RNR1 encodes the major large (alpha, R1) subunit of class Ia ribonucleotide reductase, which reduces ADP, GDP, CDP and UDP to the corresponding 2'-deoxyribonucleoside diphosphates, the rate-limiting and committed step of de novo dNTP synthesis for nuclear and mitochondrial DNA replication and repair. Rnr1 carries the catalytic site (redox-active cysteine pair and a C-terminal CXXC motif that regenerates the neighbouring monomer's active site in trans), the specificity site that binds ATP/dATP/dGTP/dTTP to select the substrate, and the ATP-cone activity site at which ATP activates and dATP inhibits the enzyme by promoting alpha6 hexamers. It acts as an alpha2 homodimer (or Rnr1-Rnr3 heterodimer after DNA damage) with the Rnr2-Rnr4 beta-beta' heterodimer that holds the diferric tyrosyl radical; reduced thioredoxin re-reduces the enzyme. RNR1 is essential, cell-cycle (G1/S) and DNA-damage induced, and the intrinsically disordered inhibitor Sml1 binds Rnr1 to restrain activity. Rnr1 is cytoplasmic, whereas the small subunits are nuclear until S phase or checkpoint activation releases them.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000166 nucleotide binding | IDA PMID:16537479 Structures of eukaryotic ribonucleotide reductase I provide ... | TOO GENERAL | Summary: Xu et al. (2006) solved Rnr1 crystal structures with AMPPNP, CDP, UDP, ADP, GDP, dGTP and TTP bound at catalytic and allosteric sites. Reason: Correct but general; the catalytic activity term carries the core meaning. Supporting Evidence: PMID:16537479 The structures of the apo-, AMPPNP only-, AMPPNP-CDP-, AMPPNP-UDP-, dGTP-ADP- and TTP-GDP-bound complexes give insight into substrate and effector binding and specificity cross-talk. |
| GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA (PTN000171388) thioredoxin-dependent ribonucleoside-diphosphate reductase activity; correct for the class Ia large subunit. Supporting Evidence: PMID:10716984 The R1 protein is the business end of the enzyme containing the active site and the binding sites for allosteric effectors. |
| GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | IDA PMID:10535923 Purification of ribonucleotide reductase subunits Y1, Y2, Y3... | ACCEPT | Summary: Nguyen et al. (1999) purified recombinant Y1 (Rnr1) and measured its specific activity in reconstituted assays. Supporting Evidence: PMID:10535923 RNR1 contains the active site for reduction and the binding sites for the nucleotide allosteric effectors. PMID:10535923 The specific activity of Y1 isolated from yeast and E. coli is 0.03 micromol.min(-1).mg(-1) |
| GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | IDA PMID:10716984 Yeast ribonucleotide reductase has a heterodimeric iron-radi... | ACCEPT | Summary: Chabes et al. (2000) reconstituted activity with Rnr1 plus the Rnr2/Rnr4 heterodimer; contributes_to is appropriate for the alpha2-beta-beta' holoenzyme. Supporting Evidence: PMID:10716984 In the presence of Rnr1p, both polypeptides of the Rnr2p/Rnr4p heterodimer cosediment at 9.7 S as expected for an alpha(2)betabeta' heterotetramer PMID:10716984 The R1 protein is the business end of the enzyme containing the active site and the binding sites for allosteric effectors. |
| GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | IDA PMID:11893751 Yeast DNA damage-inducible Rnr3 has a very low catalytic act... | ACCEPT | Summary: Domkin et al. (2002) compared Rnr1 and Rnr3 activity in vitro; Rnr1 is the active large subunit. Supporting Evidence: PMID:11893751 The in vitro activity of Rnr3 was less than 1% of the Rnr1 activity. |
| GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/RHEA:23252/EC 1.17.4.1 mapping; correct. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + [thioredoxin]- |
| GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | IMP PMID:8552025 Overexpression of the RNR1 gene rescues Saccharomyces cerevi... | ACCEPT | Summary: Multicopy RNR1 suppresses mip1 mtDNA polymerase mutants by raising dNTP supply (Lecrenier & Foury 1995), an in vivo readout of RNR activity. Supporting Evidence: PMID:8552025 has been isolated and identified as the RNR1 gene PMID:8552025 an increased supply of dNTPs in mitochondria can stimulate the mtDNA polymerase activity |
| GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | ISS GO_REF:0000024 | ACCEPT | Summary: ISS from mouse Rrm1 (P07742); orthologous large subunit, correct. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt Catalyzes the biosynthesis of deoxyribonucleotides from the |
| GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (PWY-7222-1, GDP reduction) with contributes_to; correct (the cytoplasm is_active_in from the same model is also fine). Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + [thioredoxin]- |
| GO:0005515 protein binding | IPI PMID:10716984 Yeast ribonucleotide reductase has a heterodimeric iron-radi... | REMOVE | Summary: Rnr1-Rnr2 association in the holoenzyme (Chabes et al. 2000). Reason: Uninformative protein binding term (removal does not imply the interaction is false); holoenzyme membership is captured by part_of GO:0005971. Supporting Evidence: PMID:10716984 In the presence of Rnr1p, both polypeptides of the Rnr2p/Rnr4p heterodimer cosediment at 9.7 S as expected for an alpha(2)betabeta' heterotetramer |
| GO:0005515 protein binding | IPI PMID:10716984 Yeast ribonucleotide reductase has a heterodimeric iron-radi... | REMOVE | Summary: Rnr1-Rnr4 association in the holoenzyme (Chabes et al. 2000). Reason: Uninformative protein binding term (removal does not imply the interaction is false); captured by GO:0005971. Supporting Evidence: PMID:10716984 In the presence of Rnr1p, both polypeptides of the Rnr2p/Rnr4p heterodimer cosediment at 9.7 S as expected for an alpha(2)betabeta' heterotetramer |
| GO:0005515 protein binding | IPI PMID:16317005 The Schizosaccharomyces pombe replication inhibitor Spd1 reg... | REMOVE | Summary: Rnr1-Sml1 interaction reported with the S. pombe Spd1 study (Hakansson et al. 2006; abstract-only cache). Reason: Uninformative protein binding term (removal does not imply the interaction is false); Sml1 is an inhibitor that binds Rnr1; GO has no specific MF for being bound by an inhibitor. Supporting Evidence: PMID:16317005 Spd1p inhibits fission yeast RNR activity by interacting with the Cdc22p file:yeast/RNR1/RNR1-uniprot.txt P21524; Q04964: SML1; NbExp=4; IntAct=EBI-15234, EBI-27834; |
| GO:0005515 protein binding | IPI PMID:16537480 Structures of eukaryotic ribonucleotide reductase I define g... | REMOVE | Summary: Rnr1 crystallised with an Rnr2-derived peptide (Xu et al. 2006). Reason: Uninformative protein binding term (removal does not imply the interaction is false); subunit-assembly interface, captured by complex membership. Supporting Evidence: PMID:16537480 three x-ray structures of eukaryotic Rnr1 from Saccharomyces cerevisiae |
| GO:0005515 protein binding | IPI PMID:16537480 Structures of eukaryotic ribonucleotide reductase I define g... | REMOVE | Summary: Rnr1 crystallised with an Rnr4-derived peptide (Xu et al. 2006). Reason: Uninformative protein binding term (removal does not imply the interaction is false); captured by complex membership. Supporting Evidence: PMID:16537480 three x-ray structures of eukaryotic Rnr1 from Saccharomyces cerevisiae |
| GO:0005515 protein binding | IPI PMID:17277086 Role of the C terminus of the ribonucleotide reductase large... | REMOVE | Summary: Sml1 binding to the Rnr1 N-terminal domain, competing with the R1-CTD (Zhang et al. 2007). Reason: Uninformative protein binding term (removal does not imply the interaction is false); inhibitor binding; regulatory, not an Rnr1 function. Supporting Evidence: PMID:17277086 Here we show that R1-CTD acts in trans to reduce the active site of its neighboring monomer. |
| GO:0005515 protein binding | IPI PMID:21336276 Structural basis for allosteric regulation of human ribonucl... | REMOVE | Summary: Yeast Rnr1 with Rnr2 in the alpha6-beta-beta' holocomplex EM model (Fairman et al. 2011). Reason: Uninformative protein binding term (removal does not imply the interaction is false); captured by complex membership. Supporting Evidence: PMID:21336276 In addition, we report the X-ray structure of S. cerevisiae RR1 (Yeast RR1) Ξ±6 |
