KDX1 (commonly called MLP1 in the primary literature; systematic name YKL161C) is a degenerate protein-kinase-fold protein of budding yeast, a paralog of the cell wall integrity (CWI) MAP kinase SLT2/MPK1 that arose from the whole-genome duplication. Despite retaining a recognizable protein-kinase domain, KDX1 is a catalytically inactive pseudokinase: its activation-loop DFG motif is degenerate (Asp->Asn) and it lacks the MAPK TEY dual-phosphorylation motif that activates SLT2, so it cannot function as a conventional MAP kinase. KDX1 acts in the CWI signaling pathway downstream of the Mkk1/Mkk2 MEKs. Its best-characterized activity is non-catalytic: activated (phosphorylated) KDX1, like activated SLT2, binds the DNA-binding transcription factor Swi4 and, together with Swi6 (the SBF complex), drives transcription of cell wall stress genes such as FKS2, functioning redundantly with SLT2 in this branch. KDX1 was originally identified as an Rlm1-associated protein and physically interacts with the MADS-box transcription factor Rlm1. KDX1 protein is scarce under normal growth but accumulates strongly when the cell wall is stressed, because MLP1 is itself a transcriptional target of the SLT2->Rlm1 arm of the same pathway.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: This cellular compartment is compatible with the retained CWI signaling role. Reason: Primary PMID:18268013 detects Mlp1/Kdx1 in the Swi4/Swi6 complex at the FKS2 promoter, independently supporting nuclear activity. Nuclear localization is part of the characterized transcriptional mechanism; being a cellular-component term rather than a molecular function is not a reason to call it non-core. Supporting Evidence: PMID:18268013 Activated (phosphorylated) Mpk1 and Mlp1 were detected in a complex with Swi4 and Swi6 at the FKS2 promoter. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: This cellular compartment is compatible with the retained CWI signaling role. Reason: The cytoplasmic IBA descends from PTN000623979 and is compatible with upstream CWI signaling to Kdx1/Mlp1. The characterized nuclear promoter pool does not exclude a cytoplasmic pool. No target-specific evidence of loss of this inherited localization was identified; retain the inferred location without claiming exclusive residency or a direct target microscopy assay. |
| GO:0051726 regulation of cell cycle | IBA GO_REF:0000033 | UNDECIDED | Summary: The inherited noncatalytic claim requires separate assessment from loss of protein kinase activity. Reason: Current PAINT target leaf PTN000623199 retains this annotation. The relevant source node is PANTHER:PTN001172579. PMID:20641022 distinguishes the noncatalytic CWI/SBF transcription route from ordinary G1 transcription; this limits what those assays establish but does not exclude a separate role in cell-cycle control or transitions. A specialized stress function and kinase inactivity are insufficient to refute process participation. Prior claims of wrong-paralog propagation were stronger than the reconstructed evidence. The source includes characterized cell-cycle kinases, but no complete family tree/MSA was examined to establish that ancestral node placement is wrong. A focused OpenScientist investigation has been requested; the source row is preserved pending that assessment. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN001172579 UNRESOLVED Verified ancestral IBD identifier in the source and current PAINT. Target retention or loss of this process/complex function remains unresolved independently of kinase catalytic loss. |
| GO:0000082 G1/S transition of mitotic cell cycle | IBA GO_REF:0000033 | UNDECIDED | Summary: The inherited noncatalytic claim requires separate assessment from loss of protein kinase activity. Reason: Current PAINT target leaf PTN000623199 retains this annotation. The relevant source node is PANTHER:PTN001172579. PMID:20641022 distinguishes the noncatalytic CWI/SBF transcription route from ordinary G1 transcription; this limits what those assays establish but does not exclude a separate role in cell-cycle control or transitions. A specialized stress function and kinase inactivity are insufficient to refute process participation. Prior claims of wrong-paralog propagation were stronger than the reconstructed evidence. The source includes characterized cell-cycle kinases, but no complete family tree/MSA was examined to establish that ancestral node placement is wrong. A focused OpenScientist investigation has been requested; the source row is preserved pending that assessment. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN001172579 UNRESOLVED Verified ancestral IBD identifier in the source and current PAINT. Target retention or loss of this process/complex function remains unresolved independently of kinase catalytic loss. |
