{"gene":"DERA","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":1982,"finding":"E. coli deoC gene encodes 2-deoxyribose-5-phosphate aldolase (deoxyriboaldolase), a 259-amino acid class I aldolase (MW 27,737) that forms Schiff base intermediates during catalysis; a lysine residue was tentatively identified as the active-site residue involved in Schiff base formation.","method":"DNA/protein sequencing, amino acid composition analysis, catalytic property characterization","journal":"European journal of biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — protein sequencing combined with catalytic characterization and mechanistic class assignment in a single study, but active-site lysine identification was tentative","pmids":["6749498"],"is_preprint":false},{"year":2014,"finding":"Human DERA is the deoxyribose-phosphate aldolase responsible for converting 2-deoxy-D-ribose-5-phosphate into glyceraldehyde-3-phosphate and acetaldehyde; DERA interacts with stress granule component YBX1 and is recruited to stress granules upon oxidative or mitochondrial stress; shRNA-mediated knockdown of DERA reduced stress granule formation and increased apoptosis after clotrimazole stress; DERA activity enables cells with abolished mitochondrial ATP production to use extracellular deoxyinosine to maintain ATP levels via deoxynucleoside degradation.","method":"Enzymatic activity assays, co-immunoprecipitation (DERA–YBX1), shRNA knockdown with stress granule imaging and apoptosis readouts, ATP rescue experiments","journal":"Biochimica et biophysica acta","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (enzymatic assay, Co-IP, KD with defined phenotypic readouts, metabolic rescue experiment) in a single focused study on the human protein","pmids":["25229427"],"is_preprint":false},{"year":2018,"finding":"The C-terminal tail of E. coli DERA is intrinsically disordered and samples open and catalytically relevant closed conformations; in the closed state, the terminal tyrosine residue Y259 enters the active site and is required for the proton abstraction step of catalysis; auxiliary phosphate-binding residues on the C-terminal tail help orient Y259 for catalysis.","method":"NMR spectroscopy (NOE distance restraints, H/D exchange, phosphate titration), molecular dynamics simulations, solution-state structure determination of closed state","journal":"ACS catalysis","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure determination combined with H/D exchange kinetics and MD simulations, multiple orthogonal methods establishing both conformation and mechanistic role of Y259","pmids":["30101036"],"is_preprint":false},{"year":2015,"finding":"A non-canonical phosphate-binding site in DERA, consisting of Ser238 and Ser239, contributes to catalytic efficiency; the S239P mutant showed increased enthalpy but reduced entropy at the transition state, with a concomitant loss in anticorrelated protein motions distributed across the enzyme; the degree of anticorrelated (protein-wide) motions is coupled to catalytic efficiency in the DERA retro-aldol reaction.","method":"Site-directed and site-saturation mutagenesis, kinetic analysis of mutants, molecular dynamics simulations, temperature-dependence of catalytic rates","journal":"Chemical science","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro kinetic assays with defined mutants combined with MD simulations and thermodynamic analysis, multiple orthogonal methods in a single study","pmids":["29910900"],"is_preprint":false},{"year":2017,"finding":"Cysteine 47 (C47) in DERA forms a covalent Michael adduct with crotonaldehyde (a side-product of acetaldehyde self-condensation), constituting the primary mechanism of irreversible inhibition of DERA by acetaldehyde; the C47L substitution abolishes this inhibition while preserving stereoselectivity.","method":"Site-directed mutagenesis, activity assays with acetaldehyde, identification of covalent inhibitor-adduct","journal":"Journal of biotechnology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutagenesis combined with activity assays defining the inhibitory mechanism, single lab but two methods","pmids":["28347769"],"is_preprint":false},{"year":2020,"finding":"E. coli DERA active-site and proximal residues at 24 positions govern substrate donor preference; targeted mutagenesis of these residues improved acetaldehyde (C2) donor activity 2–3-fold while abolishing activity toward the natural donor glyceraldehyde-3-phosphate; wild-type DERA can also use formaldehyde (C1) as donor substrate.","method":"Structure-guided site-directed mutagenesis (1–3 mutations), enzyme activity assays