| GO:0005515 protein binding | IPI PMID:21336276 Structural basis for allosteric regulation of human ribonucl... | REMOVE | Summary: Yeast Rnr1 with Rnr4 in the holocomplex model (Fairman et al. 2011). Reason: Uninformative protein binding term (removal does not imply the interaction is false); captured by complex membership. Supporting Evidence: PMID:21336276 In addition, we report the X-ray structure of S. cerevisiae RR1 (Yeast RR1) Ξ±6 |
| GO:0005515 protein binding | IPI PMID:27155231 Inhibition of yeast ribonucleotide reductase by Sml1 depends... | REMOVE | Summary: Sml1 binding to ScRR1 measured kinetically and by size exclusion (Misko et al. 2016). Reason: Uninformative protein binding term (removal does not imply the interaction is false); inhibitor binding. Supporting Evidence: PMID:27155231 Sml1 is an intrinsically disordered protein inhibitor of Saccharomyces cerevisiae ribonucleotide reductase (ScRR1) |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Rnr1-Rnr2 pair in the structural interactome (Michaelis et al. 2023). Reason: Uninformative protein binding term (removal does not imply the interaction is false); captured by complex membership. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt SUBUNIT: Heterotetramer of two large (R1) and two small (R2) subunits. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Rnr1-Rnr4 pair in the structural interactome (Michaelis et al. 2023). Reason: Uninformative protein binding term (removal does not imply the interaction is false); captured by complex membership. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt SUBUNIT: Heterotetramer of two large (R1) and two small (R2) subunits. |
| GO:0005524 ATP binding | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA ATP binding; ATP binds both the activity (ATP-cone) site and the specificity site of R1. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt deoxynucleoside triphosphates and ATP binding to separate specificity PMID:16537479 The structures of the apo-, AMPPNP only-, AMPPNP-CDP-, AMPPNP-UDP-, dGTP-ADP- and TTP-GDP-bound complexes give insight into substrate and effector binding and specificity cross-talk. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro ATP-cone mapping to ATP binding; correct (allosteric effector binding). Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt deoxynucleoside triphosphates and ATP binding to separate specificity |
| GO:0005634 nucleus | HDA PMID:22842922 Dissecting DNA damage response pathways by analysing protein... | MARK AS OVER ANNOTATED | Summary: Nuclear GFP signal in a high-throughput relocalization screen after replication stress (Tkach et al. 2012); Rnr1 is not discussed in the cached text. Reason: Dedicated studies show Rnr1 is predominantly cytoplasmic and remains cytoplasmic after genotoxic stress, while the small subunits are the ones that relocalise; a nuclear pool of Rnr1 is not a site of its function. Supporting Evidence: PMID:22842922 high-throughput microscopic screening of the yeast GFP fusion collection PMID:12732713 After genotoxic stress, Rnr1 remains in the cytoplasm |
| GO:0005737 cytoplasm | HDA PMID:22842922 Dissecting DNA damage response pathways by analysing protein... | ACCEPT | Summary: Cytoplasmic in the high-throughput GFP screen (Tkach et al. 2012); consistent with dedicated studies. Supporting Evidence: PMID:22842922 high-throughput microscopic screening of the yeast GFP fusion collection PMID:12732713 During the normal cell cycle, Rnr1 and Rnr3 are predominantly localized to the cytoplasm |
| GO:0005737 cytoplasm | IDA PMID:12732713 Subcellular localization of yeast ribonucleotide reductase r... | ACCEPT | Summary: Yao et al. (2003) showed by immunofluorescence that Rnr1 is predominantly cytoplasmic through the cell cycle and after DNA damage. Supporting Evidence: PMID:12732713 During the normal cell cycle, Rnr1 and Rnr3 are predominantly localized to the cytoplasm PMID:12732713 After genotoxic stress, Rnr1 remains in the cytoplasm |
