CDK5RAP3 (also known as C53, LZAP, IC53) is a 506-residue protein that, despite its name, is not a kinase and has no known catalytic activity. Its principal, well-established function is as a substrate adaptor/recruiter within the UFM1 ribosome E3 ligase (UREL) complex, a heterotrimer composed of the UFM1 E3 ligase UFL1, the ER-anchoring adaptor DDRGK1/UFBP1, and CDK5RAP3. This complex catalyzes UFMylation (covalent attachment of the ubiquitin-like modifier UFM1) of substrate proteins at the cytoplasmic surface of the endoplasmic reticulum. CDK5RAP3 directs the ligase to mono-UFMylate ribosomal protein RPL26/uL24 on the 60S subunit of ER-associated ribosomes; within reconstituted systems it constrains UFL1 activity to achieve this precise substrate selection. Through its RPL10a-binding domain it docks the complex onto the 60S subunit, and the UREL complex wraps around the 60S as a C-shaped clamp to promote release and recycling of 60S subunits from the SEC61 translocon following normal termination or ribosome stalling during co-translational translocation (ER ribosome-associated quality control). The complex also mediates UFM1-dependent reticulophagy (ER-phagy) in response to ER stress, in part through ufmylation of CYB5R3, and CDK5RAP3 binds ATG8-family proteins and UFM1 through shuffled ATG8-interacting motifs. UFMylation-dependent functions underlie its requirement for liver development and erythroid differentiation. CDK5RAP3 localizes to the ER membrane, cytosol, nucleus, centrosome and microtubules/cytoskeleton. A separate, older body of literature describes CDK5RAP3/LZAP/C53 as a putative tumor suppressor modulating NF-kappaB (RelA) signaling, ARF/MDM2/p53 regulation, the mitotic G2/M DNA-damage checkpoint (antagonizing CHEK1), p38 MAPK activity, cell invasion and apoptosis-associated nuclear envelope rupture; these roles derive mainly from overexpression/knockdown studies and are less firmly established than the UFMylation adaptor function.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0012505 endomembrane system | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA annotation placing CDK5RAP3 in the endomembrane system. CDK5RAP3 is indeed part of the ER membrane-tethered UREL complex, so endomembrane system is consistent but very general. Reason: Broad phylogenetic (IBA) localization term subsumed by the more specific and well-evidenced 'endoplasmic reticulum membrane' localization. Retained only as a general grouping term. Supporting Evidence: PMID:38383789 UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other |
| GO:0030968 endoplasmic reticulum unfolded protein response | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA annotation to ER unfolded protein response. The UFMylation pathway is broadly linked to ER homeostasis and UPR, but this is an indirect, transferred process annotation. Reason: ER stress/UPR involvement is supported for the UFM1 system but is a downstream/contextual process rather than the core molecular adaptor function. Keep as non-core. Supporting Evidence: PMID:23152784 the Ufm1 system was transcriptionally up-regulated by disturbance of the ER homeostasis and inhibition of vesicle trafficking |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA molecular function annotation: ubiquitin-like ligase-substrate adaptor activity. This matches the experimentally established core function of CDK5RAP3 as the substrate adaptor of the UREL UFM1 E3 ligase complex. Reason: This is the core molecular function of CDK5RAP3 and is strongly supported by direct experimental evidence; the IBA transfer is concordant. Supporting Evidence: PMID:36121123 CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26 PMID:37595036 CDK5RAP3, an adaptor for ufmylation of ribosomal subunit RPL26 |
| GO:0007346 regulation of mitotic cell cycle | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA annotation to regulation of mitotic cell cycle. CDK5RAP3/C53 has reported roles at the G2/M checkpoint and Cdk1 activation, but as an IBA-transferred general process term. Reason: Mitotic cell cycle regulation reflects the older C53/LZAP checkpoint literature and is a non-core, pleiotropic role relative to the UFMylation adaptor function. Supporting Evidence: PMID:19223857 C53 promotes Cdk1 activation and mitotic entry in both unperturbed cell-cycle progression and DNA damage response |
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: IEA localization to nucleus from UniProt subcellular-location mapping. Nuclear localization of CDK5RAP3/LZAP is reported experimentally. Reason: Nuclear localization is documented but is secondary to the ER/cytosolic site of the core UFMylation function. Supporting Evidence: PMID:16173922 Expression of LZAP also caused activation of p53 and a p53-dependent G1 cell-cycle arrest |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: IEA localization to cytoplasm (combined automated methods, transferred from mouse ortholog). Cytoplasmic localization is well documented. Reason: Cytoplasmic/cytosolic localization is consistent with multiple experimental reports and with the cytosolic pool of CDK5RAP3. Supporting Evidence: PMID:15790566 C53 and cyclin B1 co-localize and associate in vivo |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: IEA localization to ER membrane from UniProt subcellular-location mapping. This matches the experimentally determined ER-membrane tethering of the UREL complex. Reason: ER membrane localization is strongly supported by direct evidence; the IEA call is concordant with the core function site. Supporting Evidence: PMID:38383789 UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other |
