Complex: Ribonucleoside-diphosphate reductase variant 1
Macromolecular complex annotations are imported from the Complex Portal. These annotations have been derived from physical molecular interaction evidence extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background.
- Curated by
- IntAct
- ComplexAc
- CPX-1102
- Systematic Name
- 2xRNR1:RNR2:RNR4
- SGD ID
- SGD:S000217933
- Aliases
- 2'-deoxyribonucleoside-diphosphate:oxidized-thioredoxin 2'-oxidoreductase ; RNR ; Ribonucleoside 5'-diphosphate reductase ; Ribonucleoside diphosphate reductase ; Ribonucleotide diphosphate reductase ; Ribonucleotide reductase ; Ribonucleotide-diphosphate reductase
- Description
- Catalyzes the reduction of ribonucleotides to the corresponding deoxyribonucleotides, an essential step in the de novo synthesis of monomeric precursors for DNA replication and repair. The catalytically active form is an alpha2beta2 tetramer. The homodimeric alpha subunit, called R1, houses the active site, composed of redox-active disulfides, and binding sites for allosteric effectors, ribonucleoside diphosphates. The beta subunit, called R2, contains a di-iron cluster that in its reduced state reacts with dioxygen to form a stable tyrosyl radical (Y*) and a di-iron(III) cluster. This essential Y* is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site, that initiates ribonucleotide reduction. The enzyme is allosterically controlled by relative levels of dNTPs. This variant is found in all cell states, a related variant (CPX-1103) is only found in damaged or growth-arrested cells. the small subunit, RNR2-RNR4, is nuclear while the large subunit, RNR1, is cytoplasmic. In response to S-phase or DNA-damage, RNR2-RNR4 enters the cytoplasm to bind RNR1.
Composition
Composition view: one node per subunit type, with a ×N badge showing its stoichiometry (stated copies). Click a subunit to highlight its row in the Subunits table below. Switch to "Expanded copies" to see the original interaction diagram with every copy and its binding partners.
Notes
PDB Structure
When available from the Protein Data Bank (PDB), the physical structure of the macromolecular complex is displayed. Click on the image or link for further information about the physical structure.
| 1JK0 | 1ZZD | 2CVY |
Subunits
This table lists all participants of the complex (proteins, small molecules, nucleic acids, etc.) and their respective stoichiometry. A brief description is also provided for each participant in the table.
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| Subunit | Description | Stoichiometry |
|---|
Binding Regions
Residue-level binding regions reported for this complex. Each row gives the range of residues on the subunit that mediates binding to the partner subunit, with the region label from IntAct where available. Regions are directional, so a pair of subunits may appear twice (once for each partner's contact region).
| Subunit | Binding partner | Region (residues) | Region name |
|---|---|---|---|
| RNR1 | RNR1 | 1–888 | rnr1 |
| RNR2 | RNR4 | 1–399 | rnr4 binding region |
| RNR2 | iron cation | 145–145 | iron binding region |
| RNR2 | iron cation | 176–176 | iron binding region |
| RNR2 | iron cation | 179–179 | iron binding region |
| RNR4 | RNR2 | 338–345 | rnr2 binding region |
Gene Ontology
Gene Ontology (GO) terms that describe the function of a complex, the biological process in which it participates, or its cellular location. Click on a term for its definition and other objects annotated to that term.
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GO Slim Terms
The yeast GO Slim terms are higher level terms that best represent the major S. cerevisiae biological processes, functions, and cellular components. The GO Slim terms listed here are the broader parent terms for the specific terms to which this gene product is annotated, and thus represent the more general processes, functions, and components in which it is involved.
- ion binding, oxidoreductase activity, biosynthetic process, nucleobase-containing small molecule metabolic process, small molecule metabolic process, cytoplasm, cytosol
Biological Process
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| Evidence ID | Analyze ID | Complex Name | Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Annotation Type | Source | Assigned On | Reference |
|---|
Molecular Function
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| Evidence ID | Analyze ID | Complex Name | Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Annotation Type | Source | Assigned On | Reference |
|---|
Cellular Component
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| Evidence ID | Analyze ID | Complex Name | Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Annotation Type | Source | Assigned On | Reference |
|---|
Shared Biology
Relationships this complex shares with other yeast complexes. The "Network" shows Gene Ontology terms and subunits shared between this complex and other complexes as an interactive graph. The "Ranked list" summarizes the same relationships: the Gene Ontology terms this complex is annotated to and how many other complexes share each, plus other complexes ranked by how much biology they share with this one.
Network
Ranked list
References
List of references used specifically to curate the information on this page.
- Xu H, et al. (2006) Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly. Proc Natl Acad Sci U S A 103(11):4028-33 PMID: 16537480
- Xu H, et al. (2006) Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation. Proc Natl Acad Sci U S A 103(11):4022-7 PMID: 16537479
Resources
IntAct | ModelArchive | PDB:1JK0 | PDB:1ZZD | PDB:2CVY ... Show all Show fewer