| GO:0005737 cytoplasm | IDA PMID:9315670 Identification of RNR4, encoding a second essential small su... | ACCEPT | Summary: Cytoplasmic localization cited from the RNR4 identification paper (Huang & Elledge 1997; abstract-only cache); consistent with later studies. Supporting Evidence: PMID:12732713 During the normal cell cycle, Rnr1 and Rnr3 are predominantly localized to the cytoplasm |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SL-0086 mapping; correct. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12732713}. |
| GO:0005737 cytoplasm | NAS PMID:16537480 Structures of eukaryotic ribonucleotide reductase I define g... | ACCEPT | Summary: NAS from the Rnr1 structure paper; Rnr1 is the cytoplasmic subunit. Supporting Evidence: PMID:18851834 In Saccharomyces cerevisiae, the small subunit Rnr2-Rnr4 is nuclear, whereas the large subunit Rnr1 is cytoplasmic. |
| GO:0005737 cytoplasm | NAS PMID:18851834 Dif1 is a DNA-damage-regulated facilitator of nuclear import... | ACCEPT | Summary: NAS from Lee et al. (2008), who state the large subunit Rnr1 is cytoplasmic. Supporting Evidence: PMID:18851834 In Saccharomyces cerevisiae, the small subunit Rnr2-Rnr4 is nuclear, whereas the large subunit Rnr1 is cytoplasmic. |
| GO:0005737 cytoplasm | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA is_active_in cytoplasm (PWY-7222-1); correct for the active holoenzyme. Supporting Evidence: PMID:18851834 In Saccharomyces cerevisiae, the small subunit Rnr2-Rnr4 is nuclear, whereas the large subunit Rnr1 is cytoplasmic. |
| GO:0005971 ribonucleoside-diphosphate reductase complex | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA ribonucleoside-diphosphate reductase complex; correct. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt SUBUNIT: Heterotetramer of two large (R1) and two small (R2) subunits. |
| GO:0005971 ribonucleoside-diphosphate reductase complex | IDA PMID:10716984 Yeast ribonucleotide reductase has a heterodimeric iron-radi... | ACCEPT | Summary: Rnr1 co-sediments with Rnr2/Rnr4 as an alpha2-beta-beta' heterotetramer (Chabes et al. 2000). Supporting Evidence: PMID:10716984 In the presence of Rnr1p, both polypeptides of the Rnr2p/Rnr4p heterodimer cosediment at 9.7 S as expected for an alpha(2)betabeta' heterotetramer |
| GO:0005971 ribonucleoside-diphosphate reductase complex | IPI PMID:10716984 Yeast ribonucleotide reductase has a heterodimeric iron-radi... | ACCEPT | Summary: Same study, IPI form of the holoenzyme assembly evidence. Supporting Evidence: PMID:10716984 In the presence of Rnr1p, both polypeptides of the Rnr2p/Rnr4p heterodimer cosediment at 9.7 S as expected for an alpha(2)betabeta' heterotetramer |
| GO:0009263 deoxyribonucleotide biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER IBA deoxyribonucleotide biosynthetic process; correct. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt Catalyzes the biosynthesis of deoxyribonucleotides from the |
| GO:0009263 deoxyribonucleotide biosynthetic process | IDA PMID:10535923 Purification of ribonucleotide reductase subunits Y1, Y2, Y3... | ACCEPT | Summary: Reconstituted Rnr1 activity forming dNDPs (Nguyen et al. 1999). Supporting Evidence: PMID:10535923 The specific activity of Y1 isolated from yeast and E. coli is 0.03 micromol.min(-1).mg(-1) |
| GO:0009263 deoxyribonucleotide biosynthetic process | IDA PMID:10716984 Yeast ribonucleotide reductase has a heterodimeric iron-radi... | ACCEPT | Summary: Reconstituted holoenzyme dCDP formation (Chabes et al. 2000). Supporting Evidence: PMID:10716984 The R1 protein is the business end of the enzyme containing the active site and the binding sites for allosteric effectors. |
| GO:0009263 deoxyribonucleotide biosynthetic process | IDA PMID:5459124 Ribonucleotide reductase from Saccharomyces cerevisiae. | ACCEPT | Summary: Early characterisation of yeast ribonucleotide reductase (Vitols et al. 1970; only the title is cached, so deferring to the curator). Supporting Evidence: PMID:5459124 Ribonucleotide reductase from Saccharomyces cerevisiae. |
| GO:0009263 deoxyribonucleotide biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: ARBA/InterPro mapping; correct. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt Catalyzes the biosynthesis of deoxyribonucleotides from the |