with multiple substrates, machine-learning-guided mutagenesis rounds","journal":"Applied microbiology and biotechnology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — 3D-structure-guided mutagenesis combined with substrate specificity assays across multiple substrates, single lab","pmids":["33147349"],"is_preprint":false}],"current_model":"DERA (human) and its bacterial ortholog (E. coli deoC) encode a class I aldolase that catalyzes reversible retro-aldol cleavage of 2-deoxy-D-ribose-5-phosphate to glyceraldehyde-3-phosphate and acetaldehyde via a Schiff base intermediate at an active-site lysine; catalysis is further regulated by an intrinsically disordered C-terminal tail whose terminal tyrosine (Y259) samples a closed conformation to facilitate proton abstraction, and by protein-wide anticorrelated motions linked to a non-canonical phosphate-binding site (Ser238/Ser239); the enzyme is irreversibly inhibited by crotonaldehyde through a covalent adduct with Cys47; in human cells, DERA interacts with YBX1, is recruited to stress granules under oxidative or mitochondrial stress (with its loss increasing apoptosis), and enables ATP production from extracellular deoxyinosines via the nucleoside catabolism pathway."},"narrative":{"mechanistic_narrative":"DERA encodes a class I aldolase that catalyzes the reversible retro-aldol cleavage of 2-deoxy-D-ribose-5-phosphate into glyceraldehyde-3-phosphate and acetaldehyde, operating through a Schiff base intermediate at an active-site lysine [PMID:6749498, PMID:25229427]. Catalysis depends on an intrinsically disordered C-terminal tail that samples a catalytically competent closed conformation in which the terminal tyrosine Y259 enters the active site to drive the proton-abstraction step, with auxiliary phosphate-binding residues orienting Y259 [PMID:30101036]; a non-canonical phosphate-binding site (Ser238/Ser239) further tunes catalytic efficiency by coupling protein-wide anticorrelated motions to the transition state [PMID:29910900]. Substrate donor preference is governed by active-site and proximal residues, and the enzyme can also accept formaldehyde as a donor, while crotonaldehyde formed from acetaldehyde self-condensation irreversibly inactivates the enzyme via a covalent Michael adduct with Cys47 [PMID:28347769, PMID:33147349]. Beyond its catalytic role, human DERA links deoxynucleoside catabolism to cellular stress responses: it enables ATP production from extracellular deoxyinosine, interacts with the stress granule component YBX1, and is recruited to stress granules under oxidative or mitochondrial stress, where its loss reduces stress granule formation and increases apoptosis [PMID:25229427].","teleology":[{"year":1982,"claim":"Establishing that the deoC gene product is a class I aldolase resolved how 2-deoxyribose-5-phosphate is cleaved, identifying a Schiff base mechanism centered on an active-site lysine.","evidence":"DNA/protein sequencing, amino acid composition, and catalytic characterization of E. coli deoxyriboaldolase","pmids":["6749498"],"confidence":"Medium","gaps":["Active-site lysine was only tentatively assigned","No structural model of the catalytic site","Human ortholog not yet addressed"]},{"year":2014,"claim":"Characterizing human DERA extended the enzyme's role beyond metabolism, showing it both supports deoxynucleoside-derived ATP production and participates in stress granule biology via YBX1, linking a metabolic enzyme to cell survival under stress.","evidence":"Enzymatic assays, DERA–YBX1 co-immunoprecipitation, shRNA knockdown with stress granule imaging and apoptosis readouts, and deoxyinosine ATP-rescue experiments in human cells","pmids":["25229427"],"confidence":"High","gaps":["Mechanism of DERA recruitment to stress granules unknown","Whether YBX1 interaction is direct or scaffold-mediated not resolved","Catalytic activity not shown to be required for the stress granule function"]},{"year":2015,"claim":"Identifying a non-canonical Ser238/Ser239 phosphate-binding site and linking transition-state thermodynamics to protein-wide anticorrelated motions explained how distributed dynamics contribute to catalytic efficiency.","evidence":"Site-directed/saturation mutagenesis, kinetic and thermodynamic analysis, and MD simulations of E. coli DERA","pmids":["29910900"],"confidence":"High","gaps":["Physical basis coupling distal motions to active-site chemistry not fully defined","Relevance of these dynamics to the human enzyme untested"]},{"year":2017,"claim":"Defining the covalent Cys47–crotonaldehyde adduct explained the long-observed irreversible inactivation of DERA by acetaldehyde, and