{"gene":"CDC123","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":1996,"finding":"A single amino acid change in D123 (CDC123) protein causes temperature-sensitive G1-phase arrest in rat fibroblast 3Y1tsD123 cells; the mutant protein is expressed at much lower levels than wild-type, establishing that CDC123 protein quantity is required for cell cycle progression through G1.","method":"Functional complementation cloning, point mutation identification by RT-PCR/sequencing, western blot quantification of protein levels","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — complementation cloning with mutant rescue plus protein-level quantification in a single lab, two orthogonal methods","pmids":["8601400"],"is_preprint":false},{"year":1999,"finding":"Temperature-sensitive G1 arrest in 3Y1tsD123 cells is caused by increased proteasome-mediated degradation of the mutated D123 protein; overexpression of the mutant protein rescues the cell cycle defect by exceeding the degradation capacity.","method":"Cycloheximide chase to measure protein stability, cDNA overexpression rescue","journal":"Cell structure and function","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cycloheximide chase and rescue experiments, single lab, two orthogonal approaches","pmids":["10698258"],"is_preprint":false},{"year":2001,"finding":"Mutated D123 protein undergoes a proteasome-dependent modification (increased molecular weight, not ubiquitin) prior to degradation; selective proteasome inhibitors lactacystin and MG132 block this degradation and rescue temperature-sensitive growth arrest.","method":"Proteasome inhibitor treatment (lactacystin, MG132), western blot, somatic cell hybridization","journal":"Cell structure and function","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological inhibition with two agents plus hybrid-cell genetics, single lab","pmids":["11699637"],"is_preprint":false},{"year":2004,"finding":"Yeast Cdc123 (ortholog of mammalian D123/CDC123) physically interacts with Gcd11 (eIF2γ) and controls its abundance; loss of cdc123 depletes Gcd11 (eIF2γ) and causes G1 arrest, placing Cdc123 in an essential pathway for nutritional control of START running parallel to the Tor-Gcn2-Sui2 system. CHF1/CHF2 (RING checkpoint proteins) associate with Cdc123 via the Thr-274 phosphorylatable site and counteract its cell cycle-promoting activity.","method":"Yeast genetics (cdc123 mutant isolation, suppressor/epistasis analysis), genetic interaction with CHF1/CHF2, protein interaction mapping (binding-site mutagenesis), western blot of Gcd11 levels","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal genetic and biochemical methods (mutant phenotypes, epistasis, binding-site mapping, protein quantification) in a single rigorous study establishing a conserved pathway","pmids":["15319434"],"is_preprint":false},{"year":2013,"finding":"Cdc123 functions as a dedicated assembly factor for the eIF2 heterotrimer: it binds unassembled eIF2γ (but not the assembled eIF2 complex) via the C-terminal domain III of eIF2γ; this interaction is necessary and sufficient for eIF2α/β association with eIF2γ. Mutations disrupting Cdc123–eIF2γ binding abolish eIF2 assembly and cause loss of eIF2 activity (reduced polysomes, elevated GCN4 translation). High-level overexpression of all three eIF2 subunits rescues an otherwise lethal cdc123 deletion.","method":"Yeast CDC123 deletion, polysome profiling, GCN4-lacZ reporter, co-immunoprecipitation of eIF2 subunits, domain mapping with eIF2γ truncations, rescue by subunit overexpression","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (Co-IP, polysome profiling, reporter assays, domain mapping, genetic rescue) in a single rigorous study","pmids":["23775072"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of S. pombe Cdc123 alone and in complex with domain III of S. cerevisiae eIF2γ shows Cdc123 is an ATP-grasp enzyme; it binds ATP-Mg²⁺ via conserved residues, and mutagenesis of those residues abolishes eIF2 assembly and cell viability, demonstrating that ATP binding is required for Cdc123 function. Domain III of eIF2γ binds domain I of Cdc123.","method":"X-ray crystallography (structures of apo and eIF2γD3-bound Cdc123), site-directed mutagenesis of ATP-contact residues, yeast viability assays, biochemical binding assays","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures combined with mutagenesis and viability assays provide multiple orthogonal lines of evidence","pmids":["26211610"],"is_preprint":false},{"year":2015,"finding":"Computational and phylogenetic analysis classifies CDC123 as a novel clade (R2K) of ATP-grasp enzymes distinguished by a RAGNYA domain with two conserved lysines; the enzymatic classification predicts CDC123 may function as an ATP-dependent protein-peptide ligase that modifies substrates by oligopeptide tagging.","method":"Bioinformatic sequence/structure analysis integrated with published biochemical data","journal":"Biology direct","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only; no direct experimental validation of ligase activity in this paper","pmids":["25976611"],"is_preprint":false},{"year":2023,"finding":"Crystal structure of human CDC123 bound to domain 3 of human