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Protein

Ribonucleoside-diphosphate reductase small chain 2

Gene

RNR4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR4 is required for proper folding of RNR2 and assembly with the large subunits.1 Publication

Catalytic activityi

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

Kineticsi

    1. Vmax=2250 nmol/min/mg enzyme for cytidine 5'-diphosphate1 Publication

    Temperature dependencei

    Optimum temperature is 30 degrees Celsius.1 Publication

    Pathwayi: DNA replication

    This protein is involved in the pathway DNA replication, which is part of Genetic information processing.
    View all proteins of this organism that are known to be involved in the pathway DNA replication and in Genetic information processing.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei131PROSITE-ProRule annotation1

    GO - Molecular functioni

    • ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: SGD

    GO - Biological processi

    • cofactor biosynthetic process Source: SGD
    • deoxyribonucleotide biosynthetic process Source: SGD
    • DNA replication Source: UniProtKB-UniPathway
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Enzyme and pathway databases

    BioCyciMetaCyc:YGR180C-MONOMER.
    YEAST:YGR180C-MONOMER.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase small chain 2 (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase R2 subunit 2
    Ribonucleotide reductase small subunit 2
    Gene namesi
    Name:RNR4
    Synonyms:CRT3
    Ordered Locus Names:YGR180C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome VII

    Organism-specific databases

    EuPathDBiFungiDB:YGR180C.
    SGDiS000003412. RNR4.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: SGD
    • nucleus Source: SGD
    • ribonucleoside-diphosphate reductase complex Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001904651 – 345Ribonucleoside-diphosphate reductase small chain 2Add BLAST345

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei1N-acetylmethionineCombined sources1 Publication1
    Modified residuei169PhosphoserineCombined sources1
    Modified residuei332PhosphoserineCombined sources1
    Modified residuei334PhosphothreonineCombined sources1
    Modified residuei336PhosphoserineCombined sources1
    Cross-linki337Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources

    Keywords - PTMi

    Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP49723.
    PRIDEiP49723.
    TopDownProteomicsiP49723.

    PTM databases

    iPTMnetiP49723.

    Expressioni

    Inductioni

    Induced by DNA-damage.1 Publication

    Interactioni

    Subunit structurei

    Heterotetramer of two large (R1) and two small (R2) subunits. S.cerevisiae has two different R1 subunits (RNR1 and RNR3) and two different R2 subunits (RNR2 and RNR4). The functional form of the small subunits is a RNR2-RNR4 heterodimer, where RNR2 provides the iron-radical center and RNR4 is required for proper folding of RNR2 and assembly with the large subunits. Under normal growth conditions, the active form of the large subunits is a homodimer of the constitutively expressed RNR1. In damaged cells or cells arrested for DNA synthesis, the reductase consists of multiple species because of the association of the small subunits (RNR2-RNR4) with either the RNR1 homodimer or a heterodimer of RNR1 and the damage-inducible RNR3. Interacts with DIF1.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    RNR2P099386EBI-15251,EBI-15240
    WTM1Q123634EBI-15251,EBI-20563

    Protein-protein interaction databases

    BioGridi33432. 97 interactors.
    DIPiDIP-5381N.
    IntActiP49723. 17 interactors.
    MINTiMINT-537732.

    Structurei

    Secondary structure

    1345
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi4 – 9Combined sources6
    Helixi13 – 21Combined sources9
    Turni22 – 24Combined sources3
    Turni26 – 28Combined sources3
    Helixi43 – 54Combined sources12
    Helixi59 – 61Combined sources3
    Turni65 – 67Combined sources3
    Turni69 – 73Combined sources5
    Helixi78 – 89Combined sources12
    Helixi101 – 107Combined sources7
    Helixi111 – 138Combined sources28
    Helixi142 – 144Combined sources3
    Helixi148 – 151Combined sources4
    Helixi155 – 166Combined sources12
    Beta strandi169 – 172Combined sources4
    Helixi175 – 187Combined sources13
    Turni188 – 190Combined sources3
    Helixi191 – 200Combined sources10
    Beta strandi202 – 205Combined sources4
    Helixi207 – 232Combined sources26
    Helixi240 – 258Combined sources19
    Turni265 – 268Combined sources4
    Helixi277 – 288Combined sources12
    Helixi316 – 322Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JK0X-ray2.80B1-345[»]
    1SMSX-ray3.10A/B1-345[»]
    1ZZDX-ray2.60B337-345[»]
    DisProtiDP00488.
    ProteinModelPortaliP49723.
    SMRiP49723.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP49723.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    HOGENOMiHOG000255975.
    InParanoidiP49723.
    KOiK10808.
    OrthoDBiEOG092C3G06.

