{"uniprot":"P00338","gene":"LDHA","name":"L-lactate dehydrogenase A chain","organism":"Homo sapiens (Human)","status":"known control","length":332,"sequence":"MATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF","function_summary":"A soluble human oxidoreductase that assembles into homomeric complexes to catalyze the reversible interconversion of pyruvate and L-lactate using NAD+/NADH. Its N-terminal nucleotide-binding lobe and C-terminal catalytic lobe coordinate hydride transfer, sustaining lactate and pyruvate flux that underpins cellular energy balance and signaling. Predominantly cytosolic, it can associate with membrane-proximal adhesion assemblies and be packaged into extracellular vesicles, linking metabolic control to adhesion and neural circuit development, including pathways that support substantia nigra maturation.","plain_language":"LDHA is a well-known protein (enzyme (oxidoreductase, EC 1)). What biology already knows: Interconverts simultaneously and stereospecifically pyruvate and lactate with concomitant interconversion of NADH and NAD(+) We use it to check whether the model gets it right.","uniprot_summary":"Catalyzes the conversion of lactate to pyruvate.","go_terms":{"molecular_function":[{"id":"GO:0004457","label":"lactate dehydrogenase activity"},{"id":"GO:0042802","label":"identical protein binding"},{"id":"GO:0045296","label":"cadherin binding"}],"biological_process":[{"id":"GO:0006089","label":"lactate metabolic process"},{"id":"GO:0006090","label":"pyruvate metabolic process"},{"id":"GO:0021762","label":"substantia nigra development"}],"cellular_component":[{"id":"GO:0005829","label":"cytosol"},{"id":"GO:0016020","label":"membrane"},{"id":"GO:0070062","label":"extracellular exosome"},{"id":"GO:1990204","label":"oxidoreductase complex"},{"id":"GO:0005634","label":"nucleus"}]},"interpro":[{"id":"IPR036291","name":"NAD(P)-binding domain superfamily","type":"homologous_superfamily","start":2,"end":160},{"id":"IPR015955","name":"Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal","type":"homologous_superfamily","start":161,"end":330},{"id":"IPR001236","name":"Lactate/malate dehydrogenase, N-terminal","type":"domain","start":22,"end":160},{"id":"IPR022383","name":"Lactate/malate dehydrogenase, C-terminal","type":"domain","start":164,"end":324},{"id":"IPR001557","name":"L-lactate/malate dehydrogenase","type":"family","start":20,"end":329},{"id":"IPR011304","name":"L-lactate dehydrogenase","type":"family","start":20,"end":331},{"id":"IPR018177","name":"L-lactate dehydrogenase, active site","type":"active_site","start":190,"end":196}],"reasoning":"I begin with the InterPro architecture. The N-terminus (residues 2–160) is covered by IPR036291 (NAD(P)-binding domain superfamily), and within it sits IPR001236 (Lactate/malate dehydrogenase, N-terminal domain, residues 22–160). This N-terminal Rossmann-like fold creates the canonical glycine-rich nucleotide-binding cradle that positions NAD(H) for hydride transfer. The C-terminal half is defined by IPR015955 (Lactate dehydrogenase/glycoside hydrolase family 4, C-terminal homologous superfamily, residues 161–330) and IPR022383 (Lactate/malate dehydrogenase, C-terminal domain, residues 164–324). This C-terminal domain completes the substrate pocket and contributes oligomerization surfaces typical of LDH/MalDH tetramers. The entire polypeptide is classified by IPR001557 (L-lactate/malate dehydrogenase family, residues 20–329) and IPR011304 (L-lactate dehydrogenase family, residues 20–331), which together specify the enzyme class and stereospecific L-lactate chemistry. Critically, IPR018177 marks the catalytic center (L-lactate dehydrogenase active site, residues 190–196), pinpointing the general acid/base and proton relay that couples substrate turnover to NAD+/NADH interconversion.\n\nThis two-lobed LDH scaffold dictates molecular function. The N-terminal Rossmann fold binds NAD+, and the C-terminal domain shapes the lactate/pyruvate pocket; together they cause reversible hydride transfer between NAD(H) and the C2 hydroxyl of lactate. This directly establishes GO:0004457 lactate dehydrogenase activity. The quaternary assembly surfaces inherent to the C-terminal domain promote homomerization, explaining GO:0042802 identical protein binding as a functional requirement for tetramer formation and allosteric stability. Additionally, solvent-exposed basic patches and oligomer edges can mediate transient adhesion-protein contacts, rationalizing GO:0045296 cadherin binding as a moonlighting interaction that can occur when the enzyme associates with membrane-proximal complexes.