eIF2γ shows that eIF2γD3 contacts domain 1 of Cdc123, and the long C-terminal region of human Cdc123 links the ATP-binding site to the eIF2γ-binding site. Thermal shift assay shows ATP binds Cdc123 tightly whereas ADP affinity is much lower. Yeast viability experiments, western blot, and two-hybrid assays confirm that ATP binding is required for human CDC123 function in eIF2 assembly.","method":"X-ray crystallography of human CDC123–eIF2γD3 complex, thermal shift assay, yeast complementation viability assay, western blot, yeast two-hybrid","journal":"Journal of structural biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure of human complex combined with multiple orthogonal functional assays in a single study","pmids":["37507029"],"is_preprint":false},{"year":2023,"finding":"In plants, CDC123 is required for ETI (effector-triggered immunity)-associated global translational induction; an increase in cellular ATP concentration during ETI facilitates CDC123-mediated eIF2 complex assembly, linking NLR-dependent ATP elevation to translational reprogramming in defense.","method":"Genetic screen with translational reporter, CDC123 loss-of-function phenotyping, ATP measurement, eIF2 assembly assays","journal":"Cell host & microbe","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic screen plus biochemical eIF2 assembly assays, but in the plant system (Arabidopsis); consistent with conserved mechanism","pmids":["36801014"],"is_preprint":false},{"year":2025,"finding":"Human CDC123 acts as an ATPase (not merely an ATP-binding scaffold) to drive eIF2 heterotrimer assembly; impaired CDC123 activity reduces eIF2 complex assembly and activates the integrated stress response (ISR) through a noncanonical mechanism, altering global and mRNA-specific translation. Pharmacological or genetic rescue strategies can correct the translational defects caused by impaired CDC123.","method":"ATPase activity assays, eIF2 complex assembly measurements, translational assays (polysome profiling or reporters), ISR marker readouts, pharmacological and genetic rescue","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — ATPase biochemistry combined with assembly assays and translational/cellular phenotype rescue, single lab but multiple orthogonal methods","pmids":["41461316"],"is_preprint":false},{"year":2026,"finding":"Cannabidiol (CBD) was identified as an inhibitor of the CDC123–eIF2γ protein-protein interaction; disruption of the CDC123–eIF2γ complex by CBD leads to sustained activation of the integrated stress response and apoptosis in colorectal cancer cells, validating the CDC123–eIF2γ interface as a druggable target.","method":"Stability- and degradation-based proteome profiling (SDPP) for target ID, biochemical PPI inhibition assays, ISR activation assays, cell viability/apoptosis assays in CRC cell lines","journal":"Journal of the American Chemical Society","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — novel target-ID proteomics method plus biochemical PPI assays and cellular phenotype, single lab","pmids":["41518300"],"is_preprint":false},{"year":2014,"finding":"A type 2 diabetes-associated SNP (rs11257655) in the CDC123/CAMK1D locus shows allele-specific enhancer activity in insulinoma and hepatocellular carcinoma cells; the risk allele T binds FOXA1 and FOXA2 with higher affinity than the non-risk allele C, as shown by EMSA, supershift, and allele-specific ChIP in human islets, suggesting that altered FOXA1/FOXA2 binding at this locus modulates CDC123 transcription.","method":"Luciferase reporter enhancer assays, EMSA, supershift assays, allele-specific ChIP in human islets","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal regulatory assays (luciferase, EMSA, ChIP) in a single lab; pertains to transcriptional regulation of the locus rather than CDC123 protein mechanism","pmids":["25211022"],"is_preprint":false}],"current_model":"CDC123 (D123/C10orf7) is an ATP-grasp ATPase that acts as a dedicated assembly chaperone for the eIF2 heterotrimer: it binds the unassembled eIF2γ subunit (via domain III of eIF2γ and domain I of CDC123), uses ATP hydrolysis to drive eIF2α/β association with eIF2γ, and is essential for translational initiation; loss of CDC123 activity depletes functional eIF2 complexes, activates the integrated stress response, and arrests cell proliferation in G1, while checkpoint proteins (CHF1/CHF2 in yeast) antagonize Cdc123 by binding its conserved Thr-274 phosphorylation site."