| GO:0000307 cyclin-dependent protein kinase holoenzyme complex | IBA GO_REF:0000033 | UNDECIDED | Summary: The inherited noncatalytic claim requires separate assessment from loss of protein kinase activity. Reason: Current PAINT target leaf PTN000623199 retains this annotation. The relevant source node is PANTHER:PTN000623980. The characterized Mlp1-Swi4/Swi6 complex is not itself a cyclin-CDK holoenzyme, but that does not exclude an additional noncatalytic complex membership. A fungal NOT at PTN008603245 cannot be applied to Kdx1 without establishing the target lies below that node. Prior claims of wrong-paralog propagation were stronger than the reconstructed evidence. The source includes characterized cell-cycle kinases, but no complete family tree/MSA was examined to establish that ancestral node placement is wrong. A focused OpenScientist investigation has been requested; the source row is preserved pending that assessment. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN000623980 UNRESOLVED Verified ancestral IBD identifier in the source and current PAINT. Target retention or loss of this process/complex function remains unresolved independently of kinase catalytic loss. |
| GO:0000086 G2/M transition of mitotic cell cycle | IBA GO_REF:0000033 | UNDECIDED | Summary: The inherited noncatalytic claim requires separate assessment from loss of protein kinase activity. Reason: Current PAINT target leaf PTN000623199 retains this annotation. The relevant source node is PANTHER:PTN000623979. PMID:20641022 distinguishes the noncatalytic CWI/SBF transcription route from ordinary G1 transcription; this limits what those assays establish but does not exclude a separate role in cell-cycle control or transitions. A specialized stress function and kinase inactivity are insufficient to refute process participation. Prior claims of wrong-paralog propagation were stronger than the reconstructed evidence. The source includes characterized cell-cycle kinases, but no complete family tree/MSA was examined to establish that ancestral node placement is wrong. A focused OpenScientist investigation has been requested; the source row is preserved pending that assessment. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN000623979 UNRESOLVED Verified ancestral IBD identifier in the source and current PAINT. Target retention or loss of this process/complex function remains unresolved independently of kinase catalytic loss. |
| GO:0004693 cyclin-dependent protein serine/threonine kinase activity | IBA GO_REF:0000033 | REMOVE | Summary: Target-specific pseudokinase evidence contradicts conventional catalytic phosphotransfer. Reason: Primary PMID:18268013 and PMID:20641022 characterize Mlp1/Kdx1 as a pseudokinase with a noncatalytic transcriptional role; PMID:35420390 independently describes it as catalytically inactive. The Kdx1 sequence has NFG instead of the canonical DFG magnesium-binding motif. Retention of a protein-kinase fold does not make an assertion of kinase activity partly correct. Reject this catalytic transfer on target-specific divergence, without claiming that every hypothetical residual or promiscuous phosphotransfer reaction has been experimentally excluded. This catalytic judgment does not extend to ATP binding, signal transduction, cell-cycle regulation or complex membership. Reproducible alignment also maps the canonical SLT2 Lys54 to Kdx1 Arg54, while the adjacent Lys55 is retained. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN000623980 SUPPORTS SOURCE BUT NOT TARGET The ancestral catalytic assertion is contradicted by target-specific pseudokinase sequence and primary noncatalytic characterization. This is not an argument based on donor count or target self-inclusion. Supporting Evidence: PMID:20641022 Induction was only partially dependent on the Mlp1 pseudokinase (Figure 2), a catalytically inactive paralog of Mpk1 (Kim et al., 2008). file:yeast/KDX1/KDX1-bioinformatics/RESULTS.md The canonical SLT2 ATP-site Lys54 aligns to Arg54 in KDX1. |
| GO:0007165 signal transduction | IBA GO_REF:0000033 | ACCEPT | Summary: Kdx1 directly contributes to CWI signal transmission through a noncatalytic transcription-factor complex. Reason: The broad signal-transduction assertion is biologically correct: activated Kdx1/Mlp1 couples the CWI cascade to Swi4/Swi6-dependent transcription. The more specific cell-integrity MAPK process in core_functions complements this inherited annotation. Specificity preference does not make the broad true process an error. |
