RFC3 (YNL290W) encodes the 40-kDa small subunit of replication factor C (RFC), an essential AAA+ ATPase of the activator 1 small-subunit family. Rfc3 is one of the four small subunits (Rfc2-Rfc5) that form the shared core of the canonical clamp loader RFC (with Rfc1) and of the three alternative RFC-like complexes, in which Rfc1 is replaced by Rad24, Ctf18 (with Ctf8 and Dcc1) or Elg1. Within RFC, these complexes use ATP binding and hydrolysis to open the homotrimeric sliding clamp PCNA (Pol30) and close it around primer-template DNA, where PCNA confers processivity on DNA polymerases delta and epsilon during chromosomal DNA replication and repair synthesis. In RFC, Rfc3 makes a strong direct contact with PCNA and supplies the catalytic arginine finger for the ATP site of the neighbouring Rfc4 subunit; purified Rfc3 alone has a single-stranded-DNA-stimulated ATPase activity. As part of Rad24-RFC it contributes to loading of the Ddc1-Mec3-Rad17 (9-1-1) checkpoint clamp at primer-template junctions in the DNA damage checkpoint; as part of Ctf18-RFC it contributes to sister chromatid cohesion establishment and to PCNA unloading; and as part of Elg1-RFC it is a structural component of the complex that removes PCNA from chromatin after replication. RFC3 is essential for growth, and the protein is nuclear.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000077 DNA damage checkpoint signaling | NAS PMID:12604797 Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage ch... | ACCEPT | Summary: Rfc3 is one of the four small subunits of the Rad24-RFC complex, the clamp loader that loads the Rad17-Mec3-Ddc1 (9-1-1) checkpoint clamp onto partial duplex DNA in an ATP-dependent reaction (Majka and Burgers 2003). Loading of the checkpoint clamp is an early step of DNA damage checkpoint signaling. Reason: Majka and Burgers purified Rad24-RFC (Rad24 plus Rfc2-5) and showed directly that it loads the 9-1-1 clamp, whereas canonical RFC does not. Rfc3 is a stoichiometric subunit of the loader, so it does part of the work of the clamp-loading step, which is the step by which the checkpoint clamp is placed on DNA. This passes the participation test (the complex containing Rfc3 performs the step). The NAS code reflects that a checkpoint signaling phenotype of rfc3 alleles is not tested in this paper; the role is established for the complex. This is one of the core, complex-specific roles of the shared small subunits. Supporting Evidence: PMID:12604797 Here, we provide experimental evidence that, indeed, the RFC-Rad24 clamp loader loads the Rad17/3/1 clamp around partial duplex DNA in an ATP-dependent process. PMID:12604797 Rad24 interacts with the four small subunits of replication factor C (RFC) to form the RFC-Rad24 complex. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the clamp loader C-terminal domain (IPR008921). RFC binds primer-template DNA in a structure-specific manner, and isolated Rfc3 has an ATPase that is stimulated by single-stranded DNA, implying DNA contact. Reason: DNA binding by RFC is well established for the complex (structure-specific primer-template binding; Fien and Stillman 1992), and the single-stranded-DNA stimulation of the purified Rfc3 ATPase (Li and Burgers 1994) indicates that Rfc3 itself engages DNA. The evidence does not establish a more specific DNA-binding term for Rfc3 alone (the primer-template junction is recognised by the assembled pentamer), so the general term is retained. It is a supporting property of the clamp-loading activity rather than a core function in its own right. Supporting Evidence: PMID:8302859 Purified Rfc3p has an ATPase activity that is markedly stimulated by single-stranded DNA but not by double-stranded DNA or RNA. PMID:1346062 Like its human-cell counterpart, RFC from S. cerevisiae (scRFC) has an associated DNA-activated ATPase activity as well as a primer-template, structure-specific DNA binding activity. |