| GO:0005813 centrosome | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: IEA localization to centrosome from UniProt subcellular-location mapping; consistent with the IDA centrosome annotation (PMID:19223857). Reason: Centrosome localization is experimentally reported but reflects a non-core, cell-cycle-associated pool of the protein. Supporting Evidence: PMID:19223857 a portion of C53 protein is localized at the centrosome |
| GO:0005856 cytoskeleton | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: IEA localization to cytoskeleton from UniProt subcellular-location mapping; CDK5RAP3 associates with microtubules, especially after caspase cleavage. Reason: Cytoskeleton/microtubule association is experimentally reported (apoptosis context) but is non-core relative to the UFMylation function. Supporting Evidence: PMID:23478299 C53/LZAP bound indirectly to the microtubule (MT) |
| GO:0005515 protein binding | IPI PMID:16169070 A human protein-protein interaction network: a resource for ... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:16169070 A human protein-protein interaction network: a resource for annotating the proteome. |
| GO:0005515 protein binding | IPI PMID:17785205 LZAP, a putative tumor suppressor, selectively inhibits NF-k... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:17785205 LZAP directly bound to RelA |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:25416956 proteome-scale map of the human interactome network |
| GO:0005515 protein binding | IPI PMID:25910212 Widespread macromolecular interaction perturbations in human... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:25910212 widespread macromolecular interaction perturbations in human genetic disorders |
| GO:0005515 protein binding | IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:31515488 disruption of protein interactions by genetic variants |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:32296183 reference map of the human binary protein interactome |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:33961781 dual proteome-scale networks reveal cell-specific remodeling of the human interactome |
| GO:0005515 protein binding | IPI PMID:37595036 Mechanistic insights into the roles of the UFM1 E3 ligase co... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:37595036 The E3 complex consisting of UFL1 and UFBP1 interacted with UFC1... and, subsequently, CDK5RAP3 |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' (GO:0005515) IPI annotation from a high-throughput or pairwise interaction dataset. Uninformative regarding molecular function. Reason: Per curation guidelines, bare 'protein binding' should not be retained as a core function. Specific interactions (e.g. with UFL1/UFC1) are captured by more informative terms elsewhere in this review. Supporting Evidence: PMID:40205054 Multimodal cell maps as a foundation for structural and functional genomics. |
| GO:0001889 liver development | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA annotation to liver development, transferred from mouse ortholog (Q99LM2). Cdk5rap3 knockout mice show severe liver hypoplasia. Reason: Liver development is a downstream physiological consequence of the UFMylation adaptor role, well supported in mouse but non-core for the molecular function. Supporting Evidence: PMID:30635284 Cdk5rap3 knockout mice displayed prenatal lethality with severe liver hypoplasia, as characterized by delayed proliferation and compromised differentiation |
| GO:0034976 response to endoplasmic reticulum stress | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA annotation to response to ER stress, transferred from mouse ortholog. Consistent with UFM1-system role in ER homeostasis. Reason: ER stress response is a contextual/downstream process for the UFMylation pathway; keep as non-core. Supporting Evidence: PMID:32851973 C53, that is specifically recruited to autophagosomes during ER-stress |
| GO:0044389 ubiquitin-like protein ligase binding | IEA GO_REF:0000107 | ACCEPT | Summary: IEA annotation to ubiquitin-like protein ligase binding (UFL1 binding), transferred from mouse ortholog. Concordant with the IDA annotation from PMID:20531390 and the well-established CDK5RAP3-UFL1 interaction. Reason: Binding to the UFM1 E3 ligase UFL1 is a defining, directly evidenced interaction underlying the UREL complex; this is an informative MF distinct from bare protein binding. Supporting Evidence: PMID:38383789 the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 PMID:20164180 we identify NLBP as a novel LZAP-binding protein using tandem affinity purification |
| GO:0060318 definitive erythrocyte differentiation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA annotation to definitive erythrocyte differentiation, transferred from mouse ortholog; the UFM1 system is required for erythroid differentiation. Reason: Erythroid differentiation is a downstream physiological role of the UFMylation pathway; non-core for CDK5RAP3 molecular function. Supporting Evidence: PMID:23152784 the Ufm1-activating enzyme Uba5 is indispensible for erythroid differentiation in mice |