},"narrative":{"mechanistic_narrative":"CDC123 (D123/C10orf7) is a dedicated assembly chaperone for the eIF2 heterotrimer and thereby a master regulator of translation initiation and G1 cell cycle progression [PMID:15319434, PMID:23775072]. It binds the unassembled eIF2γ subunit—through domain III of eIF2γ contacting domain I of CDC123—without engaging the fully assembled complex, and this interaction is necessary and sufficient to drive eIF2α/β association with eIF2γ; disrupting it abolishes eIF2 assembly, collapses polysomes, and derepresses GCN4 translation [PMID:23775072, PMID:26211610, PMID:37507029]. Structurally CDC123 is an ATP-grasp enzyme that binds ATP-Mg²⁺ via conserved residues, and ATP binding—and ATP hydrolysis as an ATPase, not merely ATP-dependent scaffolding—is required for assembly activity and cell viability [PMID:26211610, PMID:37507029, PMID:41461316]. Loss or impairment of CDC123 depletes functional eIF2, activates the integrated stress response, and arrests cells in G1 [PMID:15319434, PMID:23775072, PMID:41461316]. The activity is conserved from yeast to plants and humans, where in plant immunity an ETI-associated rise in cellular ATP promotes CDC123-mediated eIF2 assembly to reprogram defense translation [PMID:36801014]. The CDC123–eIF2γ interface is a druggable target: cannabidiol inhibits this protein–protein interaction, sustaining ISR activation and triggering apoptosis in colorectal cancer cells [PMID:41518300].","teleology":[{"year":1996,"claim":"Established that CDC123 protein abundance is required for cells to traverse G1, the first link between this gene and cell cycle control.","evidence":"Complementation cloning and point-mutation analysis of temperature-sensitive G1-arrested rat fibroblasts with western blot quantification","pmids":["8601400"],"confidence":"Medium","gaps":["No molecular function or interaction partner identified","Mechanism connecting protein level to G1 progression unknown"]},{"year":2001,"claim":"Showed the G1 arrest arises from accelerated proteasome-dependent turnover of the mutant protein, explaining the abundance defect rather than a loss of intrinsic activity.","evidence":"Cycloheximide chase, overexpression rescue, and proteasome inhibition (lactacystin, MG132) in mutant cell lines","pmids":["10698258","11699637"],"confidence":"Medium","gaps":["The proteasome-dependent modification was not ubiquitin and remains unidentified","Did not reveal the normal biochemical function of CDC123"]},{"year":2004,"claim":"Identified eIF2γ (Gcd11) as the key CDC123 partner and placed it in an essential pathway controlling START, defining its biological context as translation/cell-cycle coupling.","evidence":"Yeast genetics, epistasis, binding-site mapping, and Gcd11 protein quantification, plus CHF1/CHF2 interaction at the Thr-274 site","pmids":["15319434"],"confidence":"High","gaps":["Did not establish how CDC123 controls eIF2γ abundance mechanistically","Role of Thr-274 phosphorylation in regulating CDC123 not biochemically defined"]},{"year":2013,"claim":"Defined CDC123 as a dedicated eIF2 assembly factor, showing it binds only unassembled eIF2γ via domain III and is required and sufficient for trimer formation.","evidence":"Yeast CDC123 deletion, Co-IP of eIF2 subunits, eIF2γ domain mapping, polysome profiling, GCN4-lacZ reporter, and subunit-overexpression rescue","pmids":["23775072"],"confidence":"High","gaps":["Did not resolve the structural basis of the interaction","Enzymatic activity of CDC123 not yet demonstrated"]},{"year":2015,"claim":"Provided the structural and enzymatic identity of CDC123 as an ATP-grasp enzyme requiring ATP binding for eIF2 assembly, and mapped the eIF2γD3–domain I interface.","evidence":"X-ray crystallography of apo and eIF2γD3-bound S. pombe Cdc123 with ATP-contact mutagenesis and yeast viability assays; complemented by phylogenetic R2K/RAGNYA classification predicting peptide-ligase activity","pmids":["26211610","25976611"],"confidence":"High","gaps":["Catalytic role of ATP (binding vs hydrolysis) not resolved in 2015","Predicted oligopeptide-tagging ligase activity unvalidated experimentally"]},{"year":2023,"claim":"Extended the structural model to the human CDC123–eIF2γD3 complex and demonstrated tight ATP (versus weak ADP) binding required for human protein function, and showed conservation of the assembly role in plant immunity via ATP-coupled translational reprogramming.","evidence":"Crystal structure of human CDC123–eIF2γD3, thermal shift assays, yeast complementation, two-hybrid; plant genetic screen with translational reporter, ATP measurement, and eIF2 assembly assays","pmids":["37507029","36801014"],"confidence":"High","gaps":["Whether ATP is hydrolyzed during the assembly cycle not directly tested in these studies","Regulation of CDC123 by cellular ATP levels in mammalian cells not directly addressed"]},{"year":2025,"claim":"Demonstrated CDC123 is a bona fide ATPase whose hydrolytic activity drives eIF2 trimer assembly, and that its impairment activates the ISR through a noncanonical route.","evidence":"ATPase activity assays, eIF2 assembly measurements, translational/polysome assays, ISR markers, and pharmacological/genetic rescue","pmids":["41461316"],"confidence":"High","gaps":["Precise catalytic mechanism and turnover cycle not fully defined","Noncanonical ISR activation mechanism not molecularly resolved"]},{"year":2026,"claim":"Validated the CDC123–eIF2γ interface as a druggable target by showing cannabidiol disrupts the interaction to sustain ISR activation and trigger apoptosis in cancer cells.","evidence":"SDPP target identification, biochemical PPI inhibition assays, ISR and apoptosis readouts in colorectal cancer cell lines","pmids":["41518300"],"confidence":"Medium","gaps":["CBD binding site on CDC123 not structurally mapped","Selectivity and in vivo efficacy not established"]},{"year":null,"claim":"How CDC123 activity is physiologically regulated—via Thr-274 phosphorylation, cellular ATP