RIR1_ARATH
ID RIR1_ARATH Reviewed; 816 AA.
AC Q9SJ20; O82573;
DT 21-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Ribonucleoside-diphosphate reductase large subunit {ECO:0000303|PubMed:10542051};
DE EC=1.17.4.1;
DE AltName: Full=Protein DEFECTIVE IN POLLEN DNA DEGRADATION 2 {ECO:0000303|PubMed:22239102};
DE AltName: Full=Ribonucleoside-diphosphate reductase R1 subunit {ECO:0000303|PubMed:10542051};
DE Short=AtRNR1;
GN Name=RNR1 {ECO:0000303|PubMed:10542051};
GN Synonyms=DPD2 {ECO:0000303|PubMed:22239102};
GN OrderedLocusNames=At2g21790 {ECO:0000312|Araport:AT2G21790};
GN ORFNames=F7D8.11 {ECO:0000312|EMBL:AAD20398.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBUNIT, AND ACTIVITY REGULATION.
RC TISSUE=Callus;
RX PubMed=10542051; DOI=10.1046/j.1432-1327.1999.00814.x;
RA Sauge-Merle S., Falconet D., Fontecave M.;
RT "An active ribonucleotide reductase from Arabidopsis thaliana cloning,
RT expression and characterization of the large subunit.";
RL Eur. J. Biochem. 266:62-69(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP INDUCTION.
RX PubMed=15075397; DOI=10.1105/tpc.018903;
RA Culligan K., Tissier A., Britt A.;
RT "ATR regulates a G2-phase cell-cycle checkpoint in Arabidopsis thaliana.";
RL Plant Cell 16:1091-1104(2004).
RN [6]
RP FUNCTION, MUTAGENESIS OF PRO-274; GLY-290 AND GLY-718, DISRUPTION
RP PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=17346262; DOI=10.1111/j.1365-313x.2007.03035.x;
RA Garton S., Knight H., Warren G.J., Knight M.R., Thorlby G.J.;
RT "crinkled leaves 8--a mutation in the large subunit of ribonucleotide
RT reductase--leads to defects in leaf development and chloroplast division in
RT Arabidopsis thaliana.";
RL Plant J. 50:118-127(2007).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF GLY-264.
RX PubMed=22239102; DOI=10.1111/j.1365-313x.2012.04904.x;
RA Tang L.Y., Matsushima R., Sakamoto W.;
RT "Mutations defective in ribonucleotide reductase activity interfere with
RT pollen plastid DNA degradation mediated by DPD1 exonuclease.";
RL Plant J. 70:637-649(2012).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. R1 contains the binding sites for both
CC substrates and allosteric effectors and carries out the actual
CC reduction of the ribonucleotide. Ribonucleotide reductase (RNR) complex
CC function is essential for efficient organellar DNA degradation in
CC pollen. Involved in chloroplast division. {ECO:0000269|PubMed:10542051,
CC ECO:0000269|PubMed:17346262, ECO:0000269|PubMed:22239102}.
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 to separate specificity
CC and activation sites on the large subunit. The type of nucleotide bound
CC 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. Stimulated by ATP and
CC inhibited by dATP binding to the activity site (By similarity).
CC {ECO:0000250}.
CC -!- PATHWAY: Genetic information processing; DNA replication.
CC -!- SUBUNIT: Heterotetramer of two large/R1 and two small/R2 subunits. A
CC radical transfer pathway may occur between 'Tyr-125' of protein R2 and
CC R1. {ECO:0000269|PubMed:10542051}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:22239102}.
CC -!- TISSUE SPECIFICITY: Highly expressed in actively growing tissues such
CC as young leaves, shoot apices, inflorescences and carpels. Very low
CC expression in cotyledons, adult and cauline leaves and senescent
CC leaves. {ECO:0000269|PubMed:17346262}.
CC -!- INDUCTION: Basal expression regulated by ATR/RAD3. Can be induced by
CC another pathway when dNTPs levels are low.
CC {ECO:0000269|PubMed:15075397}.
CC -!- PTM: Contains a disulfide bonds (Probable). Binding of the substrate
CC occurs primarily when the active-site cysteines are reduced.
CC {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Lethal when homozygous. RNAi-mediated knockdown
CC causes severe developmental defects in seedlings failing to develop
CC beyond the four-leaf stage. {ECO:0000269|PubMed:17346262}.
CC -!- MISCELLANEOUS: Two distinct regulatory sites have been defined: one
CC controls substrate specificity and the other regulates the overall
CC catalytic activity. A substrate-binding catalytic site, located on R1,
CC is formed only in the presence of the second subunit R2.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase large
CC chain family. {ECO:0000305}.
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DR EMBL; AF092841; AAC61773.1; -; mRNA.
DR EMBL; AC007019; AAD20398.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07222.1; -; Genomic_DNA.
DR EMBL; AY035080; AAK59585.1; -; mRNA.
DR EMBL; BT008573; AAP40400.1; -; mRNA.
DR PIR; B84605; B84605.
DR PIR; T51813; T51813.
DR RefSeq; NP_179770.1; NM_127748.4.
DR AlphaFoldDB; Q9SJ20; -.
DR SMR; Q9SJ20; -.
DR STRING; 3702.AT2G21790.1; -.
DR iPTMnet; Q9SJ20; -.
DR PaxDb; Q9SJ20; -.
DR PRIDE; Q9SJ20; -.
DR ProteomicsDB; 226841; -.
DR EnsemblPlants; AT2G21790.1; AT2G21790.1; AT2G21790.
DR GeneID; 816715; -.
DR Gramene; AT2G21790.1; AT2G21790.1; AT2G21790.
