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Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

RNR1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. Ribonucleotide reductase (RNR) complex function is essential for efficient organellar DNA degradation in pollen. Involved in chloroplast division.3 Publications

Catalytic activityi

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

Enzyme regulationi

Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding to separate specificity and activation sites on the large subunit. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Stimulated by ATP and inhibited by dATP binding to the activity site (By similarity).By similarity

Pathway:iDNA replication

This protein is involved in the pathway DNA replication, which is part of Genetic information processing.
View all proteins of this organism that are known to be involved in the pathway DNA replication and in Genetic information processing.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei5 – 51Allosteric activatorBy similarity
Binding sitei53 – 531Allosteric activatorBy similarity
Binding sitei88 – 881Allosteric activatorBy similarity
Binding sitei202 – 2021SubstrateBy similarity
Sitei218 – 2181Important for hydrogen atom transferBy similarity
Sitei226 – 2261Allosteric effector binding, determines substrate specificityBy similarity
Binding sitei247 – 2471Substrate; via amide nitrogenBy similarity
Sitei256 – 2561Allosteric effector binding, determines substrate specificityBy similarity
Active sitei427 – 4271Proton acceptorBy similarity
Active sitei429 – 4291Cysteine radical intermediateBy similarity
Active sitei431 – 4311Proton acceptorBy similarity
Sitei444 – 4441Important for hydrogen atom transferBy similarity
Sitei756 – 7561Important for electron transferBy similarity
Sitei757 – 7571Important for electron transferBy similarity
Sitei811 – 8111Interacts with thioredoxin/glutaredoxinBy similarity
Sitei814 – 8141Interacts with thioredoxin/glutaredoxinBy similarity

GO - Molecular functioni

GO - Biological processi

  • deoxyribonucleoside triphosphate biosynthetic process Source: TAIR
  • deoxyribonucleotide biosynthetic process Source: UniProtKB
  • DNA replication Source: TAIR
  • response to cadmium ion Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciARA:AT2G21790-MONOMER.
MetaCyc:AT2G21790-MONOMER.
ReactomeiREACT_294404. Synthesis and interconversion of nucleotide di- and triphosphates.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase large subunit1 Publication (EC:1.17.4.1)
Alternative name(s):
Protein DEFECTIVE IN POLLEN DNA DEGRADATION 21 Publication
Ribonucleoside-diphosphate reductase R1 subunit1 Publication
Short name:
AtRNR1
Gene namesi
Name:RNR11 Publication
Synonyms:DPD21 Publication
Ordered Locus Names:At2g21790Imported
ORF Names:F7D8.11Imported
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G21790.

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Lethal when homozygous. RNAi-mediated knockdown causes severe developmental defects in seedlings failing to develop beyond the four-leaf stage.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi264 – 2641G → D in dpd2; loss of pollen plastid DNA degradation. 1 Publication
Mutagenesisi274 – 2741P → L in cls8-3; moderate pale leaf phenotype. 1 Publication
Mutagenesisi290 – 2901G → R in cls8-2; reduced growth with bleached areas and crinckled leaves. 1 Publication
Mutagenesisi718 – 7181G → E in cls8-1; crinckled phenotype. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 816816Ribonucleoside-diphosphate reductase large subunitPRO_0000187195Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi218 ↔ 444Redox-activeBy similarity

Post-translational modificationi

Contains a disulfide bonds (Probable). Binding of the substrate occurs primarily when the active-site cysteines are reduced.Curated

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiQ9SJ20.
PRIDEiQ9SJ20.

Expressioni

Tissue specificityi

Highly expressed in actively growing tissues such as young leaves, shoot apices, inflorescences and carpels. Very low expression in cotyledons, adult and cauline leaves and senescent leaves.1 Publication

Inductioni

Basal expression regulated by ATR/RAD3. Can be induced by another pathway when dNTPs levels are low.1 Publication

Interactioni

Subunit structurei

Heterotetramer of two large/R1 and two small/R2 subunits. A radical transfer pathway may occur between 'Tyr-125' of protein R2 and R1.1 Publication

Protein-protein interaction databases

STRINGi3702.AT2G21790.1.