the C47L variant demonstrated this site can be engineered away.","evidence":"Site-directed mutagenesis, activity assays with acetaldehyde, and covalent adduct identification","pmids":["28347769"],"confidence":"Medium","gaps":["Adduct structure characterized in a single lab","Whether Cys47 inactivation occurs in human cells not tested"]},{"year":2018,"claim":"Solving the closed-state conformation of the disordered C-terminal tail established Y259 as a mobile catalytic residue that completes the active site for proton abstraction, defining a conformational gating mechanism.","evidence":"NMR solution-structure determination, H/D exchange, phosphate titration, and MD simulations of E. coli DERA","pmids":["30101036"],"confidence":"High","gaps":["Kinetics of open/closed interconversion under turnover not quantified","Tail dynamics in human DERA not examined"]},{"year":2020,"claim":"Mapping the 24 active-site and proximal residues that control donor preference defined the determinants of substrate specificity and showed the enzyme can use C1/C2 donors, informing both mechanism and engineering.","evidence":"Structure-guided and machine-learning-guided mutagenesis with multi-substrate activity assays in E. coli DERA","pmids":["33147349"],"confidence":"Medium","gaps":["Specificity determinants validated in the bacterial enzyme only","Structural basis of altered donor binding not directly resolved"]},{"year":null,"claim":"Whether DERA's catalytic activity is mechanistically required for its stress granule recruitment and pro-survival function in human cells remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No catalytically dead human DERA mutant tested in the stress granule context","Physiological source and flux of deoxyinosine substrate in vivo undefined","Structural model of human DERA C-terminal tail/Y259 not reported"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016829","term_label":"lyase activity","supporting_discovery_ids":[0,1,2,3,5]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,5]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[1]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[1]}],"complexes":[],"partners":["YBX1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y315","full_name":"Deoxyribose-phosphate aldolase","aliases":["2-deoxy-D-ribose 5-phosphate aldolase","Phosphodeoxyriboaldolase","Deoxyriboaldolase"],"length_aa":318,"mass_kda":35.2,"function":"Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. Participates in stress granule (SG) assembly. May allow ATP production from extracellular deoxyinosine in conditions of energy deprivation","subcellular_location":"Cytoplasm; Cytoplasmic granule; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9Y315/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DERA","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ALDH16A1","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/DERA","total_profiled":1310},"omim":[{"mim_id":"619668","title":"DEOXYRIBOSE-PHOSPHATE ALDOLASE; DERA","url":"https://www.omim.org/entry/619668"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"liver","ntpm":97.7}],"url":"https://www.proteinatlas.org/search/DERA"},"hgnc":{"alias_symbol":["CGI-26","DEOC"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y315","domains":[{"cath_id":"3.20.20.70","chopping":"22-315","consensus_level":"medium","plddt":96.9698,"start":22,"end":315}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y315","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y315-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y315-F1-predicted_aligned_error_v6.png","plddt_mean":96.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DERA","jax_strain_url":"https://www.jax.org/strain/search?query=DERA"},"sequence":{"accession":"Q9Y315","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y315.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y315/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y315"}},"corpus_meta":[{"pmid":"6749498","id":"PMC_6749498","title":"The primary structure of Escherichia coli K12 2-deoxyribose 5-phosphate aldolase. Nucleotide sequence of the deoC gene and the amino acid sequence of the enzyme.","date":"1982","source":"European journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/6749498","citation_count":45,"is_preprint":false},{"pmid":"6323164","id":"PMC_6323164","title":"Structure and function of the intercistronic regulatory deoC-deoA element of Escherichia coli K-12.","date":"1984","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/6323164","citation_count":33,"is_preprint":false},{"pmid":"30284013","id":"PMC_30284013","title":"2-Deoxy-D-ribose-5-phosphate