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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: -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

Miscellaneous

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

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

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

    GO - Biological processi

    Keywordsi

    Molecular functionOxidoreductase
    Biological processDNA replication

    Enzyme and pathway databases

    BioCyciMetaCyc:YGR180C-MONOMER
    YEAST:YGR180C-MONOMER
    UniPathwayi
    UPA00326

    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

    SGDiS000003412 RNR4

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    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
    PaxDbiP49723
    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

    GO - Molecular functioni

    Protein-protein interaction databases

    BioGridi33432, 200 interactors
    ComplexPortaliCPX-1102 Ribonucleoside-diphosphate reductase variant 1
    CPX-1103 Ribonucleoside-diphosphate reductase variant 2
    DIPiDIP-5381N
    IntActiP49723, 23 interactors
    MINTiP49723
    STRINGi4932.YGR180C

    Structurei

    Secondary structure

    1345
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    DisProtiDP00488
    ProteinModelPortaliP49723
    SMRiP49723
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP49723

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    HOGENOMiHOG000255975
    InParanoidiP49723
    KOiK10808
    OMAiCEFISSA
    OrthoDBiEOG092C3G06

    Family and domain databases

    CDDicd01049 RNRR2, 1 hit
    Gene3Di1.10.620.20, 1 hit
    InterProiView protein in InterPro
    IPR009078 Ferritin-like_SF
    IPR012348 RNR-like
    IPR033909 RNR_small
    IPR030475 RNR_small_AS
    IPR000358 RNR_small_fam
    PANTHERiPTHR23409 PTHR23409, 1 hit
    PfamiView protein in Pfam
    PF00268 Ribonuc_red_sm, 1 hit
    SUPFAMiSSF47240 SSF47240, 1 hit
    PROSITEiView protein in PROSITE
    PS00368 RIBORED_SMALL, 1 hit

    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

    Similar proteinsi

    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, 200 interactors
    ComplexPortaliCPX-1102 Ribonucleoside-diphosphate reductase variant 1
    CPX-1103 Ribonucleoside-diphosphate reductase variant 2
    DIPiDIP-5381N
    IntActiP49723, 23 interactors
    MINTiP49723
    STRINGi4932.YGR180C

    PTM databases

    iPTMnetiP49723

    Proteomic databases

    MaxQBiP49723
    PaxDbiP49723
    PRIDEiP49723
    TopDownProteomicsiP49723

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYGR180C; YGR180C; YGR180C
    GeneIDi853091
    KEGGisce:YGR180C

    Organism-specific databases

    SGDiS000003412 RNR4

    Phylogenomic databases

    HOGENOMiHOG000255975
    InParanoidiP49723
    KOiK10808
    OMAiCEFISSA
    OrthoDBiEOG092C3G06

    Enzyme and pathway databases

    UniPathwayi
    UPA00326

    BioCyciMetaCyc:YGR180C-MONOMER
    YEAST:YGR180C-MONOMER

    Miscellaneous databases

    EvolutionaryTraceiP49723
    PROiPR:P49723

    Family and domain databases

    CDDicd01049 RNRR2, 1 hit
    Gene3Di1.10.620.20, 1 hit
    InterProiView protein in InterPro
    IPR009078 Ferritin-like_SF
    IPR012348 RNR-like
    IPR033909 RNR_small
    IPR030475 RNR_small_AS
    IPR000358 RNR_small_fam
    PANTHERiPTHR23409 PTHR23409, 1 hit
    PfamiView protein in Pfam
    PF00268 Ribonuc_red_sm, 1 hit
    SUPFAMiSSF47240 SSF47240, 1 hit
    PROSITEiView protein in PROSITE
    PS00368 RIBORED_SMALL, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRIR4_YEAST
    AccessioniPrimary (citable) accession number: P49723
    Secondary accession number(s): D6VUW4, Q66R92
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: November 7, 2018
    This is version 189 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

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

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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
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