Q9SJ20 (RIR1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	816 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	Allosteric enzyme Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from mutant phenotype PubMed 17346262. Source: TAIR deoxyribonucleoside triphosphate biosynthetic process Inferred from mutant phenotype PubMed 17346262. Source: TAIR deoxyribonucleotide biosynthetic process Inferred from sequence or structural similarity. Source: UniProtKB response to cadmium ion Inferred from expression pattern PubMed 16502469. Source: TAIR
Cellular_component	ribonucleoside-diphosphate reductase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 816	816	Ribonucleoside-diphosphate reductase large subunit		PRO_0000187195
Regions
	Domain	1 – 92	92	ATP-cone
	Region	11 – 17	7	Allosteric activator binding By similarity
	Region	217 – 218	2	Substrate binding By similarity
	Region	285 – 288	4	Allosteric effector binding, determines substrate specificity By similarity
	Region	427 – 431	5	Substrate binding By similarity
	Region	622 – 626	5	Substrate binding By similarity
Sites
	Active site	427	1	Proton acceptor By similarity
	Active site	429	1	Cysteine radical intermediate By similarity
	Active site	431	1	Proton acceptor By similarity
	Binding site	5	1	Allosteric activator By similarity
	Binding site	53	1	Allosteric activator By similarity
	Binding site	88	1	Allosteric activator By similarity
	Binding site	202	1	Substrate By similarity
	Binding site	247	1	Substrate; via amide nitrogen By similarity
	Site	218	1	Important for hydrogen atom transfer By similarity
	Site	226	1	Allosteric effector binding, determines substrate specificity By similarity
	Site	256	1	Allosteric effector binding, determines substrate specificity By similarity
	Site	444	1	Important for hydrogen atom transfer By similarity
	Site	756	1	Important for electron transfer By similarity
	Site	757	1	Important for electron transfer By similarity
	Site	811	1	Interacts with thioredoxin/glutaredoxin By similarity
	Site	814	1	Interacts with thioredoxin/glutaredoxin By similarity
Amino acid modifications
	Disulfide bond	218 ↔ 444		Redox-active By similarity
Experimental info
	Sequence conflict	37	1	V → I in AAC61773. Ref.1
	Sequence conflict	233	1	E → G in AAC61773. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q9SJ20 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: A6769E2F210488EA	FASTA	816	91,816
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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.
IPI	IPI00525243.
PIR	B84605. T51813.
RefSeq	NP_179770.1. NM_127748.3.
UniGene	At.115.
3D structure databases
ProteinModelPortal	Q9SJ20.
SMR	Q9SJ20. Positions 1-762.
ModBase	Search...
Proteomic databases
PaxDb	Q9SJ20.
PRIDE	Q9SJ20.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT2G21790.1; AT2G21790.1; AT2G21790.
GeneID	816715.
KEGG	ath:AT2G21790.
Organism-specific databases
GeneFarm	2079.
TAIR	At2g21790.
Phylogenomic databases
eggNOG	COG0209.
HOGENOM	HOG000057035.
InParanoid	Q9SJ20.
KO	K10807.
OMA	PQARNSN.
PhylomeDB	Q9SJ20.
ProtClustDB	PLN02437.
Enzyme and pathway databases
UniPathway	UPA00326.
Gene expression databases
ArrayExpress	Q9SJ20.
Genevestigator	Q9SJ20.
GermOnline	AT2G21790. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR005144. ATP-cone. IPR013346. NrdE_NrdA. IPR000788. RNR_lg_C. IPR013509. RNR_lsu_N. IPR008926. RNR_R1-su_N. [Graphical view]
Pfam	PF03477. ATP-cone. 1 hit. PF02867. Ribonuc_red_lgC. 1 hit. PF00317. Ribonuc_red_lgN. 1 hit. [Graphical view]
PRINTS	PR01183. RIBORDTASEM1.
SUPFAM	SSF48168. Ribonucleo_red_N. 1 hit.
TIGRFAMs	TIGR02506. NrdE_NrdA. 1 hit.
PROSITE	PS51161. ATP_CONE. 1 hit. PS00089. RIBORED_LARGE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RIR1_ARATH

Accession

Primary (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 1, 2013
This is version 98 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program