Discoidin domain receptor (Ddr), the single Drosophila member of the DDR receptor family. The full-length 1054-residue product is a type I transmembrane receptor with an extracellular discoidin (F5/8 type C) domain, a single transmembrane helix and a cytoplasmic tyrosine-kinase-like domain; a shorter isoform lacks the transmembrane and kinase regions. Ddr is required in peripheral wrapping glia for ensheathment of larval axons, and glial Ddr is needed in adult wing nerves for normal axon caliber and long-term survival of sensory neurons. It interacts genetically with the type XV/XVIII collagen Multiplexin, which is a candidate ligand, but no ligand has been shown to bind or activate fly Ddr. Unlike vertebrate DDR1/DDR2, the dipteran kinase domain lacks the beta3 lysine, catalytic-loop asparagine and DFG aspartate, so Ddr is predicted to be a pseudokinase, and the residues forming the vertebrate collagen-binding pocket are not conserved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro kinase-domain mapping (IPR001245) to protein kinase activity. Ddr has a full-length kinase domain, but the 1054-residue receptor has lost the beta3 lysine, the catalytic-loop asparagine and the DFG aspartate, a pattern shared with other dipteran Ddr orthologues. Reason: The domain match is real, but the mapping assumes catalytic competence. Alignment with human DDR2 shows Ala789 at the beta3 lysine (DDR2 Lys608), Ser897 at the catalytic-loop asparagine (Asn715) and Ser910 at the DFG aspartate (Asp728); D. virilis and Anopheles Ddr have the same three losses, whereas Tribolium DDR and C. elegans ddr-2 keep all three (the honeybee model keeps two and C. elegans ddr-1 one, with a different pattern). Dipteran Ddr is therefore predicted to be a pseudokinase. Kinase activity of fly Ddr has never been assayed (PMID:36355066 studied only genetics), so the loss is a prediction rather than a measurement; the annotation is marked as an over-annotation instead of removed. Supporting Evidence: file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md D. melanogaster Ddr retains the HRD aspartate but has lost three residues that are required for phosphotransfer in canonical protein kinases file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md Dipteran Ddr is therefore predicted to be a pseudokinase |
| GO:0005518 collagen binding | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA from the DDR node PTN002400507, seeded by human/mouse/rat DDR1 and DDR2 collagen binding. No binding of any collagen to fly Ddr has been shown. Reason: The IBD at PTN002400507 is well grounded for vertebrate DDRs, and fly Ddr is inside that clade. The question is whether the inherited collagen recognition holds on the dipteran branch. Target-specific evidence argues for divergence: the DDR2 residues that line the collagen pocket (Trp52, Asp69, Thr56, Asn175) are replaced in fly Ddr (His128, Gly146, Val133, Thr252) and in every invertebrate DDR examined, and insects lack the fibrillar collagens that carry the GVMGFO DDR-binding motif. The only fly collagen candidate, Multiplexin, comes from a dominant genetic interaction that the authors present as a model, not a binding result. Collagen binding is therefore plausible but unestablished; not removed because a different binding mode for a non-fibrillar collagen cannot be excluded. Propagation Review Root cause: UNRESOLVED Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN002400507 UNRESOLVED The node correctly captures vertebrate DDR1/DDR2 collagen binding; whether it holds for dipteran Ddr is unresolved because the vertebrate collagen-binding pocket residues are not conserved and no fly binding assay exists. Supporting Evidence: file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md The pocket that recognises the GVMGFO motif of fibrillar collagens in vertebrates is thus not conserved in invertebrates PMID:36355066 the strong genetic interaction we observed between Ddr and Mp is consistent with a model in which Mp acts as a collagen ligand for Ddr during axonal ensheathment |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | UNDECIDED | Summary: InterPro kinase-domain mapping (IPR000719) to ATP binding. Reason: The glycine-rich loop (LGSGVFGE, DDR2 LGEGQFGE) is kept, but the beta3 lysine and DFG aspartate that coordinate ATP phosphates and Mg2+ are lost in fly