aldolase (DERA): applications and modifications.","date":"2018","source":"Applied microbiology and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/30284013","citation_count":29,"is_preprint":false},{"pmid":"25229427","id":"PMC_25229427","title":"DERA is the human deoxyribose phosphate aldolase and is involved in stress response.","date":"2014","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/25229427","citation_count":25,"is_preprint":false},{"pmid":"33147349","id":"PMC_33147349","title":"Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods.","date":"2020","source":"Applied microbiology and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/33147349","citation_count":19,"is_preprint":false},{"pmid":"23667462","id":"PMC_23667462","title":"A highly productive, whole-cell DERA chemoenzymatic process for production of key lactonized side-chain intermediates in statin synthesis.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23667462","citation_count":17,"is_preprint":false},{"pmid":"30101036","id":"PMC_30101036","title":"Conformational Sampling of the Intrinsically Disordered C-Terminal Tail of DERA Is Important for Enzyme Catalysis.","date":"2018","source":"ACS catalysis","url":"https://pubmed.ncbi.nlm.nih.gov/30101036","citation_count":13,"is_preprint":false},{"pmid":"28347769","id":"PMC_28347769","title":"Probing the acetaldehyde-sensitivity of 2-deoxy-ribose-5-phosphate aldolase (DERA) leads to resistant variants.","date":"2017","source":"Journal of biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/28347769","citation_count":11,"is_preprint":false},{"pmid":"31738478","id":"PMC_31738478","title":"Seed morphology using SEM techniques for identification of useful grasses in Dera Ghazi Khan, Pakistan.","date":"2019","source":"Microscopy research and technique","url":"https://pubmed.ncbi.nlm.nih.gov/31738478","citation_count":10,"is_preprint":false},{"pmid":"20229283","id":"PMC_20229283","title":"The fed-batch production of a thermophilic 2-deoxyribose-5-phosphate aldolase (DERA) in Escherichia coli by exponential feeding strategy control.","date":"2010","source":"Applied biochemistry and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/20229283","citation_count":10,"is_preprint":false},{"pmid":"29910900","id":"PMC_29910900","title":"Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA).","date":"2015","source":"Chemical science","url":"https://pubmed.ncbi.nlm.nih.gov/29910900","citation_count":9,"is_preprint":false},{"pmid":"33579093","id":"PMC_33579093","title":"A report on the molecular detection and seasonal prevalence of Trypanosoma brucei in Dromedary Camels from Dera Ghazi Khan District in Southern Punjab (Pakistan).","date":"2016","source":"Tropical biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/33579093","citation_count":6,"is_preprint":false},{"pmid":"32659474","id":"PMC_32659474","title":"Genetic variants in TKT and DERA in the nicotinamide adenine dinucleotide phosphate pathway predict melanoma survival.","date":"2020","source":"European journal of cancer (Oxford, England : 1990)","url":"https://pubmed.ncbi.nlm.nih.gov/32659474","citation_count":5,"is_preprint":false},{"pmid":"14612251","id":"PMC_14612251","title":"Mutations in deoB and deoC alter an extracellular signaling pathway required for activation of the gab operon in Escherichia coli.","date":"2003","source":"FEMS microbiology letters","url":"https://pubmed.ncbi.nlm.nih.gov/14612251","citation_count":4,"is_preprint":false},{"pmid":"17547717","id":"PMC_17547717","title":"Establishment and characterization of a cell line (DEOC-1) originating from a human malignant melanoma of the skin.","date":"2007","source":"Human cell","url":"https://pubmed.ncbi.nlm.nih.gov/17547717","citation_count":3,"is_preprint":false},{"pmid":"37750990","id":"PMC_37750990","title":"Genomic selection pressure discovery using site-frequency spectrum and reduced local variability statistics in Pakistani Dera-Din-Panah goat.","date":"2023","source":"Tropical animal health and production","url":"https://pubmed.ncbi.nlm.nih.gov/37750990","citation_count":3,"is_preprint":false},{"pmid":"33159762","id":"PMC_33159762","title":"Haematological outcomes in progression of malaria: A cohort study from district Dera Ismail Khan, Pakistan.","date":"2020","source":"JPMA. The Journal of the Pakistan Medical Association","url":"https://pubmed.ncbi.nlm.nih.gov/33159762","citation_count":3,"is_preprint":false},{"pmid":"37491848","id":"PMC_37491848","title":"Genetic basis of ß-thalassemia in families of pashtun ethnicity in Dera Ismail Khan district of Khyber Pakhtun-Khwa