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 | KEEP AS NON CORE | Summary: Phylogenetically inferred cytoplasmic localization, consistent with a soluble P-loop small-molecule kinase and with the absence of any transmembrane or targeting signal. Plausible and retained, but the localization is not the core of the gene's function. Reason: IBA localization is reasonable for a soluble cytoplasmic kinase and consistent with UniProt (no signal/transmembrane features). No experimental yeast localization is available to refine it, so it is kept as a non-core supporting annotation rather than a defining function. |
| GO:0005575 cellular_component | ND GO_REF:0000015 | KEEP AS NON CORE | Summary: Root "cellular_component" term with the ND (no biological data) code β the standard placeholder used when no specific location has been curated. It carries no information and is superseded by the IBA cytoplasm annotation. Reason: This is the conventional ND root-term stub, not an assertion to accept or remove on biological grounds. It is retained as-is per GO practice; the informative location is captured by the cytoplasm (IBA) row and in core_functions. |
| 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:0005524 ATP binding | IEA GO_REF:0000043 | NEW | Summary: ATP binding via the canonical Walker A (P-loop) motif GSPGSGKS at residues 31-38 (UniProt BINDING 31..39, ATP; ChEBI:30616). Present in UniProt as a keyword-derived IEA annotation and directly supported by the crystal structure and the intact P-loop identified bioinformatically. This is a core molecular function underlying the enzyme's ATP-dependent kinase/ATPase activity. Reason: ATP binding is a genuine UniProt annotation (GO:0005524, IEA from UniProtKB keyword) that is not present as a row in the GOA TSV; it is added here as a NEW core molecular function because it is well supported by the Walker A P-loop (structure + sequence) and is the mechanistic basis for the accepted kinase and ATP-hydrolysis activities. 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 P-loop (Walker A) glycine-rich loop is detected at |
| 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):
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