YFH7 (ORF YFR007W; alias AIM12) is a 353-residue soluble ATP-dependent small-molecule kinase of the P-loop NTPase superfamily in the budding yeast Saccharomyces cerevisiae. Its crystal structure (PDB 2GA8/2GAA) shows the phosphoribulokinase/uridine kinase/bacterial pantothenate kinase (PRK/URK/PANK) fold β with core, lid and NMP-binding subdomains β plus an additional ~100-residue alpha/beta domain of novel topology that is a lineage-specific insertion. It carries a canonical Walker A (P-loop) motif (GSPGSGKS, residues 31-38) that binds ATP and the URK-family diagnostic second block (VILEG, ~residue 263), and it hydrolyses ATP in vitro (KM approximately 1.2 mM). Although the P-loop kinase fold is ancient and pan-eukaryotic, the YFH7 protein itself is restricted to the Saccharomycetaceae. YFH7 is a soluble, moderately abundant cytoplasmic protein. Deletion is viable but has been linked in genome-wide screens to defects in endoplasmic reticulum (karmellae) biogenesis and to an increased frequency of mitochondrial genome loss. The physiological phosphoacceptor substrate of YFH7, and the pathway in which it acts, remain unidentified.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred cytoplasmic localization, placed by PAINT at the PANTHER:PTN000032154 ancestral node of the broader PTHR10285 P-loop kinase family. This broad localization is consistent with a soluble P-loop small-molecule kinase and with the absence of any transmembrane or targeting signal. Reason: Accepted as YFH7's inferred core site of action: the protein has the soluble PRK/URK/PANK P-loop kinase fold, no predicted transmembrane segment or organelle targeting sequence, and no experimental yeast localization that would refine or contradict the broad cytoplasm assignment. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000032154 Β· uridine kinase / PRK-URK-PANK family ancestral node (PTHR10285) SUPPORTS TRANSFER The IBD places a broad cytoplasmic localization at the PTHR10285 family node. YFH7 is an outlying Saccharomycetaceae-restricted branch by sequence, but its solved soluble P-loop kinase fold and lack of targeting features make this CC transfer appropriate. |
| GO:0005575 cellular_component | ND GO_REF:0000015 | ACCEPT | Summary: Root cellular component ND annotation: when it was made, no cellular component had been curated for this gene product from literature. Reason: ACCEPT under the ND acceptance rule (projects/NO_DATA.md). The evidence this review cites for the cellular component is inferred (from orthologs, family membership or sequence features) or comes from other species; none of it is literature on this gene product in this species. This was judged from the review's own content during the NO_DATA re-action pass, not from a new literature search. Earlier action: KEEP_AS_NON_CORE. Re-checked 2026-10-31: PMID:18004758, cited in core_functions, is structural and enzymatic and does not localize YFH7. The gene's search record (YFH7-notes.md) finds no experimental localization study of YFH7. Supporting Evidence: file:yeast/YFH7/YFH7-notes.md Localization: cytoplasm (GO IBA GO:0005737, GO_Central). No experimental yeast IDA |
| GO:0016301 kinase activity | ISS PMID:18004758 Crystal structure and functional analysis identify the P-loo... | ACCEPT | Summary: YFH7 is a P-loop kinase of the PRK/URK/PANK subfamily. The intact Walker A P-loop (GSPGSGKS, 31-38), the retained URK-family second block (VILEG, ~263), the solved structure, and in-vitro ATP-dependent activity together support a genuine kinase (phosphotransferase) molecular function. This is a core function. The general "kinase activity" term is appropriate and should NOT be over-specified: the crystal paper concluded "new substrate specificity", i.e. no phosphoacceptor substrate is demonstrated, so a specific kinase child term is not warranted. Reason: Well supported by structure + enzymology (PMID:18004758) and by the intact diagnostic P-loop/URK motifs in the bioinformatics analysis. Deliberately kept at the general "kinase activity" level because the physiological substrate is unknown. Supporting Evidence: PMID:18004758 Structural and ligand binding analysis combined with enzymatic assays suggest that YFH7 is an ATP-dependent small molecule kinase with new substrate specificity. file:yeast/YFH7/YFH7-bioinformatics/RESULTS.md the small-molecule-kinase catalytic scaffold is intact |
| GO:0016310 phosphorylation | ISS PMID:18004758 Crystal structure and functional analysis identify the P-loo... | ACCEPT | Summary: Biological-process counterpart of the kinase molecular function: as an ATP-dependent kinase, YFH7 is involved in phosphorylation (phosphate transfer to a small-molecule acceptor). Consistent with the ISS transfer and the intact catalytic scaffold. Reason: Directly entailed by the accepted kinase activity; the general "phosphorylation" process term is appropriate given the undetermined substrate. Retained as the BP partner of the MF annotation. Supporting Evidence: PMID:18004758 Structural and ligand binding analysis combined with enzymatic assays suggest that YFH7 is an ATP-dependent small molecule kinase with new substrate specificity. |
