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Q9SJ20

- RIR1_ARATH

UniProt

Q9SJ20 - RIR1_ARATH

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Protein

Ribonucleoside-diphosphate reductase large subunit

Gene
RNR1, At2g21790, F7D8.11
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - 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.1 Publication

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.1 Publication

Pathwayi

Sites

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

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB

GO - Biological processi

  1. deoxyribonucleoside triphosphate biosynthetic process Source: TAIR
  2. deoxyribonucleotide biosynthetic process Source: UniProtKB
  3. DNA replication Source: TAIR
  4. 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.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase large subunit (EC:1.17.4.1)
Alternative name(s):
Ribonucleoside-diphosphate reductase R1 subunit
Short name:
AtRNR1
Gene namesi
Name:RNR1
Ordered Locus Names:At2g21790
ORF Names:F7D8.11
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 2

Organism-specific databases

TAIRiAT2G21790.

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. ribonucleoside-diphosphate reductase complex Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

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-active By similarity

Post-translational modificationi

Contains a disulfide bonds Inferred. Binding of the substrate occurs primarily when the active-site cysteines are reduced.

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiQ9SJ20.
PRIDEiQ9SJ20.

Expressioni

Inductioni

Basal expression regulated by ATR/RAD3. Can be induced by another pathway when dNTPs levels are low.2 Publications

Gene expression databases

ArrayExpressiQ9SJ20.
GenevestigatoriQ9SJ20.

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

Structurei

3D structure databases

ProteinModelPortaliQ9SJ20.
SMRiQ9SJ20. Positions 1-762.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 9292ATP-coneAdd
BLAST

Region

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

Sequence similaritiesi

Contains 1 ATP-cone domain.

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000057035.
InParanoidiQ9SJ20.
KOiK10807.
OMAiLLWQMPS.
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

MYVVKRDGRQ ETVHFDKITA RLKKLSYGLS SDHCDPVLVA QKVCAGVYKG    50
VTTSQLDELA AETAAAMTCN HPDYASLAAR IAVSNLHKNT KKSFSETIKD 100
MFYHVNDRSG LKSPLIADDV FEIIMQNAAR LDSEIIYDRD FEYDYFGFKT 150
LERSYLLKVQ GTVVERPQHM LMRVAVGIHK DDIDSVIQTY HLMSQRWFTH 200
ASPTLFNAGT PRPQLSSCFL VCMKDDSIEG IYETLKECAV ISKSAGGIGV 250
SVHNIRATGS YIRGTNGTSN GIVPMLRVFN DTARYVDQGG GKRKGAFAVY 300
LEPWHADVYE FLELRKNHGK EEHRARDLFY ALWLPDLFME RVQNNGQWSL 350
FCPNEAPGLA DCWGAEFETL YTKYEREGKA KKVVQAQQLW YEILTSQVET 400
GTPYMLFKDS CNRKSNQQNL GTIKSSNLCT EIIEYTSPTE TAVCNLASIA 450
LPRFVREKGV PLDSHPPKLA GSLDSKNRYF DFEKLAEVTA TVTVNLNKII 500
DVNYYPVETA KTSNMRHRPI GIGVQGLADA FILLGMPFDS PEAQQLNKDI 550
FETIYYHALK ASTELAARLG PYETYAGSPV SKGILQPDMW NVIPSDRWDW 600
AVLRDMISKN GVRNSLLVAP MPTASTSQIL GNNECFEPYT SNIYSRRVLS 650
GEFVVVNKHL LHDLTDMGLW TPTLKNKLIN ENGSIVNVAE IPDDLKAIYR 700
TVWEIKQRTV VDMAADRGCY IDQSQSLNIH MDKPNFAKLT SLHFYTWKKG 750
LKTGMYYLRS RAAADAIKFT VDTAMLKEKP SVAEGDKEVE EEDNETKLAQ 800
MVCSLTNPEE CLACGS 816
Length:816
Mass (Da):91,816
Last modified:May 1, 2000 - v1
Checksum:iA6769E2F210488EA
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti37 – 371V → I in AAC61773. 1 Publication
Sequence conflicti233 – 2331E → G in AAC61773. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
PIRi B84605.
T51813.
RefSeqi NP_179770.1. NM_127748.3.
UniGenei At.115.

3D structure databases

ProteinModelPortali Q9SJ20.
SMRi Q9SJ20. Positions 1-762.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PaxDbi Q9SJ20.
PRIDEi Q9SJ20.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT2G21790.1 ; AT2G21790.1 ; AT2G21790 .
GeneIDi 816715.
KEGGi ath:AT2G21790.

Organism-specific databases

GeneFarmi 2079.
TAIRi AT2G21790.

Phylogenomic databases

eggNOGi COG0209.
HOGENOMi HOG000057035.
InParanoidi Q9SJ20.
KOi K10807.
OMAi LLWQMPS.
PhylomeDBi Q9SJ20.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci ARA:AT2G21790-MONOMER.
MetaCyc:AT2G21790-MONOMER.

Miscellaneous databases

PROi Q9SJ20.

Gene expression databases

ArrayExpressi Q9SJ20.
Genevestigatori Q9SJ20.

Family and domain databases

InterProi IPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view ]
Pfami PF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view ]
PRINTSi PR01183. RIBORDTASEM1.
SUPFAMi SSF48168. SSF48168. 1 hit.
TIGRFAMsi TIGR02506. NrdE_NrdA. 1 hit.
PROSITEi PS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view ]
ProtoNeti Search...

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, 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.

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: May 14, 2014
This is version 105 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

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