Ribonucleoside-diphosphate reductase large subunit

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Q03604 (RIR1_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 107. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ribonucleoside-diphosphate reductase large subunit
EC=1.17.4.1

Alternative name(s):
Ribonucleotide reductase large subunit

Gene names

Name:	rnr-1
ORF Names:	T23G5.1

Organism

Caenorhabditis elegans [Reference proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Ecdysozoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length	788 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
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.
Pathway	Genetic information processing; DNA replication.
Subunit structure	Heterodimer of a large and a small subunit.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase large chain family. Contains 1 ATP-cone domain.

Ontologies

Keywords
Biological process	DNA replication
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 electronic annotation. Source: UniProtKB-UniPathway deoxyribonucleotide biosynthetic process Inferred from sequence or structural similarity. Source: UniProtKB
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 – 788

788

Ribonucleoside-diphosphate reductase large subunit

PRO_0000187194

Regions

Domain

7 – 98

ATP-cone

Region

17 – 23

Allosteric activator binding By similarity

Region

223 – 224

Substrate binding By similarity

Region

291 – 294

Allosteric effector binding, determines substrate specificity By similarity

Region

433 – 437

Substrate binding By similarity

Region

609 – 613

Substrate binding By similarity

Sites

Active site

433

Proton acceptor By similarity

Active site

435

Cysteine radical intermediate By similarity

Active site

437

Proton acceptor By similarity

Binding site

Allosteric activator By similarity

Binding site

Allosteric activator By similarity

Binding site

Allosteric activator By similarity

Binding site

208

Substrate By similarity

Binding site

253

Substrate; via amide nitrogen By similarity

Site

224

Important for hydrogen atom transfer By similarity

Site

232

Allosteric effector binding, determines substrate specificity By similarity

Site

262

Allosteric effector binding, determines substrate specificity By similarity

Site

450

Important for hydrogen atom transfer By similarity

Site

743

Important for electron transfer By similarity

Site

744

Important for electron transfer By similarity

Site

783

Interacts with thioredoxin/glutaredoxin By similarity

Site

786

Interacts with thioredoxin/glutaredoxin By similarity

Amino acid modifications

Disulfide bond

224 ↔ 450

Redox-active By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q03604 [UniParc].

Last modified October 1, 1993. Version 1.
Checksum: B1AF398B173407D4
Show »

FASTA

788

88,970

        10         20         30         40         50         60 
MQRYNSTYVV KRDGRKEDVH FDKITSRIQK LSYGLNMDFV DPVAVAIKVI SGLYKGVTTV 

        70         80         90        100        110        120 
ELDNLAAETA ASMTTQHPEY ALLAARIAVS NLHKKTNKVF SEVMKTLHEF HHPHTGKHAP 

       130        140        150        160        170        180 
MISDETWAII EKNADKLNSA IVYDRDYSYT YFGFKTLERS YLLKINKEIV ERPQQMLMRV 

       190        200        210        220        230        240 
SIGIHGDDIT SAIETYNLMS ERYMTHASPT LFNSGTCRPQ MSSCFLLTMS EDSILGIYDT 

       250        260        270        280        290        300 
LKQCALISKS AGGIGLNVHK IRATGSVIAG TNGTSNGLIP MLRVYNNTAR YVDQGGNKRP 

       310        320        330        340        350        360 
GAFAIYLEPW HADIFEFVSL RKNTGPEEER ARDLFLALWI PDLFMKRVEK DQEWSLMCPC 

       370        380        390        400        410        420 
ECPGLDDCWG EEFEALYAKY EAEGRVRKTV KARKLWEHIV SNQIETGLPY ITYKDAANRK 

       430        440        450        460        470        480 
SNQQNLGTIK CSNLCTEIIE YSAPDEIAVC NLASIALNRY VTPEKKFDFV KLAEVTKVIT 

       490        500        510        520        530        540 
RNLNKIIDVN YYPVEEARNS NMRHRPIGLG VQGLADCFML MRYPFTSAEA RDLNKRIFET 

       550        560        570        580        590        600 
IYYAALEASC ELAELNGPYS TYEGSPVSKG QLQFDMWGVT PTDQCDWATL RKKIAKHGIR 

       610        620        630        640        650        660 
NSLLMAPMPT ASTAQILGNN ESIEPYTSNI YSRRVLSGDF QIVNPHMLKD LVERGLWTDE 

       670        680        690        700        710        720 
MKNRLIANNG SIQNIDGIPS DIKELYRTVW EISQKDIIEM AADRGAYIDQ SQSLNIHMAK 

       730        740        750        760        770        780 
PSYAGITSMH FYGWKKGLKT GMYYLRTKPA VNAVQFTVDK NALKTNQQAE TPATVAESQD 


EGCLMCSG

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References

[1]	"2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans." Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J., Burton J., Connell M., Copsey T., Cooper J., Coulson A., Craxton M., Dear S., Du Z., Durbin R., Favello A., Fraser A., Fulton L. Wohldman P. Nature 368:32-38(1994) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z19158 Genomic DNA. Translation: CAA79574.1.
PIR	S28302.
RefSeq	NP_499039.1. NM_066638.4.
3D structure databases
ProteinModelPortal	Q03604.
SMR	Q03604. Positions 21-748.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-26889N.
IntAct	Q03604. 3 interactions.
MINT	MINT-1080458.
STRING	6239.T23G5.1.2.
Proteomic databases
PaxDb	Q03604.
PRIDE	Q03604.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	T23G5.1.1; T23G5.1.1; T23G5.1. T23G5.1.2; T23G5.1.2; T23G5.1. T23G5.1.3; T23G5.1.3; T23G5.1.
GeneID	176301.
KEGG	cel:CELE_T23G5.1.
UCSC	T23G5.1.2. c. elegans.
Organism-specific databases
CTD	176301.
WormBase	T23G5.1; CE00331; WBGene00004391; rnr-1.
Phylogenomic databases
eggNOG	COG0209.
GeneTree	ENSGT00390000001372.
HOGENOM	HOG000057035.
InParanoid	Q03604.
KO	K10807.
OMA	YKYGVKT.
Enzyme and pathway databases
UniPathway	UPA00326.
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...
Other
NextBio	891992.

Entry information

Entry name

RIR1_CAEEL

Accession

Primary (citable) accession number: Q03604

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1993
Last modified:	May 1, 2013
This is version 107 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project

Relevant documents

Caenorhabditis elegans

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents