RIR3_SALTY
ID RIR3_SALTY Reviewed; 714 AA.
AC Q08698;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Ribonucleoside-diphosphate reductase 2 subunit alpha;
DE EC=1.17.4.1;
DE AltName: Full=R1E protein;
DE AltName: Full=Ribonucleotide reductase 2;
GN Name=nrdE; OrderedLocusNames=STM2807;
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], AND PROTEIN SEQUENCE OF 2-15.
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 X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEXES WITH ALLOSTERIC
RP EFFECTORS.
RX PubMed=12818204; DOI=10.1016/s0022-2836(03)00538-2;
RA Uppsten M., Farnegardh M., Jordan A., Eliasson R., Eklund H., Uhlin U.;
RT "Structure of the large subunit of class Ib ribonucleotide reductase from
RT Salmonella typhimurium and its complexes with allosteric effectors.";
RL J. Mol. Biol. 330:87-97(2003).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 2-713.
RX PubMed=16631785; DOI=10.1016/j.jmb.2006.03.035;
RA Uppsten M., Farnegardh M., Domkin V., Uhlin U.;
RT "The first holocomplex structure of ribonucleotide reductase gives new
RT insight into its mechanism of action.";
RL J. Mol. Biol. 359:365-377(2006).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. R1E contains the binding sites for both
CC substrates and allosteric effectors and carries out the actual
CC reduction of the ribonucleotide.
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. Lacks the N-terminal activity
CC site.
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 large
CC chain family. {ECO:0000305}.
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DR EMBL; X73226; CAA51699.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL21692.1; -; Genomic_DNA.
DR PIR; S34271; S34271.
DR RefSeq; NP_461733.1; NC_003197.2.
DR RefSeq; WP_000246626.1; NC_003197.2.
DR PDB; 1PEM; X-ray; 2.99 A; A=1-714.
DR PDB; 1PEO; X-ray; 3.00 A; A=1-714.
DR PDB; 1PEQ; X-ray; 2.80 A; A=1-714.
DR PDB; 1PEU; X-ray; 3.20 A; A=1-714.
DR PDB; 2BQ1; X-ray; 3.99 A; E/F=2-714.
DR PDBsum; 1PEM; -.
DR PDBsum; 1PEO; -.
DR PDBsum; 1PEQ; -.
DR PDBsum; 1PEU; -.
DR PDBsum; 2BQ1; -.
DR AlphaFoldDB; Q08698; -.
DR SMR; Q08698; -.
DR STRING; 99287.STM2807; -.
DR DrugBank; DB03258; 2'-Deoxycytidine 5'-triphosphate.
DR DrugBank; DB03222; dATP.
DR DrugBank; DB02452; Thymidine 5'-triphosphate.
DR PaxDb; Q08698; -.
DR EnsemblBacteria; AAL21692; AAL21692; STM2807.
DR GeneID; 1254330; -.
DR KEGG; stm:STM2807; -.
DR PATRIC; fig|99287.12.peg.2965; -.
DR HOGENOM; CLU_000404_4_1_6; -.
DR OMA; LEIWHID; -.
DR PhylomeDB; Q08698; -.
DR BioCyc; MetaCyc:MON-13835; -.
DR BioCyc; SENT99287:STM2807-MON; -.
DR UniPathway; UPA00326; -.
DR EvolutionaryTrace; Q08698; -.
DR Proteomes; UP000001014; 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; 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 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; Direct protein sequencing; Disulfide bond;
KW Nucleotide-binding; Oxidoreductase; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8195103"
FT CHAIN 2..714
FT /note="Ribonucleoside-diphosphate reductase 2 subunit
FT alpha"
FT /id="PRO_0000187225"
FT ACT_SITE 386
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 388
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 390
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 161
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 177..178
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 206
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 386..390
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 588..592
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 178
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 185
FT /note="Allosteric effector binding"
FT SITE 215
FT /note="Allosteric effector binding"
FT SITE 222
FT /note="Allosteric effector binding"
FT SITE 415
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 692
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 693
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 709
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 712
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT DISULFID 178..415
FT /note="Redox-active"
FT HELIX 16..21
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 35..47
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 59..68
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 74..77
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 82..94
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 102..111
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 119..122
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 126..138
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 142..153
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 156..159
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 161..166
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 179..181
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 187..201
FT /evidence="ECO:0007829|PDB:1PEQ"
FT TURN 202..204
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 206..210
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 224..226
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 232..244
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 254..260
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 266..270
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 271..273
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 279..281
FT /evidence="ECO:0007829|PDB:1PEU"
FT STRAND 287..291
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 295..301
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 305..309
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 311..318
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 322..324
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 327..336
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 342..346
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 347..361
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 365..367
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 369..375
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 378..380
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 406..408
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 416..421
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 422..426
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 431..447
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 455..464
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 467..472
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 474..480
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 488..516
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 523..525
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 527..530
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 532..534
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 535..538
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 547..556
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 563..576
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 592..596
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 600..603
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 608..612
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 615..618
FT /evidence="ECO:0007829|PDB:1PEO"
FT STRAND 620..623
FT /evidence="ECO:0007829|PDB:1PEQ"
FT TURN 629..631
FT /evidence="ECO:0007829|PDB:1PEM"
FT HELIX 632..634
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 638..641
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 643..654
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 665..667
FT /evidence="ECO:0007829|PDB:1PEQ"
FT HELIX 673..686
FT /evidence="ECO:0007829|PDB:1PEQ"
FT STRAND 694..696
FT /evidence="ECO:0007829|PDB:1PEQ"
SQ SEQUENCE 714 AA; 80587 MW; B12F79B42B05000D CRC64;
MATTTPERVM QETMDYHALN AMLNLYDKAG HIQFDKDQQA IDAFFATHVR PHSVTFASQH
ERLGTLVREG YYDDAVLARY DRAFVLRLFE HAHASGFRFQ TFLGAWKFYT SYTLKTFDGK
RYLEHFEDRV TMVALTLAQG DETLATQLTD EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL
LRIEDNMESI GRAVNSALQL SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED
AFSYANQLGA RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFRLA
KENAQMALFS PYDIQRRYGK PFGDIAISER YDELIADPHV RKTYINARDF FQTLAEIQFE
SGYPYIMFED TVNRANPIAG RINMSNLCSE ILQVNSASRY DDNLDYTHIG HDISCNLGSL
NIAHVMDSPD IGRTVETAIR GLTAVSDMSH IRSVPSIAAG NAASHAIGLG QMNLHGYLAR
EGIAYGSPEA LDFTNLYFYT ITWHAVHTSM RLARERGKTF AGFAQSRYAS GDYFTQYLQD
DWQPKTAKVR ALFARSGITL PTREMWLKLR DDVMRYGIYN QNLQAVPPTG SISYINHATS
SIHPIVAKIE IRKEGKTGRV YYPAPFMTNE NLDMYQDAYD IGPEKIIDTY AEATRHVDQG
LSLTLFFPDT ATTRDINKAQ IYAWRKGIKS LYYIRLRQLA LEGTEIEGCV SCAL