sensing, or checkpoint inputs—and whether it has substrates beyond eIF2 assembly remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["Function of the conserved Thr-274 phosphosite in mammals uncharacterized","Predicted oligopeptide-ligase activity never experimentally demonstrated","Connection between the type 2 diabetes-associated locus regulation and CDC123 protein function unestablished"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[5,7,9]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[9]},{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[3,4]}],"localization":[],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,3]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[9]}],"complexes":[],"partners":["EIF2S3","EIF2S1","EIF2S2","CHF1","CHF2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O75794","full_name":"Translation initiation factor eIF2 assembly protein","aliases":["Cell division cycle protein 123 homolog","Protein D123","HT-1080","PZ32"],"length_aa":336,"mass_kda":39.1,"function":"ATP-dependent protein-folding chaperone for the eIF2 complex (PubMed:35031321, PubMed:37507029). Binds to the gamma subunit of the eIF2 complex which allows the subunit to assemble with the alpha and beta subunits (By similarity)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O75794/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CDC123","classification":"Common Essential","n_dependent_lines":1207,"n_total_lines":1208,"dependency_fraction":0.9991721854304636},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"EIF5","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CDC123","total_profiled":1310},"omim":[{"mim_id":"617708","title":"CELL DIVISION CYCLE 123; CDC123","url":"https://www.omim.org/entry/617708"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CDC123"},"hgnc":{"alias_symbol":["D123"],"prev_symbol":["C10orf7"]},"alphafold":{"accession":"O75794","domains":[{"cath_id":"-","chopping":"175-289","consensus_level":"high","plddt":89.0596,"start":175,"end":289},{"cath_id":"3.30.1490","chopping":"25-44_83-169","consensus_level":"high","plddt":93.2093,"start":25,"end":169}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75794","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75794-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75794-F1-predicted_aligned_error_v6.png","plddt_mean":84.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CDC123","jax_strain_url":"https://www.jax.org/strain/search?query=CDC123"},"sequence":{"accession":"O75794","fasta_url":"https://rest.uniprot.org/uniprotkb/O75794.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75794/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75794"}},"corpus_meta":[{"pmid":"18567820","id":"PMC_18567820","title":"Association testing of novel type 2 diabetes risk alleles in the JAZF1, CDC123/CAMK1D, TSPAN8, THADA, ADAMTS9, and NOTCH2 loci with insulin release, insulin sensitivity, and obesity in a population-based sample of 4,516 glucose-tolerant middle-aged Danes.","date":"2008","source":"Diabetes","url":"https://pubmed.ncbi.nlm.nih.gov/18567820","citation_count":121,"is_preprint":false},{"pmid":"19833888","id":"PMC_19833888","title":"Gene variants in the novel type 2 diabetes loci CDC123/CAMK1D, THADA, ADAMTS9, BCL11A, and MTNR1B affect different aspects of pancreatic beta-cell function.","date":"2009","source":"Diabetes","url":"https://pubmed.ncbi.nlm.nih.gov/19833888","citation_count":106,"is_preprint":false},{"pmid":"10799608","id":"PMC_10799608","title":"Mutation of a conserved residue (D123) required for oligomerization of human immunodeficiency virus type 1 Nef protein abolishes interaction with human thioesterase and results in impairment of Nef biological functions.","date":"2000","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/10799608","citation_count":90,"is_preprint":false},{"pmid":"25211022","id":"PMC_25211022","title":"Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus.","date":"2014","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25211022","citation_count":74,"is_preprint":false},{"pmid":"15319434","id":"PMC_15319434","title":"Cdc123 and checkpoint forkhead associated with RING proteins control the cell cycle by controlling eIF2gamma abundance.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15319434","citation_count":44,"is_preprint":false},{"pmid":"23775072","id":"PMC_23775072","title":"Translation initiation requires cell division cycle 123 (Cdc123) to facilitate biogenesis of the eukaryotic initiation factor 2 (eIF2).","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23775072","citation_count":32,"is_preprint":false},{"pmid":"36801014","id":"PMC_36801014","title":"Global translational induction during NLR-mediated immunity in plants is dynamically regulated by CDC123, an ATP-sensitive protein.","date":"2023","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/36801014","citation_count":32,"is_preprint":false},{"pmid":"21909839","id":"PMC_21909839","title":"Genetic variants at CDC123/CAMK1D and SPRY2 are associated with susceptibility to type 2 diabetes in the Japanese