| GO:0003689 DNA clamp loader activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation from node PTN000186209 (RFC small subunits) with donors including yeast Rfc2/Rfc3/Rfc4/Rfc5 and human RFC2-5. Rfc3 itself is among the experimental donors (SGD:S000005234). Reason: RFC3 sits in PANTHER subfamily PTHR11669:SF9 (official name "replication factor C subunit 5"; the PANTHER numbering does not follow yeast gene numbering) within the RFC small-subunit clade, so it is inside the clade to which PAINT assigned this activity. The contributes_to qualifier correctly expresses that the activity belongs to the assembled heteropentamer. Rfc3's own experimental annotations (see the IDA rows) are among the descendant evidences used to place the node, which is expected rather than circular. Supporting Evidence: PMID:10799539 Eukaryotic replication factor C (RF-C) is a heteropentameric complex that is required to load the replication clamp proliferating cell nuclear antigen onto primed DNA. |
| GO:0003689 DNA clamp loader activity | IDA PMID:12604797 Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage ch... | ACCEPT | Summary: Purified Rad24-RFC (Rad24 with Rfc2-Rfc5) loads the Rad17-Mec3-Ddc1 checkpoint clamp onto gapped and partial-duplex DNA in an ATP-dependent manner and releases it upon ATP hydrolysis. Reason: Direct biochemical demonstration of clamp loading by a complex of which Rfc3 is a stoichiometric subunit; contributes_to is the correct qualifier. The paper also shows that RFC loads PCNA and Rad24-RFC loads 9-1-1 as non-exchangeable pairs, both of which contain Rfc3. Supporting Evidence: PMID:12604797 Loading of Rad17/3/1 required the presence of both the clamp loader and ATP PMID:12604797 These data suggest that the two pairs of complexes, PCNAβRFC and Rad17/3/1βRFC-Rad24, define nonexchangeable clamp-clamp loader systems which are active during DNA replication and the checkpoint response, respectively. |
| GO:0003689 DNA clamp loader activity | IDA PMID:8995429 Overproduction and affinity purification of Saccharomyces ce... | ACCEPT | Summary: RFC overproduced from all five RFC genes was purified to homogeneity by PCNA-affinity in the presence of ATP and was active, with ATP binding (not hydrolysis) driving tight PCNA binding. Reason: The cached abstract establishes that all five RFC genes, including RFC3, are needed to overproduce active RF-C and that the purified complex binds PCNA in an ATP-dependent mode, the first step of clamp loading. The curator had the full text with activity assays; the contributes_to qualifier is appropriate for a subunit of the loader. Supporting Evidence: PMID:8995429 Overexpression of all five genes was also necessary to achieve overproduction of RF-C as omission of any single gene from the plasmid gave uninduced, i.e. normal cellular levels of RF-C. PMID:8995429 Binding of ATP, but not its hydrolysis, was required for the strong binding mode as nonhydrolyzable analogs were also effective. |
| GO:0005515 protein binding | IPI PMID:10660302 A novel Rad24 checkpoint protein complex closely related to ... | REMOVE | Summary: Co-purification and reciprocal co-immunoprecipitation of Rfc3 with Rad24, defining the Rad24-RFC complex. Reason: Generic protein binding is uninformative. The interaction with Rad24 reflects stable membership of the Rad24-RFC complex, which is already captured by the GO:0031389 Rad17 RFC-like complex annotations from this same paper. Removal does not dispute the interaction. Supporting Evidence: PMID:10660302 the small RFC proteins, Rfc2, Rfc3, Rfc4 and Rfc5, interacted with Rad24, whereas the Rfc1 subunit did not |
| GO:0005515 protein binding | IPI PMID:11389843 Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative ... | REMOVE | Summary: Rfc3 co-purifies with Ctf8 as part of the Ctf18-RFC complex. Reason: Generic protein binding is uninformative; the interaction with Ctf8 reflects Ctf18-RFC complex membership, already captured by the GO:0031390 Ctf18 RFC-like complex annotations from this paper. Removal does not dispute the interaction. Supporting Evidence: PMID:11389843 Ctf18p, Ctf8p, and Dcc1p interact physically in a complex with Rfc2p, Rfc3p, Rfc4p, and Rfc5p but not with Rfc1p or Rad24p. |
