC STRAIN=LT2;
RX PubMed=2691838; DOI=10.1111/j.1365-2958.1989.tb00253.x;
RA Stirling D.A., Hulton C.S.J., Waddell L., Park S.F., Stewart G.S.A.B.,
RA Booth I.R., Higgins C.F.;
RT "Molecular characterization of the proU loci of Salmonella typhimurium and
RT Escherichia coli encoding osmoregulated glycine betaine transport
RT systems.";
RL Mol. Microbiol. 3:1025-1038(1989).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 219-319.
RX PubMed=2548994; DOI=10.1128/jb.171.9.4694-4706.1989;
RA Overdier D.G., Olson E.R., Erickson B.D., Ederer M.M., Csonka L.N.;
RT "Nucleotide sequence of the transcriptional control region of the
RT osmotically regulated proU operon of Salmonella typhimurium and
RT identification of the 5' endpoint of the proU mRNA.";
RL J. Bacteriol. 171:4694-4706(1989).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RX PubMed=9748343; DOI=10.1021/bi981380s;
RA Eriksson M., Jordan A., Eklund H.;
RT "Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its
RT oxidized and reduced forms.";
RL Biochemistry 37:13359-13369(1998).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. R2F contains the tyrosyl radical
CC required for catalysis.
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;
CC Note=Binds 2 iron ions per subunit.;
CC -!- PATHWAY: Genetic information processing; DNA replication.
CC -!- SUBUNIT: Tetramer of two alpha and two beta subunits. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase small
CC chain family. {ECO:0000305}.
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DR EMBL; X73226; CAA51695.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL21693.1; -; Genomic_DNA.
DR EMBL; X52693; CAA36920.1; -; Genomic_DNA.
DR EMBL; M26063; AAA88620.1; -; Genomic_DNA.
DR PIR; S34272; S34272.
DR RefSeq; NP_461734.1; NC_003197.2.
DR RefSeq; WP_000777903.1; NC_003197.2.
DR PDB; 1R2F; X-ray; 2.10 A; A/B=1-319.
DR PDB; 2BQ1; X-ray; 4.00 A; I/J=1-319.
DR PDB; 2R2F; X-ray; 2.25 A; A/B=1-319.
DR PDBsum; 1R2F; -.
DR PDBsum; 2BQ1; -.
DR PDBsum; 2R2F; -.
DR AlphaFoldDB; P17424; -.
DR SMR; P17424; -.
DR STRING; 99287.STM2808; -.
DR PaxDb; P17424; -.
DR EnsemblBacteria; AAL21693; AAL21693; STM2808.
DR GeneID; 1254331; -.
DR KEGG; stm:STM2808; -.
DR PATRIC; fig|99287.12.peg.2966; -.
DR HOGENOM; CLU_052495_0_0_6; -.
DR OMA; IGYKYQR; -.
DR PhylomeDB; P17424; -.
DR BioCyc; MetaCyc:MON-13836; -.
DR BioCyc; SENT99287:STM2808-MON; -.
DR UniPathway; UPA00326; -.
DR EvolutionaryTrace; P17424; -.
DR Proteomes; UP000001014; 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..319
FT /note="Ribonucleoside-diphosphate reductase 2 subunit beta"
FT /id="PRO_0000190489"
FT ACT_SITE 105
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 67
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 98
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 98
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT BINDING 101
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 158
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT BINDING 192
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT BINDING 195
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT CONFLICT 286
FT /note="L -> V (in Ref. 4; AAA88620)"
FT /evidence="ECO:0000305"
FT HELIX 17..28
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 33..35
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 38..41
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 42..46
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 50..72
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 74..79
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 85..112
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 115..127
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 129..143
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 147..159
FT /evidence="ECO:0007829|PDB:1R2F"
FT TURN 160..162
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 163..174
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 179..208
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 212..240
FT /evidence="ECO:0007829|PDB:1R2F"
FT TURN 241..244
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 247..264
FT /evidence="ECO:0007829|PDB:1R2F"
FT TURN 273..275
FT /evidence="ECO:0007829|PDB:1R2F"
FT HELIX 280..286
FT /evidence="ECO:0007829|PDB:1R2F"
SQ SEQUENCE 319 AA; 36232 MW; AFBB6E02A57C959A CRC64;
MKLSRISAIN WNKIQDDKDL EVWNRLTSNF WLPEKVPLSN DIPAWQTLSA AEQQLTIRVF
TGLTLLDTIQ NIAGAPSLMA DAITPHEEAV LSNISFMEAV HARSYSSIFS TLCQTKEVDA
AYAWSEENPP LQRKAQIILA HYVSDEPLKK KIASVFLESF LFYSGFWLPM YFSSRGKLTN
TADLIRLIIR DEAVHGYYIG YKYQIALQKL SAIEREELKL FALDLLMELY DNEIRYTEAL
YAETGWVNDV KAFLCYNANK ALMNLGYEAL FPPEMADVNP AILAALSPNA DENHDFFSGS
GSSYVMGKTV ETEDEDWNF