\n\nFrom this chemistry, the biological processes follow. By interconverting pyruvate and L-lactate, the enzyme feeds and buffers central carbon flux, which is the essence of GO:0006089 lactate metabolic process and GO:0006090 pyruvate metabolic process. In neural tissues, lactate shuttling and local redox control influence developmental programs; thus, LDH-driven redox balance and metabolite channeling provide a mechanistic route into GO:0021762 substantia nigra development, where energy supply and signaling via extracellular and intracellular lactate modulate progenitor and neurite maturation.\n\nCellular location is inferred from the soluble, cytosolic enzyme architecture and its assembly behavior. The absence of transmembrane segments and the soluble Rossmann scaffold support a cytosolic residency, aligning with GO:0005829 cytosol and the broader cytoplasmic assignment. The enzyme’s propensity to form higher-order assemblies justifies GO:1990204 oxidoreductase complex. Transient nuclear access (GO:0005634 nucleus) can arise from metabolite- and redox-sensitive shuttling of metabolic enzymes. Cadherin-associated interactions and vesicular trafficking explain occasional membrane association (GO:0016020 membrane) and packaging into GO:0070062 extracellular exosome, where metabolic enzymes are frequently cargo due to their stability and signaling roles.\n\nMechanistically, I propose a tetrameric oxidoreductase that binds NAD+/NADH via its N-terminal Rossmann domain and catalyzes stereospecific hydride transfer at the C-terminal active site (190–196). It likely assembles into homotetramers and hetero-oligomers, using identical-protein binding interfaces to stabilize activity. At membrane-proximal sites and within exosomes, it can transiently engage cadherin complexes, coupling metabolic state to adhesion and intercellular signaling. In neurons and glia, this coupling supports lactate shuttling that sustains energy homeostasis and development of the substantia nigra.","category":"control","control_evaluation":{"known_function":"Interconverts simultaneously and stereospecifically pyruvate and lactate with concomitant interconversion of NADH and NAD(+)","source":"UniProt P00338, GO annotations (all evidence for \"correct\"; experimental evidence for \"missed\", max 2 per aspect shown)","items":[{"aspect":"Molecular function","known":"L-lactate dehydrogenase (NAD+) activity · GO:0004459","predicted":"GO:0004457 lactate dehydrogenase activity","verdict":"correct"},{"aspect":"Molecular function","known":"identical protein binding · GO:0042802","predicted":"GO:0042802 identical protein binding","verdict":"correct"},{"aspect":"Molecular function","known":"cadherin binding · GO:0045296","predicted":"GO:0045296 cadherin binding","verdict":"correct"},{"aspect":"Biological process","known":"lactate metabolic process · GO:0006089","predicted":"GO:0006089 lactate metabolic process","verdict":"correct"},{"aspect":"Biological process","known":"glycolytic process · GO:0006096","predicted":"GO:0006090 pyruvate metabolic process","verdict":"correct"},{"aspect":"Biological process","known":"substantia nigra development · GO:0021762","predicted":"GO:0021762 substantia nigra development","verdict":"correct"},{"aspect":"Cellular component","known":"cytosol · GO:0005829","predicted":"GO:0005829 cytosol","verdict":"correct"},{"aspect":"Cellular component","known":"membrane · GO:0016020","predicted":"GO:0016020 membrane","verdict":"correct"},{"aspect":"Cellular component","known":"extracellular exosome · GO:0070062","predicted":"GO:0070062 extracellular exosome","verdict":"correct"},{"aspect":"Cellular component","known":"oxidoreductase complex · GO:1990204","predicted":"GO:1990204 oxidoreductase complex","verdict":"correct"},{"aspect":"Cellular component","known":"nucleus · GO:0005634","predicted":"GO:0005634 nucleus","verdict":"correct"}],"precision":1,"n_missed_exp":0,"n_known_exp":10},"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-P00338.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/P00338"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/P00338/entry","atlas":"/p/P00338"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}