province, Pakistan.","date":"2023","source":"Expert review of hematology","url":"https://pubmed.ncbi.nlm.nih.gov/37491848","citation_count":1,"is_preprint":false},{"pmid":"24696983","id":"PMC_24696983","title":"Characterization of the etiological agents of tuberculous lymphadenitis in Dera Woreda, North Showa, Ethiopia.","date":"2014","source":"Ethiopian medical journal","url":"https://pubmed.ncbi.nlm.nih.gov/24696983","citation_count":1,"is_preprint":false},{"pmid":"42117702","id":"PMC_42117702","title":"Role of the Mycoplasma bovis deoC gene in nucleoside catabolism and host cell survival.","date":"2026","source":"Applied and environmental microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/42117702","citation_count":0,"is_preprint":false},{"pmid":"40895961","id":"PMC_40895961","title":"Epidemiological Study of Dengue Fever in a Tertiary Care Hospital in Dera Ismail Khan, Pakistan.","date":"2025","source":"Cureus","url":"https://pubmed.ncbi.nlm.nih.gov/40895961","citation_count":0,"is_preprint":false},{"pmid":"40509167","id":"PMC_40509167","title":"Flow Synthesis of Pharmaceutical Intermediate Catalyzed by Immobilized DERA: Comparison of Different Immobilization Techniques and Reactor Designs.","date":"2025","source":"Molecules (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/40509167","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.07.22.666072","title":"Construction of a genome-wide pooled CRISPRi library as a resource for exploring the acid tolerance mechanism in  <i>Streptococcus mutans</i>","date":"2025-07-22","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.22.666072","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13526,"output_tokens":1770,"usd":0.033564,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8653,"output_tokens":2440,"usd":0.052132,"stage2_stop_reason":"end_turn"},"total_usd":0.085696,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1982,\n      \"finding\": \"E. coli deoC gene encodes 2-deoxyribose-5-phosphate aldolase (deoxyriboaldolase), a 259-amino acid class I aldolase (MW 27,737) that forms Schiff base intermediates during catalysis; a lysine residue was tentatively identified as the active-site residue involved in Schiff base formation.\",\n      \"method\": \"DNA/protein sequencing, amino acid composition analysis, catalytic property characterization\",\n      \"journal\": \"European journal of biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — protein sequencing combined with catalytic characterization and mechanistic class assignment in a single study, but active-site lysine identification was tentative\",\n      \"pmids\": [\"6749498\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Human DERA is the deoxyribose-phosphate aldolase responsible for converting 2-deoxy-D-ribose-5-phosphate into glyceraldehyde-3-phosphate and acetaldehyde; DERA interacts with stress granule component YBX1 and is recruited to stress granules upon oxidative or mitochondrial stress; shRNA-mediated knockdown of DERA reduced stress granule formation and increased apoptosis after clotrimazole stress; DERA activity enables cells with abolished mitochondrial ATP production to use extracellular deoxyinosine to maintain ATP levels via deoxynucleoside degradation.\",\n      \"method\": \"Enzymatic activity assays, co-immunoprecipitation (DERA–YBX1), shRNA knockdown with stress granule imaging and apoptosis readouts, ATP rescue experiments\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (enzymatic assay, Co-IP, KD with defined phenotypic readouts, metabolic rescue experiment) in a single focused study on the human protein\",\n      \"pmids\": [\"25229427\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The C-terminal tail of E. coli DERA is intrinsically disordered and samples open and catalytically relevant closed conformations; in the closed state, the terminal tyrosine residue Y259 enters the active site and is required for the proton abstraction step of catalysis; auxiliary phosphate-binding residues on the C-terminal tail help orient Y259 for catalysis.\",\n      \"method\": \"NMR spectroscopy (NOE distance restraints, H/D exchange, phosphate titration), molecular dynamics simulations, solution-state structure determination of closed state\",\n      \"journal\": \"ACS catalysis\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure determination combined with H/D exchange kinetics and MD simulations, multiple orthogonal methods establishing both conformation and mechanistic role of Y259\",\n      \"pmids\": [\"30101036\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"A non-canonical phosphate-binding site in DERA, consisting of Ser238 and Ser239, contributes to catalytic efficiency; the S239P mutant showed increased enthalpy but reduced entropy at the transition state, with a concomitant loss in anticorrelated protein motions distributed across the enzyme; the degree of anticorrelated (protein-wide) motions is coupled to catalytic efficiency in the DERA retro-aldol reaction.