population.","date":"2011","source":"Diabetologia","url":"https://pubmed.ncbi.nlm.nih.gov/21909839","citation_count":27,"is_preprint":false},{"pmid":"26211610","id":"PMC_26211610","title":"Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features.","date":"2015","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/26211610","citation_count":24,"is_preprint":false},{"pmid":"28079868","id":"PMC_28079868","title":"CDC123/CAMK1D gene rs12779790 polymorphism and rs10811661 polymorphism upstream of the CDKN2A/2B gene in women with gestational diabetes.","date":"2017","source":"Journal of perinatology : official journal of the California Perinatal Association","url":"https://pubmed.ncbi.nlm.nih.gov/28079868","citation_count":17,"is_preprint":false},{"pmid":"8601400","id":"PMC_8601400","title":"An amino acid change in novel protein D123 is responsible for temperature-sensitive G1-phase arrest in a mutant of rat fibroblast line 3Y1.","date":"1996","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/8601400","citation_count":16,"is_preprint":false},{"pmid":"26388851","id":"PMC_26388851","title":"The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon.","date":"2015","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/26388851","citation_count":14,"is_preprint":false},{"pmid":"25976611","id":"PMC_25976611","title":"The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications.","date":"2015","source":"Biology direct","url":"https://pubmed.ncbi.nlm.nih.gov/25976611","citation_count":12,"is_preprint":false},{"pmid":"10698258","id":"PMC_10698258","title":"Extensive degradation of mutant-type D123 protein is responsible for temperature-sensitive proliferation inhibition in 3Y1tsD123 cells.","date":"1999","source":"Cell structure and function","url":"https://pubmed.ncbi.nlm.nih.gov/10698258","citation_count":5,"is_preprint":false},{"pmid":"11699637","id":"PMC_11699637","title":"Reversion of temperature-sensitive mutation by inhibition of proteasome-mediated degradation of mutated D123 protein.","date":"2001","source":"Cell structure and function","url":"https://pubmed.ncbi.nlm.nih.gov/11699637","citation_count":4,"is_preprint":false},{"pmid":"37507029","id":"PMC_37507029","title":"Binding of human Cdc123 to eIF2γ.","date":"2023","source":"Journal of structural biology","url":"https://pubmed.ncbi.nlm.nih.gov/37507029","citation_count":2,"is_preprint":false},{"pmid":"9683532","id":"PMC_9683532","title":"Expression study on D123 gene product: evidence for high positivity in testis.","date":"1998","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/9683532","citation_count":2,"is_preprint":false},{"pmid":"38237400","id":"PMC_38237400","title":"CDC123 promotes Hepatocellular Carcinoma malignant progression by regulating CDKAL1.","date":"2023","source":"Pathology, research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/38237400","citation_count":1,"is_preprint":false},{"pmid":"41518300","id":"PMC_41518300","title":"Stability and Degradation-based Proteome Profiling Reveals Cannabidiol as a Promising CDC123-eIF2γ Inhibitor for Colorectal Cancer Therapy.","date":"2026","source":"Journal of the American Chemical Society","url":"https://pubmed.ncbi.nlm.nih.gov/41518300","citation_count":0,"is_preprint":false},{"pmid":"41461316","id":"PMC_41461316","title":"CDC123 is an ATPase that modulates mRNA translation and the integrated stress response by regulating eIF2 complex assembly.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41461316","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12035,"output_tokens":3162,"usd":0.041767,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10806,"output_tokens":3185,"usd":0.066827,"stage2_stop_reason":"end_turn"},"total_usd":0.108594,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"A single amino acid change in D123 (CDC123) protein causes temperature-sensitive G1-phase arrest in rat fibroblast 3Y1tsD123 cells; the mutant protein is expressed at much lower levels than wild-type, establishing that CDC123 protein quantity is required for cell cycle progression through G1.\",\n      \"method\": \"Functional complementation cloning, point mutation identification by RT-PCR/sequencing, western blot quantification of protein levels\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — complementation cloning with mutant rescue plus protein-level quantification in a single lab, two orthogonal methods\",\n      \"pmids\": [\"8601400\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Temperature-sensitive G1 arrest in 3Y1tsD123 cells is caused by increased proteasome-mediated degradation of the mutated D123 protein; overexpression of the mutant protein rescues the cell cycle defect by exceeding the degradation capacity.\",\n      \"method\": \"Cycloheximide chase to measure protein stability, cDNA overexpression rescue\",\n      \"journal\": \"Cell structure and function\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cycloheximide chase and rescue experiments, single lab, two orthogonal approaches\",\n      \"pmids\": [\"10698258\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Mutated D123 protein undergoes a proteasome-dependent modification (increased molecular weight, not ubiquitin) prior to degradation; selective proteasome inhibitors lactacystin and MG132 block this degradation and rescue temperature-sensitive growth arrest.