Structurei

3D structure databases

ProteinModelPortaliQ9SJ20.
SMRiQ9SJ20. Positions 1-762.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 9292ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni11 – 177Allosteric activator bindingBy similarity
Regioni217 – 2182Substrate bindingBy similarity
Regioni285 – 2884Allosteric effector binding, determines substrate specificityBy similarity
Regioni427 – 4315Substrate bindingBy similarity
Regioni622 – 6265Substrate bindingBy similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000057035.
InParanoidiQ9SJ20.
KOiK10807.
OMAiYELLWQM.
PhylomeDBiQ9SJ20.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9SJ20-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYVVKRDGRQ ETVHFDKITA RLKKLSYGLS SDHCDPVLVA QKVCAGVYKG
60 70 80 90 100
VTTSQLDELA AETAAAMTCN HPDYASLAAR IAVSNLHKNT KKSFSETIKD
110 120 130 140 150
MFYHVNDRSG LKSPLIADDV FEIIMQNAAR LDSEIIYDRD FEYDYFGFKT
160 170 180 190 200
LERSYLLKVQ GTVVERPQHM LMRVAVGIHK DDIDSVIQTY HLMSQRWFTH
210 220 230 240 250
ASPTLFNAGT PRPQLSSCFL VCMKDDSIEG IYETLKECAV ISKSAGGIGV
260 270 280 290 300
SVHNIRATGS YIRGTNGTSN GIVPMLRVFN DTARYVDQGG GKRKGAFAVY
310 320 330 340 350
LEPWHADVYE FLELRKNHGK EEHRARDLFY ALWLPDLFME RVQNNGQWSL
360 370 380 390 400
FCPNEAPGLA DCWGAEFETL YTKYEREGKA KKVVQAQQLW YEILTSQVET
410 420 430 440 450
GTPYMLFKDS CNRKSNQQNL GTIKSSNLCT EIIEYTSPTE TAVCNLASIA
460 470 480 490 500
LPRFVREKGV PLDSHPPKLA GSLDSKNRYF DFEKLAEVTA TVTVNLNKII
510 520 530 540 550
DVNYYPVETA KTSNMRHRPI GIGVQGLADA FILLGMPFDS PEAQQLNKDI
560 570 580 590 600
FETIYYHALK ASTELAARLG PYETYAGSPV SKGILQPDMW NVIPSDRWDW
610 620 630 640 650
AVLRDMISKN GVRNSLLVAP MPTASTSQIL GNNECFEPYT SNIYSRRVLS
660 670 680 690 700
GEFVVVNKHL LHDLTDMGLW TPTLKNKLIN ENGSIVNVAE IPDDLKAIYR
710 720 730 740 750
TVWEIKQRTV VDMAADRGCY IDQSQSLNIH MDKPNFAKLT SLHFYTWKKG
760 770 780 790 800
LKTGMYYLRS RAAADAIKFT VDTAMLKEKP SVAEGDKEVE EEDNETKLAQ
810
MVCSLTNPEE CLACGS
Length:816
Mass (Da):91,816
Last modified:May 1, 2000 - v1
Checksum:iA6769E2F210488EA
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti37 – 371V → I in AAC61773 (PubMed:10542051).Curated
Sequence conflicti233 – 2331E → G in AAC61773 (PubMed:10542051).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF092841 mRNA. Translation: AAC61773.1.
AC007019 Genomic DNA. Translation: AAD20398.1.
CP002685 Genomic DNA. Translation: AEC07222.1.
AY035080 mRNA. Translation: AAK59585.1.
BT008573 mRNA. Translation: AAP40400.1.
PIRiB84605.
T51813.
RefSeqiNP_179770.1. NM_127748.3.
UniGeneiAt.115.

Genome annotation databases

EnsemblPlantsiAT2G21790.1; AT2G21790.1; AT2G21790.
GeneIDi816715.
KEGGiath:AT2G21790.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF092841 mRNA. Translation: AAC61773.1.
AC007019 Genomic DNA. Translation: AAD20398.1.
CP002685 Genomic DNA. Translation: AEC07222.1.
AY035080 mRNA. Translation: AAK59585.1.
BT008573 mRNA. Translation: AAP40400.1.
PIRiB84605.
T51813.
RefSeqiNP_179770.1. NM_127748.3.
UniGeneiAt.115.

3D structure databases

ProteinModelPortaliQ9SJ20.
SMRiQ9SJ20. Positions 1-762.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT2G21790.1.

Proteomic databases

PaxDbiQ9SJ20.
PRIDEiQ9SJ20.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G21790.1; AT2G21790.1; AT2G21790.
GeneIDi816715.
KEGGiath:AT2G21790.

Organism-specific databases

GeneFarmi2079.
TAIRiAT2G21790.

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000057035.
InParanoidiQ9SJ20.
KOiK10807.
OMAiYELLWQM.
PhylomeDBiQ9SJ20.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciARA:AT2G21790-MONOMER.
MetaCyc:AT2G21790-MONOMER.
ReactomeiREACT_294404. Synthesis and interconversion of nucleotide di- and triphosphates.

Miscellaneous databases

PROiQ9SJ20.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "An active ribonucleotide reductase from Arabidopsis thaliana cloning, expression and characterization of the large subunit."
    Sauge-Merle S., Falconet D., Fontecave M.
    Eur. J. Biochem. 266:62-69(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBUNIT, ENZYME REGULATION.
    Tissue: Callus.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "ATR regulates a G2-phase cell-cycle checkpoint in Arabidopsis thaliana."
    Culligan K., Tissier A., Britt A.
    Plant Cell 16:1091-1104(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  6. "crinkled leaves 8--a mutation in the large subunit of ribonucleotide reductase--leads to defects in leaf development and chloroplast division in Arabidopsis thaliana."
    Garton S., Knight H., Warren G.J., Knight M.R., Thorlby G.J.
    Plant J. 50:118-127(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF PRO-274; GLY-290 AND GLY-718, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY.
  7. "Mutations defective in ribonucleotide reductase activity interfere with pollen plastid DNA degradation mediated by DPD1 exonuclease."
    Tang L.Y., Matsushima R., Sakamoto W.
    Plant J. 70:637-649(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF GLY-264.

Entry informationi

Entry nameiRIR1_ARATH
AccessioniPrimary (citable) accession number: Q9SJ20
Secondary accession number(s): O82573
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: May 1, 2000
Last modified: June 24, 2015
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Two distinct regulatory sites have been defined: one controls substrate specificity and the other regulates the overall catalytic activity. A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2.

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.