id: A0A9L0K2P4 gene_symbol: NADK2 taxon: id: NCBITaxon:9793 label: Equus asinus status: COMPLETE description: 'Assessment of 3 ProtNLM2 GO predictions for donkey NADK2 (A0A9L0K2P4), scored for this exact sequence. A0A9L0K2P4 is the isoform-2-like splice product of the donkey NADK2 gene: it lacks the segment equivalent to human 288-319, which carries the TGSxAW NAD+-binding motif (W319) and the second-monomer active-site residue S306, while it keeps the GGDG motif, the ATP-contacting residues (human K76, S188, D161) and the extension-3/EMKA dimerization element (human 325-367). The full-length canonical-equivalent product of the same gene is A0A8C4M4D0. Predictions are judged against donkey GOA on any NADK2 product (NAD+ kinase activity, mitochondrion, mitochondrial matrix, NAD+ metabolic process) and the human ortholog Q4G0N4 (PMID:23212377, PMID:35868311, PMID:35733246). ATP binding and protein homodimerization are retained by this product and absent from donkey GOA (COR); phosphorylation, which here means phosphorylation of NAD+, is uncertain for this product because it lacks the NAD+-binding segment but keeps the ATP site and dimerization element, and its activity is untested (UNC). Non-GO ProtNLM2 outputs, not scored: subcellular location ''Mitochondrion'' and function text ''Mitochondrial NAD(+) kinase that phosphorylates NAD(+) to yield NADP(+). Can use both ATP or inorganic polyphosphate as the phosphoryl donor'', which reproduces the human Swiss-Prot function statement.' source_documents: - projects/PROTNLM_EVALUATION/donkey40/donkey40-predictions.tsv - genes/EQUAS/NADK2/NADK2-goa.tsv - genes/human/NADK2/NADK2-uniprot.txt - genes/EQUAS/NADK2/NADK2-bioinformatics/RESULTS.md - genes/EQUAS/NADK2/NADK2-bioinformatics/RESULTS-rereview.md predictions: - source_method: ProtNLM2 source_version: UniProt API snapshot 2026-10-14 predicted_term: id: GO:0042803 label: protein homodimerization activity predicted_term_type: GO_MF review: assessment: COR confidence_score: 2 summary: 'Not in donkey GOA, nor on the sibling donkey product A0A8C4M4D0. Human NADK2 (same PANTHER subfamily PTHR13158:SF5) is a homodimer by crystal structure, SAXS and SEC-MALS (PMID:35868311), and an independent structure shows the same symmetrical homodimer (PMID:35733246). The element that mediates dimerization is extension 3/EMKA (human 325-367); deleting it gives a monomer. This accession retains that element: donkey 384-506 aligns to human 320-442. The segment it lacks (human 288-319) contributes S306 and A288 to the composite active site but is not the identified dimerization interface, so the product keeps the feature the prediction needs and the transfer stands.' supported_by: - reference_id: PMID:35868311 supporting_text: NADK2 formed a dimer with a perfect 2-fold symmetry, in contrast to the tetrameric structures observed in cytosolic NADK crystals - reference_id: PMID:35868311 supporting_text: extension 3 (residues 325–367) mediates NADK2 dimerization - reference_id: PMID:35733246 supporting_text: Thus, the EMKA/EMKA interface is essential for stable self-association of NADK2. - reference_id: PMID:35733246 supporting_text: The resulting symmetrical homodimer creates two composite active sites - reference_id: file:EQUAS/NADK2/NADK2-bioinformatics/RESULTS.md supporting_text: '384-506 : 320-442' - source_method: ProtNLM2 source_version: UniProt API snapshot 2026-10-14 predicted_term: id: GO:0005524 label: ATP binding predicted_term_type: GO_MF review: assessment: COR confidence_score: 2 summary: Human NADK2 uses ATP as the phosphoryl donor (PMID:23212377). In the human structure the ATP site is formed by K76 next to the ATP triphosphate, S188 stabilising its phosphates, and the GGDG catalytic motif (PMID:35868311). All of these lie in human 1-287, which aligns to donkey 97-383 of this accession, and the GGDG motif is conserved (donkey 255-258). The segment this product lacks (human 288-319) contacts NAD+, not ATP, so the product keeps the ATP-binding features. ATP