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Q03604

- RIR1_CAEEL

UniProt

Q03604 - RIR1_CAEEL

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Protein

Ribonucleoside-diphosphate reductase large subunit

Gene
rnr-1, T23G5.1
Organism
Caenorhabditis elegans
Status
Reviewed - Annotation score: 4 out of 5 - Protein inferred from homologyi

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.

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.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111Allosteric activator By similarity
Binding sitei59 – 591Allosteric activator By similarity
Binding sitei94 – 941Allosteric activator By similarity
Binding sitei208 – 2081Substrate By similarity
Sitei224 – 2241Important for hydrogen atom transfer By similarity
Sitei232 – 2321Allosteric effector binding, determines substrate specificity By similarity
Binding sitei253 – 2531Substrate; via amide nitrogen By similarity
Sitei262 – 2621Allosteric effector binding, determines substrate specificity By similarity
Active sitei433 – 4331Proton acceptor By similarity
Active sitei435 – 4351Cysteine radical intermediate By similarity
Active sitei437 – 4371Proton acceptor By similarity
Sitei450 – 4501Important for hydrogen atom transfer By similarity
Sitei743 – 7431Important for electron transfer By similarity
Sitei744 – 7441Important for electron transfer By similarity
Sitei783 – 7831Interacts with thioredoxin/glutaredoxin By similarity
Sitei786 – 7861Interacts 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. deoxyribonucleotide biosynthetic process Source: UniProtKB
  2. DNA replication Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase large subunit (EC:1.17.4.1)
Alternative name(s):
Ribonucleotide reductase large subunit
Gene namesi
Name:rnr-1
ORF Names:T23G5.1
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
ProteomesiUP000001940: Chromosome III

Organism-specific databases

WormBaseiT23G5.1; CE00331; WBGene00004391; rnr-1.

Subcellular locationi

GO - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 788788Ribonucleoside-diphosphate reductase large subunitPRO_0000187194Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi224 ↔ 450Redox-active By similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiQ03604.
PRIDEiQ03604.

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

BioGridi41500. 3 interactions.
DIPiDIP-26889N.
IntActiQ03604. 3 interactions.
MINTiMINT-1080458.
STRINGi6239.T23G5.1.2.

Structurei

3D structure databases

ProteinModelPortaliQ03604.
SMRiQ03604. Positions 21-748.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 9892ATP-coneAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni17 – 237Allosteric activator binding By similarity
Regioni223 – 2242Substrate binding By similarity
Regioni291 – 2944Allosteric effector binding, determines substrate specificity By similarity
Regioni433 – 4375Substrate binding By similarity
Regioni609 – 6135Substrate binding By similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.

Phylogenomic databases

eggNOGiCOG0209.
GeneTreeiENSGT00390000001372.
HOGENOMiHOG000057035.
InParanoidiQ03604.
KOiK10807.
OMAiEACLMCQ.
PhylomeDBiQ03604.

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.

Q03604-1 [UniParc]FASTAAdd to Basket

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MQRYNSTYVV KRDGRKEDVH FDKITSRIQK LSYGLNMDFV DPVAVAIKVI    50
SGLYKGVTTV ELDNLAAETA ASMTTQHPEY ALLAARIAVS NLHKKTNKVF 100
SEVMKTLHEF HHPHTGKHAP MISDETWAII EKNADKLNSA IVYDRDYSYT 150
YFGFKTLERS YLLKINKEIV ERPQQMLMRV SIGIHGDDIT SAIETYNLMS 200
ERYMTHASPT LFNSGTCRPQ MSSCFLLTMS EDSILGIYDT LKQCALISKS 250
AGGIGLNVHK IRATGSVIAG TNGTSNGLIP MLRVYNNTAR YVDQGGNKRP 300
GAFAIYLEPW HADIFEFVSL RKNTGPEEER ARDLFLALWI PDLFMKRVEK 350
DQEWSLMCPC ECPGLDDCWG EEFEALYAKY EAEGRVRKTV KARKLWEHIV 400
SNQIETGLPY ITYKDAANRK SNQQNLGTIK CSNLCTEIIE YSAPDEIAVC 450
NLASIALNRY VTPEKKFDFV KLAEVTKVIT RNLNKIIDVN YYPVEEARNS 500
NMRHRPIGLG VQGLADCFML MRYPFTSAEA RDLNKRIFET IYYAALEASC 550
ELAELNGPYS TYEGSPVSKG QLQFDMWGVT PTDQCDWATL RKKIAKHGIR 600
NSLLMAPMPT ASTAQILGNN ESIEPYTSNI YSRRVLSGDF QIVNPHMLKD 650
LVERGLWTDE MKNRLIANNG SIQNIDGIPS DIKELYRTVW EISQKDIIEM 700
AADRGAYIDQ SQSLNIHMAK PSYAGITSMH FYGWKKGLKT GMYYLRTKPA 750
VNAVQFTVDK NALKTNQQAE TPATVAESQD EGCLMCSG 788
Length:788
Mass (Da):88,970
Last modified:October 1, 1993 - v1
Checksum:iB1AF398B173407D4
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z19158 Genomic DNA. Translation: CAA79574.1.
PIRiS28302.
RefSeqiNP_499039.1. NM_066638.4.
UniGeneiCel.7791.

Genome annotation databases

EnsemblMetazoaiT23G5.1.1; T23G5.1.1; WBGene00004391.
T23G5.1.2; T23G5.1.2; WBGene00004391.
GeneIDi176301.
KEGGicel:CELE_T23G5.1.
UCSCiT23G5.1.2. c. elegans.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z19158 Genomic DNA. Translation: CAA79574.1 .
PIRi S28302.
RefSeqi NP_499039.1. NM_066638.4.
UniGenei Cel.7791.

3D structure databases

ProteinModelPortali Q03604.
SMRi Q03604. Positions 21-748.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 41500. 3 interactions.
DIPi DIP-26889N.
IntActi Q03604. 3 interactions.
MINTi MINT-1080458.
STRINGi 6239.T23G5.1.2.

Proteomic databases

PaxDbi Q03604.
PRIDEi Q03604.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblMetazoai T23G5.1.1 ; T23G5.1.1 ; WBGene00004391 .
T23G5.1.2 ; T23G5.1.2 ; WBGene00004391 .
GeneIDi 176301.
KEGGi cel:CELE_T23G5.1.
UCSCi T23G5.1.2. c. elegans.

Organism-specific databases

CTDi 176301.
WormBasei T23G5.1 ; CE00331 ; WBGene00004391 ; rnr-1.

Phylogenomic databases

eggNOGi COG0209.
GeneTreei ENSGT00390000001372.
HOGENOMi HOG000057035.
InParanoidi Q03604.
KOi K10807.
OMAi EACLMCQ.
PhylomeDBi Q03604.

Enzyme and pathway databases

UniPathwayi UPA00326 .

Miscellaneous databases

NextBioi 891992.
PROi Q03604.

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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.
  2. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.

Entry informationi

Entry nameiRIR1_CAEEL
AccessioniPrimary (citable) accession number: Q03604
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: June 11, 2014
This is version 113 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  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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