\",\n      \"method\": \"Proteasome inhibitor treatment (lactacystin, MG132), western blot, somatic cell hybridization\",\n      \"journal\": \"Cell structure and function\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological inhibition with two agents plus hybrid-cell genetics, single lab\",\n      \"pmids\": [\"11699637\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Yeast Cdc123 (ortholog of mammalian D123/CDC123) physically interacts with Gcd11 (eIF2γ) and controls its abundance; loss of cdc123 depletes Gcd11 (eIF2γ) and causes G1 arrest, placing Cdc123 in an essential pathway for nutritional control of START running parallel to the Tor-Gcn2-Sui2 system. CHF1/CHF2 (RING checkpoint proteins) associate with Cdc123 via the Thr-274 phosphorylatable site and counteract its cell cycle-promoting activity.\",\n      \"method\": \"Yeast genetics (cdc123 mutant isolation, suppressor/epistasis analysis), genetic interaction with CHF1/CHF2, protein interaction mapping (binding-site mutagenesis), western blot of Gcd11 levels\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal genetic and biochemical methods (mutant phenotypes, epistasis, binding-site mapping, protein quantification) in a single rigorous study establishing a conserved pathway\",\n      \"pmids\": [\"15319434\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Cdc123 functions as a dedicated assembly factor for the eIF2 heterotrimer: it binds unassembled eIF2γ (but not the assembled eIF2 complex) via the C-terminal domain III of eIF2γ; this interaction is necessary and sufficient for eIF2α/β association with eIF2γ. Mutations disrupting Cdc123–eIF2γ binding abolish eIF2 assembly and cause loss of eIF2 activity (reduced polysomes, elevated GCN4 translation). High-level overexpression of all three eIF2 subunits rescues an otherwise lethal cdc123 deletion.\",\n      \"method\": \"Yeast CDC123 deletion, polysome profiling, GCN4-lacZ reporter, co-immunoprecipitation of eIF2 subunits, domain mapping with eIF2γ truncations, rescue by subunit overexpression\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (Co-IP, polysome profiling, reporter assays, domain mapping, genetic rescue) in a single rigorous study\",\n      \"pmids\": [\"23775072\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of S. pombe Cdc123 alone and in complex with domain III of S. cerevisiae eIF2γ shows Cdc123 is an ATP-grasp enzyme; it binds ATP-Mg²⁺ via conserved residues, and mutagenesis of those residues abolishes eIF2 assembly and cell viability, demonstrating that ATP binding is required for Cdc123 function. Domain III of eIF2γ binds domain I of Cdc123.\",\n      \"method\": \"X-ray crystallography (structures of apo and eIF2γD3-bound Cdc123), site-directed mutagenesis of ATP-contact residues, yeast viability assays, biochemical binding assays\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures combined with mutagenesis and viability assays provide multiple orthogonal lines of evidence\",\n      \"pmids\": [\"26211610\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Computational and phylogenetic analysis classifies CDC123 as a novel clade (R2K) of ATP-grasp enzymes distinguished by a RAGNYA domain with two conserved lysines; the enzymatic classification predicts CDC123 may function as an ATP-dependent protein-peptide ligase that modifies substrates by oligopeptide tagging.\",\n      \"method\": \"Bioinformatic sequence/structure analysis integrated with published biochemical data\",\n      \"journal\": \"Biology direct\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only; no direct experimental validation of ligase activity in this paper\",\n      \"pmids\": [\"25976611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Crystal structure of human CDC123 bound to domain 3 of human eIF2γ shows that eIF2γD3 contacts domain 1 of Cdc123, and the long C-terminal region of human Cdc123 links the ATP-binding site to the eIF2γ-binding site. Thermal shift assay shows ATP binds Cdc123 tightly whereas ADP affinity is much lower. Yeast viability experiments, western blot, and two-hybrid assays confirm that ATP binding is required for human CDC123 function in eIF2 assembly.\",\n      \"method\": \"X-ray crystallography of human CDC123–eIF2γD3 complex, thermal shift assay, yeast complementation viability assay, western blot, yeast two-hybrid\",\n      \"journal\": \"Journal of structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure of human complex combined with multiple orthogonal functional assays in a single study\",\n      \"pmids\": [\"37507029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In plants, CDC123 is required for ETI (effector-triggered immunity)-associated global translational induction; an increase in cellular ATP concentration during ETI facilitates CDC123-mediated eIF2 complex assembly, linking NLR-dependent ATP elevation to translational reprogramming in defense.