binding is not in donkey GOA, and NAD+ kinase activity is not a GO descendant of ATP binding, so this is a novel correct term rather than LSP. supported_by: - reference_id: PMID:23212377 supporting_text: showing that C5orf33 protein has NADK activity using ATP and poly(P) as phosphoryl donors - reference_id: PMID:35868311 supporting_text: K76 is located in the vicinity of the metal ion (7.4 Å) and is predicted to lie next to the triphosphate moiety of ATP - reference_id: PMID:35868311 supporting_text: as well as the S188, which appears to be readily available to stabilize the three phosphate groups of the phosphodonor ATP - reference_id: file:EQUAS/NADK2/NADK2-bioinformatics/RESULTS.md supporting_text: '97-383 : 1-287' - source_method: ProtNLM2 source_version: UniProt API snapshot 2026-10-14 predicted_term: id: GO:0016310 label: phosphorylation predicted_term_type: GO_BP review: assessment: UNC confidence_score: 1 summary: 'For NADK2 this process is the phosphorylation of NAD+ to NADP+ (PMID:23212377). This accession provably lacks the segment equivalent to human 288-319: the donkey-human alignment aligns 0 of its 32 residues. The segment carries the TGSxAW NADK motif (human 314-319), whose W319 stacks the nicotinamide ring, and S306, which the second monomer contributes to the nicotinamide contacts (PMID:35868311). The product cannot form a complete NAD+ site of its own. The requirement of this segment for catalysis is inferred from the crystal structures; no mutagenesis of W319, S306 or the 288-319 segment and no activity assay of the isoform-2-equivalent product exist. The product keeps the GGDG catalytic motif, the ATP-site residues K76 and S188, the EMKA dimerization element and E379, which also contacts the nicotinamide in trans as E379-prime. It could therefore heterodimerize with the full-length product A0A8C4M4D0 and contribute residues to that partner''s composite active site. This contribution is neither shown nor excluded. There is no positive refutation, and the missing segment does not fully account for the mechanism, so the call is uncertain rather than incorrect.' supported_by: - reference_id: PMID:23212377 supporting_text: showing that C5orf33 protein has NADK activity using ATP and poly(P) as phosphoryl donors - reference_id: PMID:35868311 supporting_text: This motif provides an aromatic side chain (tryptophan W319 on NADK2 or a tyrosine on other NADKs) for stacking the nicotinamide moiety - reference_id: PMID:35868311 supporting_text: The latter forms hydrogen bonds with the side chains of asparagine N322 and serine S306′ (from a second monomer) and with the backbone carbonyl of glutamate E379′ - reference_id: PMID:35733246 supporting_text: The resulting symmetrical homodimer creates two composite active sites - reference_id: file:EQUAS/NADK2/NADK2-bioinformatics/RESULTS-rereview.md supporting_text: catalytically active is untested (no isoform 2 activity data exist for human either) - reference_id: file:EQUAS/NADK2/NADK2-bioinformatics/RESULTS.md supporting_text: The donkey model lacks the segment corresponding to human residues 288-319 - reference_id: file:EQUAS/NADK2/NADK2-bioinformatics/RESULTS.md supporting_text: '384-506 : 320-442' references: - id: file:EQUAS/NADK2/NADK2-goa.tsv title: Donkey NADK2 GOA annotations findings: [] - id: file:EQUAS/NADK2/NADK2-bioinformatics/RESULTS.md title: 'NADK2: donkey-human sequence comparison' findings: [] - id: file:EQUAS/NADK2/NADK2-bioinformatics/RESULTS-rereview.md title: 'NADK2 (donkey): comparison of all donkey NADK2 gene models with human NADK2' findings: [] - id: PMID:23212377 title: Identification and characterization of a human mitochondrial NAD kinase. findings: [] - id: PMID:35868311 title: Crystal structure of human NADK2 reveals a dimeric organization and active site occlusion by lysine acetylation. findings: [] - id: PMID:35733246 title: Structure of human NADK2 reveals atypical assembly and regulation of NAD kinases from animal mitochondria. findings: []