| GO:0016887 ATP hydrolysis activity | IDA PMID:18004758 Crystal structure and functional analysis identify the P-loo... | ACCEPT | Summary: Directly measured in vitro: YFH7 turns over ATP, with a determined KM of ~1.2 mM for ATP (UniProt BIOPHYSICOCHEMICAL PROPERTIES from PMID:18004758). This experimental ATP-turnover activity is the empirical basis for classifying YFH7 as an ATP-dependent kinase and is a core molecular function. Reason: Experimental (IDA) measurement of ATP hydrolysis/turnover from the same structure/enzymology study; consistent with the intact Walker A P-loop. Kept as a core MF annotation. (The measured ATP turnover reflects the enzyme's ATP-dependent catalytic cycle; whether it is coupled to a productive phosphoacceptor is part of the substrate knowledge gap, but the ATPase activity itself is directly observed.) Supporting Evidence: PMID:18004758 Structural and ligand binding analysis combined with enzymatic assays suggest that YFH7 is an ATP-dependent small molecule kinase with new substrate specificity. |
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Download this section (compressed HTML)Q: What is the physiological small-molecule phosphoacceptor substrate of YFH7? The crystal structure and enzymology established an ATP-dependent kinase but "new substrate specificity" β the acceptor is unidentified.
Q: Is the ER-biogenesis (karmellae) and/or mitochondrial-genome-loss phenotype of yfh7Ξ a direct consequence of a missing phosphorylation event, or an indirect/pleiotropic effect?
Q: Does the lineage-specific ~100-residue insertion (the "additional alpha/beta domain of novel topology") confer the substrate specificity that distinguishes YFH7 from other PRK/URK/PANK-family kinases?
Experiment: Broad in-vitro phosphotransfer substrate screen (metabolomic / small-molecule library kinase assay, e.g. coupled ADP-detection) against purified recombinant YFH7 to identify the phosphoacceptor; follow up with steady-state kinetics on the best hits.
Experiment: Structure-guided mutagenesis of the Walker A lysine (in GSPGSGKS) and candidate catalytic acidic residue, with an ATPase/kinase-dead allele tested for rescue of the yfh7Ξ ER-biogenesis and mitochondrial-genome-loss phenotypes, to test whether those phenotypes require catalytic activity.
Experiment: Untargeted comparative metabolomics of wild-type vs yfh7Ξ (and a catalytic-dead knock-in) to detect an accumulating substrate or missing phosphorylated product.
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The physiological phosphoacceptor substrate of YFH7 is unknown. It is established as an ATP-dependent small-molecule kinase, but what small molecule it phosphorylates β and therefore the metabolic pathway and biological process it serves β has never been identified.
OPEN BIOLOGY BP_DARK
What is known: Firmly known: YFH7 is a soluble cytoplasmic protein with the PRK/URK/PANK P-loop kinase fold (crystal structures 2GA8/2GAA), an intact Walker A P-loop (GSPGSGKS, 31-38) that binds ATP, the retained URK-family diagnostic second block (VILEG, ~263), measured in-vitro ATP turnover (KM ~1.2 mM for ATP), and a lineage-specific ~100-residue insertion. Deletion is viable and has been associated in genome-wide screens with impaired ER (karmellae) biogenesis and increased mitochondrial genome loss. Unknown: the small-molecule acceptor phosphorylated by the enzyme, the pathway it belongs to, and whether the deletion phenotypes are direct consequences of a lost phosphorylation.
Significance: YFH7 is a structurally solved, catalytically plausible enzyme whose reaction is unassigned β a clean example of a "known activity, unknown substrate/purpose" (BP-dark) enzyme in one of the best-studied eukaryotes. Identifying its substrate would convert a decades-old orphan kinase into an annotated metabolic step and could explain the ER- and mitochondrial-maintenance phenotypes.
What would resolve it: A broad in-vitro small-molecule phosphotransfer substrate screen on recombinant YFH7 followed by kinetic confirmation; comparative wild-type-vs-yfh7Ξ metabolomics to detect an accumulating substrate or missing phosphorylated product; catalytic-dead separation-of-function alleles to test whether the deletion phenotypes require the kinase activity.
Provenance (the field's own admissions):
Putative kinase with similarity to the PRK/URK/PANK kinase subfamily; the PRK/URK/PANK subfamily of P-loop kinases is also known as phosphoribulokinase/uridine kinase/bacterial pantothenate kinase
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