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | REMOVE | Summary: Target-specific pseudokinase evidence contradicts conventional catalytic phosphotransfer. Reason: Primary PMID:18268013 and PMID:20641022 characterize Mlp1/Kdx1 as a pseudokinase with a noncatalytic transcriptional role; PMID:35420390 independently describes it as catalytically inactive. The Kdx1 sequence has NFG instead of the canonical DFG magnesium-binding motif. Retention of a protein-kinase fold does not make an assertion of kinase activity partly correct. Reject this catalytic transfer on target-specific divergence, without claiming that every hypothetical residual or promiscuous phosphotransfer reaction has been experimentally excluded. This catalytic judgment does not extend to ATP binding, signal transduction, cell-cycle regulation or complex membership. Reproducible alignment also maps the canonical SLT2 Lys54 to Kdx1 Arg54, while the adjacent Lys55 is retained. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Supporting Evidence: PMID:18268013 its pseudokinase paralog (Mlp1) use a noncatalytic mechanism to activate transcription of the FKS2 gene file:yeast/KDX1/KDX1-bioinformatics/RESULTS.md The canonical SLT2 ATP-site Lys54 aligns to Arg54 in KDX1. |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000120 | REMOVE | Summary: Target-specific pseudokinase evidence contradicts conventional catalytic phosphotransfer. Reason: Primary PMID:18268013 and PMID:20641022 characterize Mlp1/Kdx1 as a pseudokinase with a noncatalytic transcriptional role; PMID:35420390 independently describes it as catalytically inactive. The Kdx1 sequence has NFG instead of the canonical DFG magnesium-binding motif. Retention of a protein-kinase fold does not make an assertion of kinase activity partly correct. Reject this catalytic transfer on target-specific divergence, without claiming that every hypothetical residual or promiscuous phosphotransfer reaction has been experimentally excluded. This catalytic judgment does not extend to ATP binding, signal transduction, cell-cycle regulation or complex membership. Reproducible alignment also maps the canonical SLT2 Lys54 to Kdx1 Arg54, while the adjacent Lys55 is retained. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Supporting Evidence: PMID:35420390 triggered by the binding of phosphorylated forms of both Slt2 and a catalytically inactive pseudokinase (Mlp1) file:yeast/KDX1/KDX1-bioinformatics/RESULTS.md The canonical SLT2 ATP-site Lys54 aligns to Arg54 in KDX1. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | UNDECIDED | Summary: ATP binding remains unresolved independently of catalytic inactivity. Reason: Reproducible alignment of cached Kdx1/P36005 with SLT2/Q00772 maps the canonical beta3 ATP-site Lys54 to Arg54 in Kdx1; the neighboring Lys55 is retained. The earlier claim that K55 establishes retention of the invariant ATP-site lysine was therefore incorrect. Primary PMID:20641022 characterizes the equivalent Mpk1-K54R mutant as catalytically inactive. These substitutions strengthen the pseudokinase interpretation but do not establish inability to bind ATP. Preserve this separate biochemical question as UNDECIDED pending direct binding evidence and the focused report. Supporting Evidence: file:yeast/KDX1/KDX1-bioinformatics/RESULTS.md The canonical SLT2 ATP-site Lys54 aligns to Arg54 in KDX1. |
| GO:0007165 signal transduction | IEA GO_REF:0000117 | ACCEPT | Summary: Kdx1 directly contributes to CWI signal transmission through a noncatalytic transcription-factor complex. Reason: The broad signal-transduction assertion is biologically correct: activated Kdx1/Mlp1 couples the CWI cascade to Swi4/Swi6-dependent transcription. The more specific cell-integrity MAPK process in core_functions complements this inherited annotation. Specificity preference does not make the broad true process an error. |
| GO:0009272 fungal-type cell wall biogenesis | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: KDX1 contributes to the transcriptional response that maintains/remodels the cell wall under stress (e.g. FKS2 induction with SBF), so a role in fungal-type cell wall biogenesis is defensible, if indirect. Retained as a non-core biological-process annotation. Reason: Kdx1 directly regulates the transcriptional response controlling cell-wall-maintenance genes such as FKS2. Retain fungal cell-wall biogenesis as a broader physiological output of that mechanism, while the core function records its immediate noncatalytic signaling and transcription-factor interaction. Supporting Evidence: PMID:20641022 a common mechanism that involves activation of Mpk1 and Mlp1 to engage Swi4 and Swi6 |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | REMOVE | Summary: Target-specific pseudokinase evidence contradicts conventional catalytic phosphotransfer. Reason: Primary PMID:18268013 and PMID:20641022 characterize Mlp1/Kdx1 as a pseudokinase with a noncatalytic transcriptional role; PMID:35420390 independently describes it as catalytically inactive. The Kdx1 sequence has NFG instead of the canonical DFG magnesium-binding motif. Retention of a protein-kinase fold does not make an assertion of kinase activity partly correct. Reject this catalytic transfer on target-specific divergence, without claiming that every hypothetical residual or promiscuous phosphotransfer reaction has been experimentally excluded. This catalytic judgment does not extend to ATP binding, signal transduction, cell-cycle regulation or complex membership. Reproducible alignment also maps the canonical SLT2 Lys54 to Kdx1 Arg54, while the adjacent Lys55 is retained. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Supporting Evidence: file:yeast/KDX1/KDX1-bioinformatics/RESULTS.md The canonical SLT2 ATP-site Lys54 aligns to Arg54 in KDX1. |
| GO:0008150 biological_process | ND GO_REF:0000015 | REMOVE | Summary: Root-level placeholder (ND) indicating no biological-process data at time of assignment. Superseded by the specific CWI/transcription annotations in this review. Reason: Uninformative root placeholder; standard handling is removal once specific annotations exist. |
| GO:0004674 protein serine/threonine kinase activity | ISS PMID:20489023 A global protein kinase and phosphatase interaction network ... | REMOVE | Summary: Target-specific pseudokinase evidence contradicts conventional catalytic phosphotransfer. Reason: Primary PMID:18268013 and PMID:20641022 characterize Mlp1/Kdx1 as a pseudokinase with a noncatalytic transcriptional role; PMID:35420390 independently describes it as catalytically inactive. The Kdx1 sequence has NFG instead of the canonical DFG magnesium-binding motif. Retention of a protein-kinase fold does not make an assertion of kinase activity partly correct. Reject this catalytic transfer on target-specific divergence, without claiming that every hypothetical residual or promiscuous phosphotransfer reaction has been experimentally excluded. This catalytic judgment does not extend to ATP binding, signal transduction, cell-cycle regulation or complex membership. Reproducible alignment also maps the canonical SLT2 Lys54 to Kdx1 Arg54, while the adjacent Lys55 is retained. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Supporting Evidence: PMID:20641022 Induction was only partially dependent on the Mlp1 pseudokinase (Figure 2), a catalytically inactive paralog of Mpk1 (Kim et al., 2008). file:yeast/KDX1/KDX1-bioinformatics/RESULTS.md The canonical SLT2 ATP-site Lys54 aligns to Arg54 in KDX1. |
| GO:0005575 cellular_component | ND GO_REF:0000015 | REMOVE | Summary: Root-level placeholder (ND). Superseded by the nucleus/cytoplasm localization annotations. Reason: Uninformative root placeholder; standard handling is removal once specific annotations exist. |
| GO:0140297 DNA-binding transcription factor binding | IPI PMID:18268013 Yeast Mpk1 mitogen-activated protein kinase activates transc... | NEW | Summary: Proposed new annotation capturing KDX1/Mlp1's actual, experimentally supported molecular function: activated (phosphorylated) KDX1 binds the DNA-binding transcription factor Swi4 (and is detected in a Swi4/Swi6 complex at the FKS2 promoter), a non-catalytic scaffold role that replaces the mis-propagated catalytic kinase functions. This is the MF used in core_functions. Reason: KDX1 is a pseudokinase whose characterized function is binding a DNA-binding transcription factor (Swi4) rather than phosphotransfer; this term expresses that function and avoids the uninformative "protein binding". Supporting Evidence: PMID:18268013 Activated (phosphorylated) Mpk1 and Mlp1 were detected in a complex with Swi4 and Swi6 at the FKS2 promoter. PMID:20641022 the binding of activated (phosphorylated) Mpk1, or its pseudokinase paralog, Mlp1, to the Swi4 transcription factor |
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Download this section (compressed HTML)Q: Does KDX1/Mlp1 retain any Mg-ATP-dependent phosphotransfer activity in vitro, or is it biochemically catalytically dead as its degenerate DFG motif and the pseudokinase literature predict?
Suggested experts: Yeast cell wall integrity / MAP kinase signaling biologists, Pseudokinase biochemists
Q: Beyond redundancy with SLT2 in the SBF branch, does KDX1 have any non-overlapping, stress-specific function that explains retention of this whole-genome-duplication paralog?