\",\n      \"method\": \"Site-directed and site-saturation mutagenesis, kinetic analysis of mutants, molecular dynamics simulations, temperature-dependence of catalytic rates\",\n      \"journal\": \"Chemical science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro kinetic assays with defined mutants combined with MD simulations and thermodynamic analysis, multiple orthogonal methods in a single study\",\n      \"pmids\": [\"29910900\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Cysteine 47 (C47) in DERA forms a covalent Michael adduct with crotonaldehyde (a side-product of acetaldehyde self-condensation), constituting the primary mechanism of irreversible inhibition of DERA by acetaldehyde; the C47L substitution abolishes this inhibition while preserving stereoselectivity.\",\n      \"method\": \"Site-directed mutagenesis, activity assays with acetaldehyde, identification of covalent inhibitor-adduct\",\n      \"journal\": \"Journal of biotechnology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis combined with activity assays defining the inhibitory mechanism, single lab but two methods\",\n      \"pmids\": [\"28347769\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"E. coli DERA active-site and proximal residues at 24 positions govern substrate donor preference; targeted mutagenesis of these residues improved acetaldehyde (C2) donor activity 2–3-fold while abolishing activity toward the natural donor glyceraldehyde-3-phosphate; wild-type DERA can also use formaldehyde (C1) as donor substrate.\",\n      \"method\": \"Structure-guided site-directed mutagenesis (1–3 mutations), enzyme activity assays with multiple substrates, machine-learning-guided mutagenesis rounds\",\n      \"journal\": \"Applied microbiology and biotechnology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — 3D-structure-guided mutagenesis combined with substrate specificity assays across multiple substrates, single lab\",\n      \"pmids\": [\"33147349\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DERA (human) and its bacterial ortholog (E. coli deoC) encode a class I aldolase that catalyzes reversible retro-aldol cleavage of 2-deoxy-D-ribose-5-phosphate to glyceraldehyde-3-phosphate and acetaldehyde via a Schiff base intermediate at an active-site lysine; catalysis is further regulated by an intrinsically disordered C-terminal tail whose terminal tyrosine (Y259) samples a closed conformation to facilitate proton abstraction, and by protein-wide anticorrelated motions linked to a non-canonical phosphate-binding site (Ser238/Ser239); the enzyme is irreversibly inhibited by crotonaldehyde through a covalent adduct with Cys47; in human cells, DERA interacts with YBX1, is recruited to stress granules under oxidative or mitochondrial stress (with its loss increasing apoptosis), and enables ATP production from extracellular deoxyinosines via the nucleoside catabolism pathway.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DERA encodes a class I aldolase that catalyzes the reversible retro-aldol cleavage of 2-deoxy-D-ribose-5-phosphate into glyceraldehyde-3-phosphate and acetaldehyde, operating through a Schiff base intermediate at an active-site lysine [#0, #1]. Catalysis depends on an intrinsically disordered C-terminal tail that samples a catalytically competent closed conformation in which the terminal tyrosine Y259 enters the active site to drive the proton-abstraction step, with auxiliary phosphate-binding residues orienting Y259 [#2]; a non-canonical phosphate-binding site (Ser238/Ser239) further tunes catalytic efficiency by coupling protein-wide anticorrelated motions to the transition state [#3]. Substrate donor preference is governed by active-site and proximal residues, and the enzyme can also accept formaldehyde as a donor, while crotonaldehyde formed from acetaldehyde self-condensation irreversibly inactivates the enzyme via a covalent Michael adduct with Cys47 [#4, #5]. Beyond its catalytic role, human DERA links deoxynucleoside catabolism to cellular stress responses: it enables ATP production from extracellular deoxyinosine, interacts with the stress granule component YBX1, and is recruited to stress granules under oxidative or mitochondrial stress, where its loss reduces stress granule formation and increases apoptosis [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 1982,\n      \"claim\": \"Establishing that the deoC gene product is a class I aldolase resolved how 2-deoxyribose-5-phosphate is cleaved, identifying a Schiff base mechanism centered on an active-site lysine.