| GO:0005515 protein binding | IPI PMID:11486023 Chl12 (Ctf18) forms a novel replication factor C-related com... | REMOVE | Summary: Rfc3 co-immunoprecipitates with Chl12/Ctf18, forming an RFC-related complex distinct from RFC and Rad24-RFC. Reason: Generic protein binding is uninformative; the Ctf18 interaction is complex membership, captured by the GO:0031390 Ctf18 RFC-like complex annotations. Removal does not dispute the interaction. Supporting Evidence: PMID:11486023 We also show that Chl12 interacts physically with Rfc2, Rfc3, Rfc4, and Rfc5 and forms an RFC-related complex which is distinct from the RFC and RAD24 complexes. |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | REMOVE | Summary: High-throughput affinity purification/mass spectrometry (HMS-PCI) recovered Rfc3 with Rad24. Reason: Generic protein binding from a large-scale complex screen; the association reflects Rad24-RFC membership, already annotated with the informative GO:0031389 term. Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | REMOVE | Summary: High-throughput affinity purification/mass spectrometry recovered Rfc3 with Rfc2. Reason: Generic protein binding; Rfc2-Rfc3 association reflects co-membership of the RFC and RFC-like complexes, which is captured by the complex (CC) annotations. Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:12665596 Mechanical link between cohesion establishment and DNA repli... | REMOVE | Summary: Chromatographic co-fractionation of the cohesion establishment acetyltransferase Ctf7/Eco1 with Rfc2-Rfc5 and with Ctf18. Reason: Generic protein binding is uninformative. The Eco1 association is with RFC complexes generally (Ctf18-RFC, RFC and Rad24-RFC) and does not establish a specific molecular function of Rfc3; no informative replacement MF is supported. Removal does not dispute the association. Supporting Evidence: PMID:12665596 By chromatographic methods, Ctf7p/Eco1p was found to associate with Chl12/Ctf18p and with Rfc2p, Rfc3p, Rfc4p, and Rfc5p. |
| GO:0005515 protein binding | IPI PMID:12912927 Elg1 forms an alternative RFC complex important for DNA repl... | REMOVE | Summary: Immunoprecipitates of Rfc3 contain Elg1, defining the Elg1-RFC complex. Reason: Generic protein binding; the Elg1 interaction is Elg1-RFC complex membership, already captured by the GO:0031391 Elg1 RFC-like complex annotations from this paper. Removal does not dispute the interaction. Supporting Evidence: PMID:12912927 In contrast, immunoprecipitates of Rfc2, Rfc3, Rfc4 or Rfc5 all contained Elg1 |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: Proteome-wide TAP purification recovered Rfc3 with Rfc2. Reason: Generic protein binding from a large-scale complex survey reflecting RFC complex co-membership, captured by the CC annotations. Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: Proteome-wide TAP purification recovered Rfc3 with Ctf18. Reason: Generic protein binding reflecting Ctf18-RFC membership, captured by GO:0031390. Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:18467557 An in vivo map of the yeast protein interactome. | REMOVE | Summary: In vivo protein-fragment complementation (DHFR PCA) screen detected Rfc3-Rfc2 proximity. Reason: Generic protein binding from a proteome-scale screen; Rfc2 and Rfc3 are adjacent subunits of the RFC pentamer, a relationship captured by the complex annotations. Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:18719252 High-quality binary protein interaction map of the yeast int... | REMOVE | Summary: Yeast two-hybrid binary interactome detected Rfc3-Rfc2. Reason: Generic protein binding from a large-scale binary screen, reflecting the known Rfc2-Rfc3 subunit contact in RFC; captured by complex annotations. Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Large-scale interactome/structural modelling study supporting Rfc3-Rad24 association. Reason: Generic protein binding reflecting Rad24-RFC complex membership (GO:0031389). Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Large-scale interactome study supporting Rfc3-Ctf8 association. Reason: Generic protein binding reflecting Ctf18-RFC complex membership (GO:0031390). Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Large-scale interactome study supporting Rfc3-Rfc2 association. Reason: Generic protein binding reflecting RFC/RFC-like complex co-membership. Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Large-scale interactome study supporting Rfc3-Ctf18 association. Reason: Generic protein binding reflecting Ctf18-RFC complex membership (GO:0031390). Removal does not dispute the interaction. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Large-scale interactome study supporting Rfc3-Elg1 association. Reason: Generic protein binding reflecting Elg1-RFC complex membership (GO:0031391). Removal does not dispute the interaction. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the AAA ATPase core domain. Rfc3 has a Walker A (P-loop) motif and binds ATP-gamma-S in cryo-EM structures of RFC-like complexes. Reason: ATP binding by Rfc3 is supported directly by structure (Rfc3 is one of the four ATP-gamma-S-bound subunits in Elg1-RFC, with the same nucleotide pattern as RFC) and by the conserved ATP-binding motif identified when the gene was cloned. ATP binding is mechanistically central to clamp opening. Supporting Evidence: PMID:38427736 In all three Elg1-RFC structures, we found five bound nucleotides: four ATPΞ³S in Rfc2, Rfc3, Rfc4, and Elg1, and one ADP in Rfc5 PMID:8302859 Among the conserved regions are the A motif of ATP binding proteins |
| GO:0005634 nucleus | HDA PMID:11914276 Subcellular localization of the yeast proteome. | ACCEPT | Summary: Proteome-scale immunolocalization of epitope-tagged yeast proteins placed Rfc3 in the nucleus. Reason: Consistent with its role in chromosomal DNA replication; nuclear localization is supported by several independent studies (also IDA from PMID:22932476). Supporting Evidence: PMID:11914276 By high-throughput immunolocalization of tagged gene products, we have determined the subcellular localization of 2744 yeast proteins. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of nuclear activity to the eukaryotic RFC small-subunit clade. Reason: RFC acts on chromosomal DNA in the nucleus; the IBA agrees with the direct yeast localization data. Supporting Evidence: PMID:11914276 By high-throughput immunolocalization of tagged gene products, we have determined the subcellular localization of 2744 yeast proteins. |
| GO:0005634 nucleus | IDA PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to... | ACCEPT | Summary: Rfc3 is among the nuclear proteins tracked in a study of oxygen-regulated nuclear protein localization; it is nuclear under normoxia and returns to the nucleus on reoxygenation. Reason: Rfc3 is listed among proteins that recovered nuclear localization after reoxygenation, confirming nuclear localization under normal growth conditions. Supporting Evidence: PMID:22932476 Proteins that recovered their nuclear locations in response to oxygen in a shorter time period |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping (Nucleus). Reason: Agrees with experimental localization data. Supporting Evidence: PMID:11914276 By high-throughput immunolocalization of tagged gene products, we have determined the subcellular localization of 2744 yeast proteins. |
| GO:0005634 nucleus | IPI PMID:23499004 The Elg1 replication factor C-like complex functions in PCNA... | ACCEPT | Summary: Kubota et al. studied Elg1-RLC-dependent unloading of PCNA from chromatin; the Elg1-RFC complex containing Rfc3 acts on nuclear chromatin. Reason: The localization is correct; the curator, who read the full text, linked Rfc3 nuclear (chromatin) association to this paper. The abstract-only cache supports that Elg1-RLC acts on chromatin during replication. Nucleus is not in doubt. Supporting Evidence: PMID:23499004 Using an improved degron system we show that without Elg1, PCNA accumulates on Saccharomyces cerevisiae chromatin during replication. |
| GO:0005634 nucleus | NAS PMID:12604797 Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage ch... | ACCEPT | Summary: Author statement placing the RFC/Rad24-RFC clamp loaders at the nuclear replication fork and sites of damage. Reason: Consistent with all other localization evidence. Supporting Evidence: PMID:12604797 RFC is a heteropentameric complex, consisting of a large subunit, Rfc1, and the four small Rfc2-5 subunits, that clamps PCNA around the DNA at primer/template junctions in an ATP-dependent process |
