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Q03604

- RIR1_CAEEL

UniProt

Q03604 - RIR1_CAEEL

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Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

rnr-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).By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111Allosteric activatorBy similarity
Binding sitei59 – 591Allosteric activatorBy similarity
Binding sitei94 – 941Allosteric activatorBy similarity
Binding sitei208 – 2081SubstrateBy similarity
Sitei224 – 2241Important for hydrogen atom transferBy similarity
Sitei232 – 2321Allosteric effector binding, determines substrate specificityBy similarity
Binding sitei253 – 2531Substrate; via amide nitrogenBy similarity
Sitei262 – 2621Allosteric effector binding, determines substrate specificityBy similarity
Active sitei433 – 4331Proton acceptorBy similarity
Active sitei435 – 4351Cysteine radical intermediateBy similarity
Active sitei437 – 4371Proton acceptorBy similarity
Sitei450 – 4501Important for hydrogen atom transferBy similarity
Sitei743 – 7431Important for electron transferBy similarity
Sitei744 – 7441Important for electron transferBy similarity
Sitei783 – 7831Interacts with thioredoxin/glutaredoxinBy similarity
Sitei786 – 7861Interacts with thioredoxin/glutaredoxinBy 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

ReactomeiREACT_245077. Synthesis and interconversion of nucleotide di- and triphosphates.
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.

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-activeBy 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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 9892ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

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

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

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

« Hide

        10         20         30         40         50
MQRYNSTYVV KRDGRKEDVH FDKITSRIQK LSYGLNMDFV DPVAVAIKVI
60 70 80 90 100
SGLYKGVTTV ELDNLAAETA ASMTTQHPEY ALLAARIAVS NLHKKTNKVF
110 120 130 140 150
SEVMKTLHEF HHPHTGKHAP MISDETWAII EKNADKLNSA IVYDRDYSYT
160 170 180 190 200
YFGFKTLERS YLLKINKEIV ERPQQMLMRV SIGIHGDDIT SAIETYNLMS
210 220 230 240 250
ERYMTHASPT LFNSGTCRPQ MSSCFLLTMS EDSILGIYDT LKQCALISKS
260 270 280 290 300
AGGIGLNVHK IRATGSVIAG TNGTSNGLIP MLRVYNNTAR YVDQGGNKRP
310 320 330 340 350
GAFAIYLEPW HADIFEFVSL RKNTGPEEER ARDLFLALWI PDLFMKRVEK
360 370 380 390 400
DQEWSLMCPC ECPGLDDCWG EEFEALYAKY EAEGRVRKTV KARKLWEHIV
410 420 430 440 450
SNQIETGLPY ITYKDAANRK SNQQNLGTIK CSNLCTEIIE YSAPDEIAVC
460 470 480 490 500
NLASIALNRY VTPEKKFDFV KLAEVTKVIT RNLNKIIDVN YYPVEEARNS
510 520 530 540 550
NMRHRPIGLG VQGLADCFML MRYPFTSAEA RDLNKRIFET IYYAALEASC
560 570 580 590 600
ELAELNGPYS TYEGSPVSKG QLQFDMWGVT PTDQCDWATL RKKIAKHGIR
610 620 630 640 650
NSLLMAPMPT ASTAQILGNN ESIEPYTSNI YSRRVLSGDF QIVNPHMLKD
660 670 680 690 700
LVERGLWTDE MKNRLIANNG SIQNIDGIPS DIKELYRTVW EISQKDIIEM
710 720 730 740 750
AADRGAYIDQ SQSLNIHMAK PSYAGITSMH FYGWKKGLKT GMYYLRTKPA
760 770 780
VNAVQFTVDK NALKTNQQAE TPATVAESQD EGCLMCSG
Length:788
Mass (Da):88,970
Last modified:October 1, 1993 - v1
Checksum:iB1AF398B173407D4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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 .
Reactomei REACT_245077. Synthesis and interconversion of nucleotide di- and triphosphates.

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: November 26, 2014
This is version 116 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