\",\n      \"evidence\": \"DNA/protein sequencing, amino acid composition, and catalytic characterization of E. coli deoxyriboaldolase\",\n      \"pmids\": [\"6749498\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Active-site lysine was only tentatively assigned\",\n        \"No structural model of the catalytic site\",\n        \"Human ortholog not yet addressed\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Characterizing human DERA extended the enzyme's role beyond metabolism, showing it both supports deoxynucleoside-derived ATP production and participates in stress granule biology via YBX1, linking a metabolic enzyme to cell survival under stress.\",\n      \"evidence\": \"Enzymatic assays, DERA–YBX1 co-immunoprecipitation, shRNA knockdown with stress granule imaging and apoptosis readouts, and deoxyinosine ATP-rescue experiments in human cells\",\n      \"pmids\": [\"25229427\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Mechanism of DERA recruitment to stress granules unknown\",\n        \"Whether YBX1 interaction is direct or scaffold-mediated not resolved\",\n        \"Catalytic activity not shown to be required for the stress granule function\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identifying a non-canonical Ser238/Ser239 phosphate-binding site and linking transition-state thermodynamics to protein-wide anticorrelated motions explained how distributed dynamics contribute to catalytic efficiency.\",\n      \"evidence\": \"Site-directed/saturation mutagenesis, kinetic and thermodynamic analysis, and MD simulations of E. coli DERA\",\n      \"pmids\": [\"29910900\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Physical basis coupling distal motions to active-site chemistry not fully defined\",\n        \"Relevance of these dynamics to the human enzyme untested\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defining the covalent Cys47–crotonaldehyde adduct explained the long-observed irreversible inactivation of DERA by acetaldehyde, and the C47L variant demonstrated this site can be engineered away.\",\n      \"evidence\": \"Site-directed mutagenesis, activity assays with acetaldehyde, and covalent adduct identification\",\n      \"pmids\": [\"28347769\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Adduct structure characterized in a single lab\",\n        \"Whether Cys47 inactivation occurs in human cells not tested\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Solving the closed-state conformation of the disordered C-terminal tail established Y259 as a mobile catalytic residue that completes the active site for proton abstraction, defining a conformational gating mechanism.\",\n      \"evidence\": \"NMR solution-structure determination, H/D exchange, phosphate titration, and MD simulations of E. coli DERA\",\n      \"pmids\": [\"30101036\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Kinetics of open/closed interconversion under turnover not quantified\",\n        \"Tail dynamics in human DERA not examined\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Mapping the 24 active-site and proximal residues that control donor preference defined the determinants of substrate specificity and showed the enzyme can use C1/C2 donors, informing both mechanism and engineering.\",\n      \"evidence\": \"Structure-guided and machine-learning-guided mutagenesis with multi-substrate activity assays in E. coli DERA\",\n      \"pmids\": [\"33147349\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Specificity determinants validated in the bacterial enzyme only\",\n        \"Structural basis of altered donor binding not directly resolved\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether DERA's catalytic activity is mechanistically required for its stress granule recruitment and pro-survival function in human cells remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No catalytically dead human DERA mutant tested in the stress granule context\",\n        \"Physiological source and flux of deoxyinosine substrate in vivo undefined\",\n        \"Structural model of human DERA C-terminal tail/Y259 not reported\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016829\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"YBX1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}