DR KEGG; ath:AT2G21790; -.
DR Araport; AT2G21790; -.
DR TAIR; locus:2052469; AT2G21790.
DR eggNOG; KOG1112; Eukaryota.
DR HOGENOM; CLU_000404_1_0_1; -.
DR InParanoid; Q9SJ20; -.
DR OMA; YIVYRDQ; -.
DR OrthoDB; 156716at2759; -.
DR PhylomeDB; Q9SJ20; -.
DR BioCyc; ARA:AT2G21790-MON; -.
DR BioCyc; MetaCyc:AT2G21790-MON; -.
DR UniPathway; UPA00326; -.
DR PRO; PR:Q9SJ20; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9SJ20; baseline and differential.
DR Genevisible; Q9SJ20; AT.
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; ISS:UniProtKB.
DR GO; GO:0009202; P:deoxyribonucleoside triphosphate biosynthetic process; IMP:TAIR.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; ISS:UniProtKB.
DR GO; GO:0006260; P:DNA replication; IMP:TAIR.
DR InterPro; IPR005144; ATP-cone_dom.
DR InterPro; IPR013346; NrdE_NrdA.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013509; RNR_lsu_N.
DR InterPro; IPR008926; RNR_R1-su_N.
DR InterPro; IPR039718; Rrm1.
DR PANTHER; PTHR11573; PTHR11573; 1.
DR Pfam; PF03477; ATP-cone; 1.
DR Pfam; PF02867; Ribonuc_red_lgC; 1.
DR Pfam; PF00317; Ribonuc_red_lgN; 1.
DR PRINTS; PR01183; RIBORDTASEM1.
DR SUPFAM; SSF48168; SSF48168; 1.
DR TIGRFAMs; TIGR02506; NrdE_NrdA; 1.
DR PROSITE; PS51161; ATP_CONE; 1.
DR PROSITE; PS00089; RIBORED_LARGE; 1.
PE 1: Evidence at protein level;
KW Allosteric enzyme; ATP-binding; Cytoplasm; Deoxyribonucleotide synthesis;
KW Disulfide bond; Nucleotide-binding; Oxidoreductase; Reference proteome.
FT CHAIN 1..816
FT /note="Ribonucleoside-diphosphate reductase large subunit"
FT /id="PRO_0000187195"
FT DOMAIN 1..92
FT /note="ATP-cone"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00492"
FT ACT_SITE 427
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 429
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 431
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 5..6
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 11..17
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 53
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 202
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 217
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 226..228
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 243
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 256
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 263..264
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 427
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 431
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 623..626
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT SITE 218
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 444
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 756
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 757
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 811
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 814
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT DISULFID 218..444
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT MUTAGEN 264
FT /note="G->D: In dpd2; loss of pollen plastid DNA
FT degradation."
FT /evidence="ECO:0000269|PubMed:22239102"
FT MUTAGEN 274
FT /note="P->L: In cls8-3; moderate pale leaf phenotype."
FT /evidence="ECO:0000269|PubMed:17346262"
FT MUTAGEN 290
FT /note="G->R: In cls8-2; reduced growth with bleached areas
FT and crinckled leaves."
FT /evidence="ECO:0000269|PubMed:17346262"
FT MUTAGEN 718
FT /note="G->E: In cls8-1; crinckled phenotype."
FT /evidence="ECO:0000269|PubMed:17346262"
FT CONFLICT 37
FT /note="V -> I (in Ref. 1; AAC61773)"
FT /evidence="ECO:0000305"
FT CONFLICT 233
FT /note="E -> G (in Ref. 1; AAC61773)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 816 AA; 91816 MW; A6769E2F210488EA CRC64;
MYVVKRDGRQ ETVHFDKITA RLKKLSYGLS SDHCDPVLVA QKVCAGVYKG VTTSQLDELA
AETAAAMTCN HPDYASLAAR IAVSNLHKNT KKSFSETIKD MFYHVNDRSG LKSPLIADDV
FEIIMQNAAR LDSEIIYDRD FEYDYFGFKT LERSYLLKVQ GTVVERPQHM LMRVAVGIHK
DDIDSVIQTY HLMSQRWFTH ASPTLFNAGT PRPQLSSCFL VCMKDDSIEG IYETLKECAV
ISKSAGGIGV SVHNIRATGS YIRGTNGTSN GIVPMLRVFN DTARYVDQGG GKRKGAFAVY
LEPWHADVYE FLELRKNHGK EEHRARDLFY ALWLPDLFME RVQNNGQWSL FCPNEAPGLA
DCWGAEFETL YTKYEREGKA KKVVQAQQLW YEILTSQVET GTPYMLFKDS CNRKSNQQNL
GTIKSSNLCT EIIEYTSPTE TAVCNLASIA LPRFVREKGV PLDSHPPKLA GSLDSKNRYF
DFEKLAEVTA TVTVNLNKII DVNYYPVETA KTSNMRHRPI GIGVQGLADA FILLGMPFDS
PEAQQLNKDI FETIYYHALK ASTELAARLG PYETYAGSPV SKGILQPDMW NVIPSDRWDW
AVLRDMISKN GVRNSLLVAP MPTASTSQIL GNNECFEPYT SNIYSRRVLS GEFVVVNKHL
LHDLTDMGLW TPTLKNKLIN ENGSIVNVAE IPDDLKAIYR TVWEIKQRTV VDMAADRGCY
IDQSQSLNIH MDKPNFAKLT SLHFYTWKKG LKTGMYYLRS RAAADAIKFT VDTAMLKEKP
SVAEGDKEVE EEDNETKLAQ MVCSLTNPEE CLACGS