Suggested experts: Yeast CWI signaling biologists
Q: Can the known Kdx1-Swi4 transcriptional mechanism be represented with existing transcription-factor-binding or coactivator concepts rather than a bespoke pseudokinase scaffold term?
Experiment: Purify recombinant KDX1 (and, as a positive control, active SLT2) and assay Mg-ATP-dependent autophosphorylation and phosphorylation of candidate substrates (e.g. Rlm1, generic MAPK substrates) in vitro, including a nucleotide-binding assay to test whether the intact beta3 lysine still supports ATP binding despite the degenerate DFG.
Hypothesis: KDX1/Mlp1 is catalytically inactive and cannot phosphorylate protein substrates.
Type: in vitro kinase / nucleotide-binding assay
Experiment: Complement an mpk1-delta mlp1-delta strain with wild-type KDX1 versus a KDX1 variant mutated at its (pseudo)active site or at the MEK-phosphoacceptor residues, and measure FKS2/CHA1/ YLR042c reporter induction under cell wall stress to separate the requirement for KDX1 binding from any residual catalysis.
Hypothesis: KDX1 activates Swi4/Swi6-dependent transcription purely non-catalytically, via its ability to bind Swi4 when phosphorylated by the upstream MEKs.
Type: genetic complementation with transcriptional reporters
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Whether KDX1/Mlp1 has any residual protein kinase catalytic (phosphotransfer) activity in vivo is undetermined; no physiological substrate has been demonstrated and the field treats it as catalytically dead.
OPEN BIOLOGY MF_DARK
What is known: Reproducible SLT2-Kdx1 alignment places canonical SLT2 K54 at Kdx1 R54 and D171 at N171, whereas neighboring K55 and catalytic-loop D153 remain. Mlp1 is consistently described as a catalytically inactive pseudokinase with a noncatalytic transcriptional role. Retention of adjacent K55 does not restore the canonical ATP-site lysine; direct nucleotide binding and any residual phosphotransfer remain distinct questions.
Significance: Determine whether this divergent pseudokinase retains nucleotide-dependent conformational regulation or a residual activity outside its established noncatalytic role; sequence fold retention alone cannot support a conventional kinase annotation.
What would resolve it: In vitro kinase assay with recombinant KDX1 (and active SLT2 as positive control) testing autophosphorylation and phosphorylation of candidate substrates, plus a nucleotide-binding assay.
Provenance (the field's own admissions):
Gap: The full set of KDX1/Mlp1 direct binding partners and any additional (non-Swi4, non-Rlm1) scaffolding targets are unknown.
OPEN BIOLOGYCURATION MF_DARK
What is known: KDX1 is documented to bind Swi4 (contributing to SBF-dependent FKS2 transcription) and to physically associate with the MADS-box transcription factor Rlm1, and it appears in the global yeast kinase/phosphatase interaction network. A comprehensive, KDX1-specific interactome distinguishing direct from indirect partners has not been reported.
Significance: Identifying KDX1's direct partners would define whether its scaffolding role extends beyond the Swi4/Swi6 and Rlm1 branches of CWI signaling and could reveal a function not shared with SLT2.
What would resolve it: Targeted affinity-purification/proximity-labeling of tagged KDX1 under cell wall stress, with validation of direct interactions.
Provenance (the field's own admissions):
Gap: The non-redundant (unique) biological role of KDX1/Mlp1 relative to SLT2/MPK1 is undefined: no phenotype has been shown to depend on KDX1 with SLT2 intact.
OPEN BIOLOGY BP_DARK
What is known: In every characterized context KDX1 is only partially required and functionally overlaps with SLT2; the non-catalytic SBF branch is fully abolished only in an mpk1-delta mlp1-delta double mutant, and KDX1's own expression depends on the SLT2->Rlm1 arm, so little KDX1 protein is present unless SLT2 signaling is active.
Significance: Whether KDX1 provides genuine redundancy/robustness, dosage amplification, or a distinct stress-specific function determines why the whole-genome-duplication paralog was retained and whether it has any non-overlapping role worth targeting or curating separately from SLT2.
What would resolve it: Systematic phenotyping of mlp1-delta (with SLT2 intact) across cell wall and other stresses, and identification of any KDX1-only-dependent transcriptional or phenotypic output.
Provenance (the field's own admissions):
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