Ddr. Pseudokinases differ in whether they still bind nucleotide, and no nucleotide-binding assay on fly Ddr exists, so this cannot be decided from sequence. Supporting Evidence: file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md D. melanogaster Ddr retains the HRD aspartate but has lost three residues that are required for phosphotransfer in canonical protein kinases |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from the receptor tyrosine kinase node PTN001230349 for plasma membrane. Reason: Ddr has the receptor architecture of its family: extracellular discoidin domain, a single predicted transmembrane helix (Phobius 501-525) and a cytoplasmic kinase-like domain. Corty et al. treat it as a cell-surface receptor of wrapping glia whose function depends on its presence in those cells. Kinase-domain degeneration does not affect the membrane location claim. Accept; the IBA is the location of the core receptor function. Supporting Evidence: file:DROME/Ddr/Ddr-uniprot.txt TRANSMEM 501..525 PMID:36355066 Drosophila Ddr encodes a cell surface receptor tyrosine kinase homologous to vertebrate Ddr1 and Ddr2. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0039 cell membrane) to plasma membrane. Reason: The UniProt location line is an ARBA prediction, but it agrees with the Phobius transmembrane segment and with the domain architecture of a type I receptor; consistent with the accepted IBA row for the same term. Supporting Evidence: file:DROME/Ddr/Ddr-uniprot.txt TRANSMEM 501..525 |
| GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway | IBA GO_REF:0000033 | UNDECIDED | Summary: PAINT IBA from the receptor tyrosine kinase node PTN001230349 for cell surface receptor protein tyrosine kinase signaling pathway. Reason: Fly Ddr is a family member of the receptor tyrosine kinases and is required in wrapping glia, alongside EGFR and Heartless, for axon ensheathment, so participation in a receptor-tyrosine-kinase-type pathway is plausible. But its kinase domain lacks the catalytic residues, and nothing is known about its ligand, its phosphorylation or its downstream effectors. Pseudokinase receptors (e.g. ERBB3) can signal through kinase-active partners, so the term is not excluded; equally it is not supported by any fly data. Left undecided pending an experiment on Ddr phosphorylation and partners. Propagation Review Root cause: UNRESOLVED Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN001230349 UNRESOLVED The receptor tyrosine kinase node is sound for catalytically active members; whether a dipteran Ddr with lost catalytic residues still takes part in receptor-tyrosine-kinase signalling (for example through a kinase-active partner) is untested. Supporting Evidence: file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md Dipteran Ddr is therefore predicted to be a pseudokinase PMID:36355066 Ddr joins two other receptor tyrosine kinases – EGFR and FGFR – as important and conserved regulators of axon ensheathment |
| GO:0038062 protein tyrosine kinase collagen receptor activity | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBA from the DDR node PTN002400507 for protein tyrosine kinase collagen receptor activity, seeded by human DDR1/DDR2 (IDA) and mouse/rat orthologues. Reason: The term claims three things: a transmembrane receptor, a tyrosine kinase, and collagen as ligand. Only the first is supported for fly Ddr. The IBD is sound for vertebrate DDRs, and the target is inside the clade, but there is target-specific evidence of divergence: dipteran Ddr has lost the beta3 lysine, catalytic-loop asparagine and DFG aspartate (predicted pseudokinase), and the vertebrate collagen-binding pocket is not conserved. No collagen has been shown to bind or activate fly Ddr; Multiplexin is a genetic candidate only (module collagen_ddr_signaling records this as a knowledge gap). The receptor part is supported by the type I transmembrane architecture and by the requirement for Ddr within wrapping glia, rescued by glial Ddr. Replace with transmembrane signaling receptor activity, which keeps the receptor claim without asserting kinase activity or a collagen ligand. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN002400507 SUPPORTS SOURCE BUT NOT TARGET The node is well grounded by vertebrate DDR1/DDR2 IDA, but fly Ddr has lost the kinase catalytic residues (shared with other Diptera) and the vertebrate collagen-pocket residues, so the kinase and collagen parts of the term do not transfer. Proposed replacements: transmembrane signaling receptor activity Supporting Evidence: file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md D. melanogaster Ddr retains the HRD aspartate but has lost three residues that are required for phosphotransfer in canonical protein kinases file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md The pocket that recognises the GVMGFO motif of fibrillar collagens in vertebrates is thus not conserved in invertebrates PMID:36355066 Similar phenotypes were observed in Ddr loss-of-function animals and could be rescued by resupplying Ddr specifically in wrapping glia, confirming the specificity of our RNAi results. file:DROME/Ddr/Ddr-uniprot.txt TRANSMEM 501..525 |
| GO:0038063 collagen-activated tyrosine kinase receptor signaling pathway | IEA GO_REF:0000108 | MARK AS OVER ANNOTATED | Summary: Inter-ontology inference (GO_REF:0000108) from GO:0038062 to collagen-activated tyrosine kinase receptor signaling pathway. Reason: This row is derived mechanically from the GO:0038062 IBA, which this review modifies to a receptor activity without kinase or collagen components. No collagen has been shown to activate fly Ddr, and the kinase domain is predicted to be catalytically inactive. The genetic interaction with the collagen Multiplexin in axon ensheathment keeps a collagen-Ddr pathway plausible, so the row is marked as an over-annotation rather than removed. Supporting Evidence: PMID:36355066 the strong genetic interaction we observed between Ddr and Mp is consistent with a model in which Mp acts as a collagen ligand for Ddr during axonal ensheathment file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md Dipteran Ddr is therefore predicted to be a pseudokinase |
| GO:0043235 signaling receptor complex | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA from the receptor tyrosine kinase node PTN001230349 for signaling receptor complex. Reason: Receptor tyrosine kinases, including DDR1 and DDR2, act as dimers or larger receptor assemblies, and a pseudokinase receptor would be expected to work in a complex with a partner. No complex containing fly Ddr has been characterised, so the broad term is kept as a phylogenetic inference but not as a core annotation. Supporting Evidence: PMID:24725424 The DDRs are unusual RTKs in that they form ligand-independent stable dimers that are non-covalently linked |
| GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA from node PTN008618212 (donors rat and human receptor tyrosine kinases, e.g. NTRK3) for positive regulation of PI3K/AKT signal transduction. Reason: This is a downstream output of active receptor tyrosine kinase signalling in vertebrates. No PI3K/Akt link has been examined for fly Ddr, and its kinase domain is predicted to be inactive, which removes the usual route (phosphotyrosine docking sites for PI3K regulatory subunits). The human DDR2 review keeps this as non-core because DDR2 is an active kinase; for fly Ddr the propagation is not supported. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN008618212 SUPPORTS SOURCE BUT NOT TARGET Node donors are active vertebrate receptor tyrosine kinases; the downstream PI3K/AKT output depends on kinase activity that dipteran Ddr is predicted to lack. Supporting Evidence: file:DROME/Ddr/Ddr-bioinformatics/RESULTS.md Dipteran Ddr is therefore predicted to be a pseudokinase |
| GO:0032285 non-myelinated axon ensheathment | IMP PMID:36355066 Discoidin domain receptor regulates ensheathment, survival a... | NEW | Summary: Ddr is required in Drosophila peripheral wrapping glia for ensheathment of larval axons; null mutants and glial RNAi reduce wrapping, and wrapping-glia-specific Ddr rescues the mutant. Reason: Participation test: Ddr acts in the wrapping glia, the cells that perform the ensheathment, and glial re-expression rescues the defect, so it is part of the ensheathing cell machinery rather than a substrate or a remote requirement. Fly wrapping glia ensheath axons without myelin, so non-myelinated axon ensheathment is the right specificity; GO:0032294 was avoided because its definition is restricted to Schwann cells. Comparator: FlyBase annotates other wrapping-glia genes (e.g. bdl, wrapper, fray, Nrg) to the parent GO:0008366 axon ensheathment by IMP; this paper has not been curated to GO for Ddr. Supporting Evidence: PMID:36355066 In an in vivo RNA interference screen to identify glial genes required for axon ensheathment, we identified the conserved receptor tyrosine kinase Discoidin domain receptor (Ddr). PMID:36355066 Similar phenotypes were observed in Ddr loss-of-function animals and could be rescued by resupplying Ddr specifically in wrapping glia, confirming the specificity of our RNAi results. PMID:36355066 In larval peripheral nerves, loss of Ddr resulted in severely reduced ensheathment of axons and reduced axon caliber |