| GO:0005663 DNA replication factor C complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of RFC complex membership to the RFC small-subunit node, with yeast Rfc3 among the experimental donors. Reason: RFC3 is in the RFC small-subunit clade (PTHR11669:SF9) and is experimentally a subunit of yeast RFC. Supporting Evidence: PMID:8995429 Yeast replication factor C (RF-C) is a heteropentamer encoded by the RFC1-5 genes. |
| GO:0005663 DNA replication factor C complex | IDA PMID:7651383 Characterization of the five replication factor C genes of S... | ACCEPT | Summary: Cloning of the five yeast RFC genes, including RFC3, by peptide sequencing of purified ScRFC or by similarity to human cDNAs; all five are essential. Reason: Establishes Rfc3 as a subunit of purified yeast RFC. Supporting Evidence: PMID:7651383 Here we report the cloning, by either peptide sequencing or by sequence similarity to the human cDNAs, of the S. cerevisiae genes RFC1, RFC2, RFC3, RFC4, and RFC5. |
| GO:0005663 DNA replication factor C complex | IPI PMID:10799539 Overproduction in Escherichia coli and characterization of y... | ACCEPT | Summary: Co-expression of RFC1-deltaN with RFC2-5 in E. coli yields a homogeneous, active heteropentameric RF-C. Reason: Reconstitution of RFC from its five subunits, including Rfc3, confirms complex membership. Supporting Evidence: PMID:10799539 The other four RFC genes were cloned into the latter plasmid to yield a single plasmid that overproduced RF-C to moderate levels. |
| GO:0005829 cytosol | IDA PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to... | KEEP AS NON CORE | Summary: In this hypoxia study, Rfc3 relocalized from the nucleus under hypoxia and returned on reoxygenation. Reason: The cytosolic signal is condition-specific (hypoxia-induced relocalization) and not where Rfc3 acts; its functional site is the nucleus. Not wrong as an observation under that condition, so kept as non-core rather than removed. Supporting Evidence: PMID:22932476 YNL290WRFC3Subunit of heteropentameric Replication factor C |
| GO:0006260 DNA replication | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping for the clamp loader C-terminal domain. Reason: Correct; RFC3 is an essential gene for growth and Rfc3 is part of the clamp loader required for processive replication by pol delta and pol epsilon. The broader term is compatible with the more specific DNA-templated DNA replication and strand-elongation annotations. Supporting Evidence: PMID:8302859 Yeast replication factor C (RF-C) is a multi-polypeptide complex required for processive DNA replication by DNA polymerases delta and epsilon. |
| GO:0006261 DNA-templated DNA replication | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation from PTN000186208 (an ancestral clamp-loader node including bacterial gamma/tau and delta-prime donors and eukaryotic RFC subunits). Reason: Rfc3 is inside the clade; clamp loading for replicative polymerases is the ancestral function of this family and is experimentally supported for yeast RFC. Supporting Evidence: PMID:1346062 RFC from S. cerevisiae was purified by its ability to stimulate yeast DNA polymerase delta on a primed single-stranded DNA template in the presence of yeast PCNA and RPA. |
| GO:0006261 DNA-templated DNA replication | IDA PMID:10799539 Overproduction in Escherichia coli and characterization of y... | ACCEPT | Summary: Recombinant RF-C reconstituted from Rfc1-deltaN and Rfc2-5 is active in PCNA-dependent DNA replication assays. Reason: Direct biochemical evidence that the Rfc3-containing complex functions in DNA-templated DNA synthesis. Supporting Evidence: PMID:10799539 In some assays, the Rfc1-DeltaN containing RF-C from E. coli showed an increased activity compared with the full-length enzyme from yeast |