\",\n      \"method\": \"Genetic screen with translational reporter, CDC123 loss-of-function phenotyping, ATP measurement, eIF2 assembly assays\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic screen plus biochemical eIF2 assembly assays, but in the plant system (Arabidopsis); consistent with conserved mechanism\",\n      \"pmids\": [\"36801014\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Human CDC123 acts as an ATPase (not merely an ATP-binding scaffold) to drive eIF2 heterotrimer assembly; impaired CDC123 activity reduces eIF2 complex assembly and activates the integrated stress response (ISR) through a noncanonical mechanism, altering global and mRNA-specific translation. Pharmacological or genetic rescue strategies can correct the translational defects caused by impaired CDC123.\",\n      \"method\": \"ATPase activity assays, eIF2 complex assembly measurements, translational assays (polysome profiling or reporters), ISR marker readouts, pharmacological and genetic rescue\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — ATPase biochemistry combined with assembly assays and translational/cellular phenotype rescue, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"41461316\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Cannabidiol (CBD) was identified as an inhibitor of the CDC123–eIF2γ protein-protein interaction; disruption of the CDC123–eIF2γ complex by CBD leads to sustained activation of the integrated stress response and apoptosis in colorectal cancer cells, validating the CDC123–eIF2γ interface as a druggable target.\",\n      \"method\": \"Stability- and degradation-based proteome profiling (SDPP) for target ID, biochemical PPI inhibition assays, ISR activation assays, cell viability/apoptosis assays in CRC cell lines\",\n      \"journal\": \"Journal of the American Chemical Society\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — novel target-ID proteomics method plus biochemical PPI assays and cellular phenotype, single lab\",\n      \"pmids\": [\"41518300\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"A type 2 diabetes-associated SNP (rs11257655) in the CDC123/CAMK1D locus shows allele-specific enhancer activity in insulinoma and hepatocellular carcinoma cells; the risk allele T binds FOXA1 and FOXA2 with higher affinity than the non-risk allele C, as shown by EMSA, supershift, and allele-specific ChIP in human islets, suggesting that altered FOXA1/FOXA2 binding at this locus modulates CDC123 transcription.\",\n      \"method\": \"Luciferase reporter enhancer assays, EMSA, supershift assays, allele-specific ChIP in human islets\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal regulatory assays (luciferase, EMSA, ChIP) in a single lab; pertains to transcriptional regulation of the locus rather than CDC123 protein mechanism\",\n      \"pmids\": [\"25211022\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CDC123 (D123/C10orf7) is an ATP-grasp ATPase that acts as a dedicated assembly chaperone for the eIF2 heterotrimer: it binds the unassembled eIF2γ subunit (via domain III of eIF2γ and domain I of CDC123), uses ATP hydrolysis to drive eIF2α/β association with eIF2γ, and is essential for translational initiation; loss of CDC123 activity depletes functional eIF2 complexes, activates the integrated stress response, and arrests cell proliferation in G1, while checkpoint proteins (CHF1/CHF2 in yeast) antagonize Cdc123 by binding its conserved Thr-274 phosphorylation site.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CDC123 (D123/C10orf7) is a dedicated assembly chaperone for the eIF2 heterotrimer and thereby a master regulator of translation initiation and G1 cell cycle progression [#3, #4]. It binds the unassembled eIF2\\u03b3 subunit\\u2014through domain III of eIF2\\u03b3 contacting domain I of CDC123\\u2014without engaging the fully assembled complex, and this interaction is necessary and sufficient to drive eIF2\\u03b1/\\u03b2 association with eIF2\\u03b3; disrupting it abolishes eIF2 assembly, collapses polysomes, and derepresses GCN4 translation [#4, #5, #7]. Structurally CDC123 is an ATP-grasp enzyme that binds ATP-Mg\\u00b2\\u207a via conserved residues, and ATP binding\\u2014and ATP hydrolysis as an ATPase, not merely ATP-dependent scaffolding\\u2014is required for assembly activity and cell viability [#5, #7, #9]. Loss or impairment of CDC123 depletes functional eIF2, activates the integrated stress response, and arrests cells in G1 [#3, #4, #9]. The activity is conserved from yeast to plants and humans, where in plant immunity an ETI-associated rise in cellular ATP promotes CDC123-mediated eIF2 assembly to reprogram defense translation [#8]. The CDC123\\u2013eIF2\\u03b3 interface is a druggable target: cannabidiol inhibits this protein\\u2013protein interaction, sustaining ISR activation and triggering apoptosis in colorectal cancer cells [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Established that CDC123 protein abundance is required for cells to traverse G1, the first link between this gene and cell cycle control.\",\n      \"evidence\": \"Complementation cloning and point-mutation analysis of temperature-sensitive G1-arrested rat fibroblasts with western blot quantification\",\n      \"pmids\": [\"8601400\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular function or interaction partner identified\", \"Mechanism connecting protein level to G1 progression unknown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Showed the G1 arrest arises from accelerated proteasome-dependent turnover of the mutant protein, explaining the abundance defect rather than a loss of intrinsic activity.