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Q9SJ20 (RIR1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 105. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribonucleoside-diphosphate reductase large subunit

EC=1.17.4.1
Alternative name(s):
Ribonucleoside-diphosphate reductase R1 subunit
Short name=AtRNR1
Gene names
Name:RNR1
Ordered Locus Names:At2g21790
ORF Names:F7D8.11
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length816 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1

Catalytic activity

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

Enzyme regulation

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. Ref.1

Pathway

Genetic information processing; DNA replication.

Subunit structure

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

Subcellular location

Cytoplasm By similarity.

Induction

Basal expression regulated by ATR/RAD3. Can be induced by another pathway when dNTPs levels are low. Ref.1 Ref.5

Post-translational modification

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

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.

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase large chain family.

Contains 1 ATP-cone domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 816816Ribonucleoside-diphosphate reductase large subunit
PRO_0000187195

Regions

Domain1 – 9292ATP-cone
Region11 – 177Allosteric activator binding By similarity
Region217 – 2182Substrate binding By similarity
Region285 – 2884Allosteric effector binding, determines substrate specificity By similarity
Region427 – 4315Substrate binding By similarity
Region622 – 6265Substrate binding By similarity

Sites

Active site4271Proton acceptor By similarity
Active site4291Cysteine radical intermediate By similarity
Active site4311Proton acceptor By similarity
Binding site51Allosteric activator By similarity
Binding site531Allosteric activator By similarity
Binding site881Allosteric activator By similarity
Binding site2021Substrate By similarity
Binding site2471Substrate; via amide nitrogen By similarity
Site2181Important for hydrogen atom transfer By similarity
Site2261Allosteric effector binding, determines substrate specificity By similarity
Site2561Allosteric effector binding, determines substrate specificity By similarity
Site4441Important for hydrogen atom transfer By similarity
Site7561Important for electron transfer By similarity
Site7571Important for electron transfer By similarity
Site8111Interacts with thioredoxin/glutaredoxin By similarity
Site8141Interacts with thioredoxin/glutaredoxin By similarity

Amino acid modifications

Disulfide bond218 ↔ 444Redox-active By similarity

Experimental info

Sequence conflict371V → I in AAC61773. Ref.1
Sequence conflict2331E → G in AAC61773. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Q9SJ20 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: A6769E2F210488EA

FASTA81691,816
        10         20         30         40         50         60 
MYVVKRDGRQ ETVHFDKITA RLKKLSYGLS SDHCDPVLVA QKVCAGVYKG VTTSQLDELA 

        70         80         90        100        110        120 
AETAAAMTCN HPDYASLAAR IAVSNLHKNT KKSFSETIKD MFYHVNDRSG LKSPLIADDV 

       130        140        150        160        170        180 
FEIIMQNAAR LDSEIIYDRD FEYDYFGFKT LERSYLLKVQ GTVVERPQHM LMRVAVGIHK 

       190        200        210        220        230        240 
DDIDSVIQTY HLMSQRWFTH ASPTLFNAGT PRPQLSSCFL VCMKDDSIEG IYETLKECAV 

       250        260        270        280        290        300 
ISKSAGGIGV SVHNIRATGS YIRGTNGTSN GIVPMLRVFN DTARYVDQGG GKRKGAFAVY 

       310        320        330        340        350        360 
LEPWHADVYE FLELRKNHGK EEHRARDLFY ALWLPDLFME RVQNNGQWSL FCPNEAPGLA 

       370        380        390        400        410        420 
DCWGAEFETL YTKYEREGKA KKVVQAQQLW YEILTSQVET GTPYMLFKDS CNRKSNQQNL 

       430        440        450        460        470        480 
GTIKSSNLCT EIIEYTSPTE TAVCNLASIA LPRFVREKGV PLDSHPPKLA GSLDSKNRYF 

       490        500        510        520        530        540 
DFEKLAEVTA TVTVNLNKII DVNYYPVETA KTSNMRHRPI GIGVQGLADA FILLGMPFDS 

       550        560        570        580        590        600 
PEAQQLNKDI FETIYYHALK ASTELAARLG PYETYAGSPV SKGILQPDMW NVIPSDRWDW 

       610        620        630        640        650        660 
AVLRDMISKN GVRNSLLVAP MPTASTSQIL GNNECFEPYT SNIYSRRVLS GEFVVVNKHL 

       670        680        690        700        710        720 
LHDLTDMGLW TPTLKNKLIN ENGSIVNVAE IPDDLKAIYR TVWEIKQRTV VDMAADRGCY 

       730        740        750        760        770        780 
IDQSQSLNIH MDKPNFAKLT SLHFYTWKKG LKTGMYYLRS RAAADAIKFT VDTAMLKEKP 

       790        800        810 
SVAEGDKEVE EEDNETKLAQ MVCSLTNPEE CLACGS 

« Hide

References

« Hide 'large scale' references
[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]"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana."
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. expand/collapse author list , Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.
Nature 402:761-768(1999) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRB84605.
T51813.
RefSeqNP_179770.1. NM_127748.3.
UniGeneAt.115.

3D structure databases

ProteinModelPortalQ9SJ20.
SMRQ9SJ20. Positions 1-762.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PaxDbQ9SJ20.
PRIDEQ9SJ20.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT2G21790.1; AT2G21790.1; AT2G21790.
GeneID816715.
KEGGath:AT2G21790.

Organism-specific databases

GeneFarm2079.
TAIRAT2G21790.

Phylogenomic databases

eggNOGCOG0209.
HOGENOMHOG000057035.
InParanoidQ9SJ20.
KOK10807.
OMALLWQMPS.
PhylomeDBQ9SJ20.

Enzyme and pathway databases

BioCycARA:AT2G21790-MONOMER.
MetaCyc:AT2G21790-MONOMER.
UniPathwayUPA00326.

Gene expression databases

ArrayExpressQ9SJ20.
GenevestigatorQ9SJ20.

Family and domain databases

InterProIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSPR01183. RIBORDTASEM1.
SUPFAMSSF48168. SSF48168. 1 hit.
TIGRFAMsTIGR02506. NrdE_NrdA. 1 hit.
PROSITEPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROQ9SJ20.

Entry information

Entry nameRIR1_ARATH
AccessionPrimary (citable) accession number: Q9SJ20
Secondary accession number(s): O82573
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names