| GO:0006271 DNA strand elongation involved in DNA replication | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning annotation. Reason: Although the source is an ARBA prediction, the claim is independently supported by experimental data in yeast; RFC loads PCNA so that pol delta/epsilon synthesize processively along primed templates, i.e. the elongation phase of replication. Supporting Evidence: PMID:8302859 Yeast replication factor C (RF-C) is a multi-polypeptide complex required for processive DNA replication by DNA polymerases delta and epsilon. PMID:1346062 RFC from S. cerevisiae was purified by its ability to stimulate yeast DNA polymerase delta on a primed single-stranded DNA template in the presence of yeast PCNA and RPA. |
| GO:0006272 leading strand elongation | IDA PMID:1346062 Identification of replication factor C from Saccharomyces ce... | KEEP AS NON CORE | Summary: Yeast RFC was purified by its ability to stimulate pol delta on primed single-stranded DNA with PCNA and RPA; by analogy with SV40 and T4 systems these factors were proposed to form a leading-strand replication complex. Reason: The experiment shows primed-template elongation in vitro; the leading-strand designation is by analogy with SV40 in vitro replication. RFC/PCNA in fact act on both strands (PCNA must be loaded at every Okazaki fragment), so the strand-specific term captures only part of the role. Not wrong (RFC loads PCNA for leading-strand pol epsilon too), and as an experimental curator call it is kept, but the general DNA strand elongation term is the core one. Supporting Evidence: PMID:1346062 By analogy with the phage T4 and SV40 DNA replication in vitro systems, the yeast RFC, PCNA, RPA, and DNA polymerase delta activities function together as a leading-strand DNA replication complex. |
| GO:0006281 DNA repair | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT propagation from the RFC small-subunit node, seeded by S. pombe small-subunit donors. Reason: RFC loads PCNA for repair DNA synthesis and the Rfc2-5-containing Rad24-RFC loads the 9-1-1 clamp in the damage response, so the small subunits do participate in DNA repair through clamp loading. Rfc3 is within the clade the node covers. In budding yeast the direct repair evidence is complex-level and mostly inferred from RFC's general clamp-loading role, so this is a supporting rather than core process; no more specific repair sub-process is experimentally established for Rfc3 here. Supporting Evidence: PMID:10660302 subunits of replication factor C (RFC), a five subunit protein that is required for the loading of polymerases onto DNA during replication and repair |
| GO:0006298 mismatch repair | TAS PMID:10072354 Eukaryotic DNA mismatch repair. | KEEP AS NON CORE | Summary: Review of eukaryotic mismatch repair listing RFC among the replication factors implicated in MMR. Reason: RFC (via PCNA loading) is implicated in the resynthesis step of MMR, which supports participation of the clamp loader complex; the review does not present RFC3-specific data. Kept as a peripheral process; the core function is clamp loading. Supporting Evidence: PMID:10072354 A number of other proteins have been implicated in MMR, including DNA polymerase delta, RPA (replication protein A), PCNA (proliferating cell nuclear antigen), RFC (replication factor C) |
| GO:0007064 mitotic sister chromatid cohesion | NAS PMID:11389843 Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative ... | KEEP AS NON CORE | Summary: Rfc3 is a subunit of Ctf18-RFC (Ctf18, Ctf8, Dcc1 with Rfc2-5), which is required for sister chromatid cohesion; rfc4 temperature-sensitive mutants show precocious sister separation. Reason: Rfc3 is a structural subunit of the Ctf18-RFC complex that acts in cohesion establishment, and Eco1 associates with Rfc2-5. However, no rfc3 allele was assayed for cohesion in the cited work (the mutant phenotype is for rfc4, and rfc5-1 in PMID:12665596), and the cohesion-specific function lies with the Ctf18/Ctf8/Dcc1 module. The annotation is accepted as a complex-level participation but is not a core function of Rfc3. Supporting Evidence: PMID:11389843 Ctf18p, Ctf8p, and Dcc1p interact physically in a complex with Rfc2p, Rfc3p, Rfc4p, and Rfc5p but not with Rfc1p or Rad24p. PMID:11389843 Furthermore, temperature-sensitive mutations in RFC4 result in precocious sister chromatid separation. |