| GO:0031133 regulation of axon diameter | IMP PMID:36355066 Discoidin domain receptor regulates ensheathment, survival a... | NEW | Summary: Glial Ddr is required for normal caliber of the identified dTSM sensory axon in the adult wing nerve, even where ensheathment looks normal. Reason: Both whole-animal Ddr mutants and wrapping-glia-specific RNAi reduce dTSM axon caliber by up to about 50%, separable from the larval wrapping defect. The effect is non-cell-autonomous (glia to axon), which fits a regulation term. Kept out of core functions because the signal from glia to axon is unknown. Supporting Evidence: PMID:36355066 We found that in both glial-specific Ddr knockdown and Ddr whole animal mutant nerves the caliber of the dTSM axon was significantly reduced compared with controls PMID:36355066 The reductions in caliber were similar between Ddr mutants and glial-specific DdrRNAi, supporting a non-cell-autonomous role for glial Ddr in regulating axon caliber. |
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Download this section (compressed HTML)Q: Is Drosophila Ddr a pseudokinase, and does it act as a co-receptor for EGFR or Heartless in wrapping glia?
Q: Should the PAINT DDR node PTN002400507 carry an IRD/loss for kinase activity and collagen binding on the dipteran branch, given the shared loss of the catalytic lysine, asparagine and DFG aspartate?
Q: What is the role of the 380-residue extracellular-only Ddr isoform: a decoy receptor or a secreted matrix-binding protein?
Experiment: Test kinase activity and ATP binding of the purified Ddr intracellular domain (thermal-shift with ATP/Mg2+, autophosphorylation), with human DDR1 as positive control.
Experiment: Test direct binding of the Ddr ectodomain to Multiplexin and to collagen IV, and whether Mp increases Ddr tyrosine phosphorylation in cultured cells or glia.
Experiment: Rescue Ddr nulls in wrapping glia with kinase-domain-deleted Ddr and with a variant restoring Lys789, to ask whether the kinase-like domain is needed for ensheathment and axon caliber.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The extracellular ligand of Drosophila Ddr is unknown: no collagen or other matrix protein has been shown to bind or activate it, and the vertebrate collagen-binding pocket is not conserved.
BIOLOGY MF_DARK
What is known: Established: Ddr is required in wrapping glia for larval axon ensheathment and interacts genetically (dominantly) with the type XV/XVIII collagen Multiplexin. Not established: any physical interaction.
Significance: Decides whether the collagen-DDR pathway exists in insects, and whether the IBA collagen-binding annotation holds for the dipteran branch.
What would resolve it: Binding assays of the Ddr ectodomain with Multiplexin and collagen IV (Col4a1/viking), and Ddr phosphorylation or partner recruitment after ligand exposure in S2 cells or glia.
Gap: How Ddr signals is unknown: its kinase domain lacks the beta3 lysine, catalytic-loop asparagine and DFG aspartate, and no phosphorylation, partner or downstream effector has been identified.
BIOLOGY MF_DARK
What is known: Established by sequence: full kinase-like domain with lost catalytic residues, conserved in Diptera. Established genetically: Ddr acts in the same glia as EGFR and Heartless, which are each required for ensheathment.
Significance: Determines whether Ddr is a scaffold or pseudokinase co-receptor (as ERBB3 is) and which pathway terms apply.
What would resolve it: In vitro kinase and nucleotide-binding assays of the Ddr intracellular domain; rescue of Ddr mutants with kinase-domain deletion or with the beta3 Ala reverted to Lys; co-immunoprecipitation with EGFR and Heartless from glia.
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