    Family and domain databases

    CDDicd01049. RNRR2. 1 hit.
    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR033909. RNR_small.
    IPR030475. RNR_small_AS.
    IPR000358. RNR_small_fam.
    [Graphical view]
    PANTHERiPTHR23409. PTHR23409. 1 hit.
    PfamiPF00268. Ribonuc_red_sm. 1 hit.
    [Graphical view]
    SUPFAMiSSF47240. SSF47240. 1 hit.
    PROSITEiPS00368. RIBORED_SMALL. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P49723-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEAHNQFLKT FQKERHDMKE AEKDEILLME NSRRFVMFPI KYHEIWAAYK
    60 70 80 90 100
    KVEASFWTAE EIELAKDTED FQKLTDDQKT YIGNLLALSI SSDNLVNKYL
    110 120 130 140 150
    IENFSAQLQN PEGKSFYGFQ IMMENIYSEV YSMMVDAFFK DPKNIPLFKE
    160 170 180 190 200
    IANLPEVKHK AAFIERWISN DDSLYAERLV AFAAKEGIFQ AGNYASMFWL
    210 220 230 240 250
    TDKKIMPGLA MANRNICRDR GAYTDFSCLL FAHLRTKPNP KIIEKIITEA
    260 270 280 290 300
    VEIEKEYYSN SLPVEKFGMD LKSIHTYIEF VADGLLQGFG NEKYYNAVNP
    310 320 330 340
    FEFMEDVATA GKTTFFEKKV SDYQKASDMS KSATPSKEIN FDDDF
    Length:345
    Mass (Da):40,055
    Last modified:October 1, 1996 - v1
    Checksum:i712853F2D87D3972
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti127Y → H in AAU09736 (PubMed:17322287).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U30385 Genomic DNA. Translation: AAB72236.1.
    Z72965 Genomic DNA. Translation: CAA97206.1.
    AY723819 Genomic DNA. Translation: AAU09736.1.
    BK006941 Genomic DNA. Translation: DAA08275.1.
    PIRiS59744.
    RefSeqiNP_011696.3. NM_001181309.3.

    Genome annotation databases

    EnsemblFungiiYGR180C; YGR180C; YGR180C.
    GeneIDi853091.
    KEGGisce:YGR180C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U30385 Genomic DNA. Translation: AAB72236.1.
    Z72965 Genomic DNA. Translation: CAA97206.1.
    AY723819 Genomic DNA. Translation: AAU09736.1.
    BK006941 Genomic DNA. Translation: DAA08275.1.
    PIRiS59744.
    RefSeqiNP_011696.3. NM_001181309.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JK0X-ray2.80B1-345[»]
    1SMSX-ray3.10A/B1-345[»]
    1ZZDX-ray2.60B337-345[»]
    DisProtiDP00488.
    ProteinModelPortaliP49723.
    SMRiP49723.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi33432. 97 interactors.
    DIPiDIP-5381N.
    IntActiP49723. 17 interactors.
    MINTiMINT-537732.

    PTM databases

    iPTMnetiP49723.

    Proteomic databases

    MaxQBiP49723.
    PRIDEiP49723.
    TopDownProteomicsiP49723.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYGR180C; YGR180C; YGR180C.
    GeneIDi853091.
    KEGGisce:YGR180C.

    Organism-specific databases

    EuPathDBiFungiDB:YGR180C.
    SGDiS000003412. RNR4.

    Phylogenomic databases

    HOGENOMiHOG000255975.
    InParanoidiP49723.
    KOiK10808.
    OrthoDBiEOG092C3G06.

    Enzyme and pathway databases

    UniPathwayiUPA00326.
    BioCyciMetaCyc:YGR180C-MONOMER.
    YEAST:YGR180C-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP49723.
    PROiP49723.

    Family and domain databases

    CDDicd01049. RNRR2. 1 hit.
    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR033909. RNR_small.
    IPR030475. RNR_small_AS.
    IPR000358. RNR_small_fam.
    [Graphical view]
    PANTHERiPTHR23409. PTHR23409. 1 hit.
    PfamiPF00268. Ribonuc_red_sm. 1 hit.
    [Graphical view]
    SUPFAMiSSF47240. SSF47240. 1 hit.
    PROSITEiPS00368. RIBORED_SMALL. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRIR4_YEAST
    AccessioniPrimary (citable) accession number: P49723
    Secondary accession number(s): D6VUW4, Q66R92
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: November 30, 2016
    This is version 174 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 88884 molecules/cell in log phase SD medium.1 Publication
    Lacks 3 iron-binding residues conserved in all other R2 subunits.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.