| GO:0016887 ATP hydrolysis activity | IDA PMID:8302859 Molecular cloning and expression of the Saccharomyces cerevi... | ACCEPT | Summary: Purified recombinant Rfc3p alone has ATPase activity, markedly stimulated by single-stranded DNA. Reason: Direct demonstration of ATP hydrolysis by the isolated subunit. In the assembled complex, ATP sites are bipartite and Rfc3 supplies the catalytic arginine finger to the Rfc4 ATP site (Yao et al. 2003), so Rfc3 contributes catalytic residues to RFC ATP hydrolysis as well. Supporting Evidence: PMID:8302859 Purified Rfc3p has an ATPase activity that is markedly stimulated by single-stranded DNA but not by double-stranded DNA or RNA. PMID:14530260 We find that the RFC(3/4) complex is a DNA-dependent ATPase, and we use this activity to determine that RFC3 supplies a catalytic arginine to the ATP site of RFC4. |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the AAA ATPase core domain. Reason: Agrees with the direct biochemical evidence for Rfc3 ATPase activity. Supporting Evidence: PMID:8302859 Purified Rfc3p has an ATPase activity that is markedly stimulated by single-stranded DNA but not by double-stranded DNA or RNA. |
| GO:0031389 Rad17 RFC-like complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation from PTN000912313 with yeast Rfc3 (SGD:S000005234) as the experimental donor. Reason: Rfc3's own experimental annotation seeds this node, which is expected rather than circular. The IBA additionally asserts that membership of the Rad17/Rad24 RFC-like complex is inherited across the subfamily, which agrees with the conservation of Rad17-RFC in fission yeast and human. Supporting Evidence: PMID:10660302 the small RFC proteins, Rfc2, Rfc3, Rfc4 and Rfc5, interacted with Rad24, whereas the Rfc1 subunit did not |
| GO:0031389 Rad17 RFC-like complex | IDA PMID:10660302 A novel Rad24 checkpoint protein complex closely related to ... | ACCEPT | Summary: Purification of the Rad24 complex identified Rfc2 and Rfc3 by mass spectrometry. Reason: Direct identification of Rfc3 in the purified Rad24 complex. Supporting Evidence: PMID:10660302 The 40 kDa species was found by mass spectrometry to contain Rfc2 and Rfc3, subunits of replication factor C (RFC) |
| GO:0031389 Rad17 RFC-like complex | IDA PMID:12604797 Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage ch... | ACCEPT | Summary: Rad24-RFC was overproduced from GST-Rad24 plus Rfc2-5 and purified as a stable 1:1 complex. Reason: Stable co-purification of Rfc2-5 with Rad24 at defined stoichiometry. Supporting Evidence: PMID:12604797 Copurification on the GST-affinity column of Rfc2-5 with GST-Rad24, and of Rad17 and Ddc1 with Mec3, indicates that the two complexes are stable. |
| GO:0031389 Rad17 RFC-like complex | IPI PMID:10660302 A novel Rad24 checkpoint protein complex closely related to ... | ACCEPT | Summary: Reciprocal co-immunoprecipitation of Rfc3 with Rad24. Reason: Supports Rad24-RFC membership. Supporting Evidence: PMID:10660302 the small RFC proteins, Rfc2, Rfc3, Rfc4 and Rfc5, interacted with Rad24, whereas the Rfc1 subunit did not |
| GO:0031389 Rad17 RFC-like complex | IPI PMID:12604797 Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage ch... | ACCEPT | Summary: Rad24 interacts with the four small RFC subunits to form RFC-Rad24. Reason: Supports Rad24-RFC membership. Supporting Evidence: PMID:12604797 Rad24 interacts with the four small subunits of replication factor C (RFC) to form the RFC-Rad24 complex. |
| GO:0031390 Ctf18 RFC-like complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation from PTN000912313 with yeast Rfc3 as the experimental donor. Reason: Rfc3 itself is the donor; membership is experimentally established in yeast. Supporting Evidence: PMID:11389843 Ctf18p, Ctf8p, and Dcc1p interact physically in a complex with Rfc2p, Rfc3p, Rfc4p, and Rfc5p but not with Rfc1p or Rad24p. |