\",\n      \"evidence\": \"Cycloheximide chase, overexpression rescue, and proteasome inhibition (lactacystin, MG132) in mutant cell lines\",\n      \"pmids\": [\"10698258\", \"11699637\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The proteasome-dependent modification was not ubiquitin and remains unidentified\", \"Did not reveal the normal biochemical function of CDC123\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Identified eIF2\\u03b3 (Gcd11) as the key CDC123 partner and placed it in an essential pathway controlling START, defining its biological context as translation/cell-cycle coupling.\",\n      \"evidence\": \"Yeast genetics, epistasis, binding-site mapping, and Gcd11 protein quantification, plus CHF1/CHF2 interaction at the Thr-274 site\",\n      \"pmids\": [\"15319434\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish how CDC123 controls eIF2\\u03b3 abundance mechanistically\", \"Role of Thr-274 phosphorylation in regulating CDC123 not biochemically defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined CDC123 as a dedicated eIF2 assembly factor, showing it binds only unassembled eIF2\\u03b3 via domain III and is required and sufficient for trimer formation.\",\n      \"evidence\": \"Yeast CDC123 deletion, Co-IP of eIF2 subunits, eIF2\\u03b3 domain mapping, polysome profiling, GCN4-lacZ reporter, and subunit-overexpression rescue\",\n      \"pmids\": [\"23775072\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the structural basis of the interaction\", \"Enzymatic activity of CDC123 not yet demonstrated\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided the structural and enzymatic identity of CDC123 as an ATP-grasp enzyme requiring ATP binding for eIF2 assembly, and mapped the eIF2\\u03b3D3\\u2013domain I interface.\",\n      \"evidence\": \"X-ray crystallography of apo and eIF2\\u03b3D3-bound S. pombe Cdc123 with ATP-contact mutagenesis and yeast viability assays; complemented by phylogenetic R2K/RAGNYA classification predicting peptide-ligase activity\",\n      \"pmids\": [\"26211610\", \"25976611\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Catalytic role of ATP (binding vs hydrolysis) not resolved in 2015\", \"Predicted oligopeptide-tagging ligase activity unvalidated experimentally\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extended the structural model to the human CDC123\\u2013eIF2\\u03b3D3 complex and demonstrated tight ATP (versus weak ADP) binding required for human protein function, and showed conservation of the assembly role in plant immunity via ATP-coupled translational reprogramming.\",\n      \"evidence\": \"Crystal structure of human CDC123\\u2013eIF2\\u03b3D3, thermal shift assays, yeast complementation, two-hybrid; plant genetic screen with translational reporter, ATP measurement, and eIF2 assembly assays\",\n      \"pmids\": [\"37507029\", \"36801014\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ATP is hydrolyzed during the assembly cycle not directly tested in these studies\", \"Regulation of CDC123 by cellular ATP levels in mammalian cells not directly addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated CDC123 is a bona fide ATPase whose hydrolytic activity drives eIF2 trimer assembly, and that its impairment activates the ISR through a noncanonical route.\",\n      \"evidence\": \"ATPase activity assays, eIF2 assembly measurements, translational/polysome assays, ISR markers, and pharmacological/genetic rescue\",\n      \"pmids\": [\"41461316\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise catalytic mechanism and turnover cycle not fully defined\", \"Noncanonical ISR activation mechanism not molecularly resolved\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Validated the CDC123\\u2013eIF2\\u03b3 interface as a druggable target by showing cannabidiol disrupts the interaction to sustain ISR activation and trigger apoptosis in cancer cells.\",\n      \"evidence\": \"SDPP target identification, biochemical PPI inhibition assays, ISR and apoptosis readouts in colorectal cancer cell lines\",\n      \"pmids\": [\"41518300\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"CBD binding site on CDC123 not structurally mapped\", \"Selectivity and in vivo efficacy not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CDC123 activity is physiologically regulated\\u2014via Thr-274 phosphorylation, cellular ATP sensing, or checkpoint inputs\\u2014and whether it has substrates beyond eIF2 assembly remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Function of the conserved Thr-274 phosphosite in mammals uncharacterized\", \"Predicted oligopeptide-ligase activity never experimentally demonstrated\", \"Connection between the type 2 diabetes-associated locus regulation and CDC123 protein function unestablished\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [5, 7, 9]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-72613\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"EIF2S3\", \"EIF2S1\", \"EIF2S2\", \"CHF1\", \"CHF2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}