| GO:0009263 deoxyribonucleotide biosynthetic process | ISS GO_REF:0000024 | ACCEPT | Summary: ISS from mouse Rrm1; correct. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt Catalyzes the biosynthesis of deoxyribonucleotides from the |
| GO:0042802 identical protein binding | IPI PMID:16537479 Structures of eukaryotic ribonucleotide reductase I provide ... | KEEP AS NON CORE | Summary: Rnr1 dimers in the crystal structures (Xu et al. 2006, 16537479). Reason: Self-association (alpha2 catalytic dimer, alpha6 regulatory hexamer) is real but is a structural property; non-core. Supporting Evidence: PMID:16537479 The alpha subunit, Rnr1, contains catalytic and regulatory sites. |
| GO:0042802 identical protein binding | IPI PMID:16537480 Structures of eukaryotic ribonucleotide reductase I define g... | KEEP AS NON CORE | Summary: Rnr1 dimer in the GemdP/peptide structures (Xu et al. 2006, 16537480). Reason: Structural self-association; non-core. Supporting Evidence: PMID:16537480 Rnr1, the alpha subunit, contains regulatory and catalytic sites |
| GO:0042802 identical protein binding | IPI PMID:17277086 Role of the C terminus of the ribonucleotide reductase large... | KEEP AS NON CORE | Summary: Interallelic complementation and two-hybrid data show the R1-CTD of one monomer acts on its neighbour (Zhang et al. 2007). Reason: Functionally meaningful dimer interface (in trans active-site regeneration) but still a self-binding term; non-core. Supporting Evidence: PMID:17277086 Here we show that R1-CTD acts in trans to reduce the active site of its neighboring monomer. |
| GO:0042802 identical protein binding | IPI PMID:21336276 Structural basis for allosteric regulation of human ribonucl... | KEEP AS NON CORE | Summary: Yeast RR1 alpha6 hexamer structure (Fairman et al. 2011). Reason: dATP/ATP-induced hexamerisation is the allosteric regulatory mechanism; self-binding term non-core. Supporting Evidence: PMID:21336276 In addition, we report the X-ray structure of S. cerevisiae RR1 (Yeast RR1) Ξ±6 |
| GO:0042802 identical protein binding | IPI PMID:27155231 Inhibition of yeast ribonucleotide reductase by Sml1 depends... | KEEP AS NON CORE | Summary: Size-exclusion analysis of dimeric and hexameric ScRR1 (Misko et al. 2016). Reason: Non-core structural property. Supporting Evidence: PMID:27155231 Sml1 is an intrinsically disordered protein inhibitor of Saccharomyces cerevisiae ribonucleotide reductase (ScRR1) |
| GO:0106387 'de novo' GMP biosynthetic process | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA from PWY-7222-1 (guanosine deoxyribonucleotides de novo biosynthesis) mapped to 'de novo' GMP biosynthetic process. Reason: Superpathway/frame mis-mapping: RNR consumes GDP to make dGDP and takes no part in de novo GMP (IMP to GMP) synthesis. The appropriate process, deoxyribonucleotide biosynthetic process, is already annotated. Supporting Evidence: file:yeast/RNR1/RNR1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + [thioredoxin]- file:yeast/RNR1/RNR1-uniprot.txt Catalyzes the biosynthesis of deoxyribonucleotides from the |
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Download this section (compressed HTML)Q: How are dNTPs produced by cytoplasmic Rnr1-containing RNR delivered to mitochondria for mtDNA replication, given that RNR1 overexpression rescues mip1 mutants?
Experiment: Use in-cell crosslinking or FRET between Rnr1 monomers in wild-type, sml1 and dATP-feedback-insensitive (activity-site) mutants, correlating oligomer state with dNTP pools across the cell cycle.
Hypothesis: In vivo alpha6 hexamer formation by Rnr1 tracks dATP levels and limits activity
Type: in vivo biophysics / metabolomics
Major isoform of large subunit of ribonucleotide-diphosphate reductase; the RNR complex catalyzes rate-limiting step in dNTP synthesis, regulated by DNA replication and DNA damage checkpoint pathways via localization of small subunits; relative distribution to the nucleus increases upon DNA replication stress; RNR1 has a paralog, RNR3, that arose from the whole genome duplication
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