| GO:0031390 Ctf18 RFC-like complex | IPI PMID:11389843 Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative ... | ACCEPT | Summary: Ctf18, Ctf8 and Dcc1 physically associate with Rfc2-5 but not with Rfc1 or Rad24. Reason: Direct evidence of Rfc3 membership in Ctf18-RFC, later reconstituted as a seven-subunit complex (Bylund and Burgers 2005). Supporting Evidence: PMID:11389843 Ctf18p, Ctf8p, and Dcc1p interact physically in a complex with Rfc2p, Rfc3p, Rfc4p, and Rfc5p but not with Rfc1p or Rad24p. PMID:15964801 This seven-subunit Ctf18-RFC complex consists of the four small subunits of RFC, together with Ctf18, Dcc1, and Ctf8. |
| GO:0031390 Ctf18 RFC-like complex | IPI PMID:11389843 Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative ... | ACCEPT | Summary: Co-purification of Rfc3 with Ctf18-RFC subunits. Reason: Supports Ctf18-RFC membership. Supporting Evidence: PMID:11389843 Ctf18p, Ctf8p, and Dcc1p interact physically in a complex with Rfc2p, Rfc3p, Rfc4p, and Rfc5p but not with Rfc1p or Rad24p. |
| GO:0031391 Elg1 RFC-like complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation from PTN000912313 with yeast Rfc3 and a fission yeast small subunit as donors. Reason: Rfc3 itself is a donor; membership is experimentally established in yeast. Supporting Evidence: PMID:12912927 Elg1 associates with Rfc2, Rfc3, Rfc4 and Rfc5, forming a fourth eukaryotic RFC-like complex that is functionally distinct from the canonical RFC, and from Rad24-RFC and Ctf18-RFC. |
| GO:0031391 Elg1 RFC-like complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning annotation. Reason: The claim is independently established experimentally in yeast (co-immunoprecipitation and cryo-EM structure of Elg1-RFC containing Rfc3). Supporting Evidence: PMID:12912927 Elg1 associates with Rfc2, Rfc3, Rfc4 and Rfc5, forming a fourth eukaryotic RFC-like complex that is functionally distinct from the canonical RFC, and from Rad24-RFC and Ctf18-RFC. |
| GO:0031391 Elg1 RFC-like complex | IPI PMID:12912927 Elg1 forms an alternative RFC complex important for DNA repl... | ACCEPT | Summary: Immunoprecipitates of Rfc3 contain Elg1. Reason: Direct evidence of Elg1-RFC membership. Supporting Evidence: PMID:12912927 In contrast, immunoprecipitates of Rfc2, Rfc3, Rfc4 or Rfc5 all contained Elg1 |
| GO:0031391 Elg1 RFC-like complex | IPI PMID:38427736 Structure of the PCNA unloader Elg1-RFC. | ACCEPT | Summary: Cryo-EM structures of purified Elg1-RFC (Elg1 with Rfc2-5), alone and bound to PCNA, show Rfc3 as an integral ATP-gamma-S-bound subunit that stabilizes the Elg1 locking loop and plug and contacts PCNA. Reason: Structural confirmation of Rfc3 as a subunit of the Elg1-RFC PCNA unloader. Supporting Evidence: PMID:38427736 In the top region, the Elg1 plug is stabilized by Rfc3 and Rfc5 and several intra-Elg1 plug H-bonds. PMID:38427736 In the structure of Elg1-RFC bound to a closed PCNA ring, the first three subunitsβElg1, Rfc4, and Rfc3βinteract with PCNA |
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Download this section (compressed HTML)Q: Should the small RFC subunits in budding yeast carry contributes_to GO:0061860 DNA clamp unloader activity on the basis of the Elg1-RFC and Ctf18-RFC unloading data? In yeast this activity is currently annotated to the Elg1-RFC complex (ComplexPortal CPX-422) and the PAINT IBA sits on the large-subunit (Elg1/ATAD5, RFC1) nodes, whereas PomBase annotates the fission yeast small subunits (including rfc3) by IC. Which convention should apply to shared small subunits?
Q: Does Rfc3 contribute catalytically to clamp unloading by Elg1-RFC, given that nucleotide binding but not hydrolysis is reported to suffice for unloading?
Experiment: Test arginine-finger (catalytic) point mutants of Rfc3 in reconstituted RFC, Rad24-RFC, Ctf18-RFC and Elg1-RFC to separate its catalytic contribution to PCNA/9-1-1 loading from its structural contribution to PCNA unloading, and assay the corresponding alleles in vivo for replication, checkpoint activation and cohesion defects.
Subunit of heteropentameric Replication factor C (RF-C); which is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon; relocalizes to the cytosol in response to hypoxia
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