| GO:0071569 protein ufmylation | IEA GO_REF:0000107 | ACCEPT | Summary: IEA annotation to protein ufmylation, transferred from mouse ortholog. This is the core biological process of CDK5RAP3 and is strongly supported by direct human evidence. Reason: Protein ufmylation is the central pathway in which CDK5RAP3 acts as substrate adaptor; concordant with multiple IDA annotations. Supporting Evidence: PMID:36121123 CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26 |
| GO:0005829 cytosol | IDA GO_REF:0000052 | ACCEPT | Summary: IDA localization to cytosol from HPA immunofluorescence. Consistent with the cytosolic pool of CDK5RAP3 that is recruited to the ER/autophagosomes. Reason: Cytosolic localization is directly supported and consistent with the reported behaviour of CDK5RAP3 as a cytosolic protein engaging the ER membrane. Supporting Evidence: PMID:32851973 we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress |
| GO:0071569 protein ufmylation | IDA PMID:36121123 A non-canonical scaffold-type E3 ligase complex mediates pro... | ACCEPT | Summary: IDA annotation to protein ufmylation (ComplexPortal) based on the reconstituted UFM1 E3 ligase complex. Directly supports the core ufmylation role. Reason: Direct biochemical reconstitution demonstrates CDK5RAP3 participation in protein ufmylation as part of the active E3 complex. Supporting Evidence: PMID:36121123 CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26 |
| GO:1990234 transferase complex | IPI PMID:36121123 A non-canonical scaffold-type E3 ligase complex mediates pro... | ACCEPT | Summary: IPI annotation: CDK5RAP3 is part of a transferase complex (the UFM1 E3 ligase / UREL complex). Reason: CDK5RAP3 is a bona fide subunit of the UREL UFM1 transferase complex (ComplexPortal CPX-8304); part_of is appropriate. Supporting Evidence: PMID:36121123 CDK5RAP3 that binds to and forms an integral part of the ligase complex |
| GO:0072344 rescue of stalled cytosolic ribosome | IMP PMID:32851973 A cross-kingdom conserved ER-phagy receptor maintains endopl... | ACCEPT | Summary: IMP annotation to rescue of stalled cytosolic ribosome. CDK5RAP3, via UFMylation, promotes recycling/rescue of stalled ribosomes at the ER. Reason: Ribosome rescue/recycling is a core function of the UREL complex; supported by IMP here and by structural/biochemical IDA evidence (PMID:38383785, PMID:38383789). Supporting Evidence: PMID:38383785 UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes |
| GO:0140501 positive regulation of reticulophagy | IMP PMID:32851973 A cross-kingdom conserved ER-phagy receptor maintains endopl... | ACCEPT | Summary: IMP annotation to positive regulation of reticulophagy (ER-phagy). C53/CDK5RAP3 acts as an ER-phagy receptor maintaining ER homeostasis during stress. Reason: Reticulophagy promotion is a directly evidenced function of CDK5RAP3 as an ATG8-binding ER-phagy receptor. Supporting Evidence: PMID:32851973 Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:36121123 A non-canonical scaffold-type E3 ligase complex mediates pro... | ACCEPT | Summary: IDA annotation: ubiquitin-like ligase-substrate adaptor activity. Direct experimental demonstration that CDK5RAP3 is the substrate adaptor of the UREL UFM1 E3 ligase complex. Reason: This is the core, well-evidenced molecular function of CDK5RAP3; multiple independent studies converge on it. Supporting Evidence: PMID:36121123 CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26 |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:36543799 The UFM1 system regulates ER-phagy through the ufmylation of... | ACCEPT | Summary: IDA annotation: ubiquitin-like ligase-substrate adaptor activity. Direct experimental demonstration that CDK5RAP3 is the substrate adaptor of the UREL UFM1 E3 ligase complex. Reason: This is the core, well-evidenced molecular function of CDK5RAP3; multiple independent studies converge on it. Supporting Evidence: PMID:36543799 The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3 |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:37595036 Mechanistic insights into the roles of the UFM1 E3 ligase co... | ACCEPT | Summary: IDA annotation: ubiquitin-like ligase-substrate adaptor activity. Direct experimental demonstration that CDK5RAP3 is the substrate adaptor of the UREL UFM1 E3 ligase complex. Reason: This is the core, well-evidenced molecular function of CDK5RAP3; multiple independent studies converge on it. Supporting Evidence: PMID:37595036 CDK5RAP3, an adaptor for ufmylation of ribosomal subunit RPL26 |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:38383785 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits ... | ACCEPT | Summary: IDA annotation: ubiquitin-like ligase-substrate adaptor activity. Direct experimental demonstration that CDK5RAP3 is the substrate adaptor of the UREL UFM1 E3 ligase complex. Reason: This is the core, well-evidenced molecular function of CDK5RAP3; multiple independent studies converge on it. Supporting Evidence: PMID:38383785 UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:38383789 The UFM1 E3 ligase recognizes and releases 60S ribosomes fro... | ACCEPT | Summary: IDA annotation: ubiquitin-like ligase-substrate adaptor activity. Direct experimental demonstration that CDK5RAP3 is the substrate adaptor of the UREL UFM1 E3 ligase complex. Reason: This is the core, well-evidenced molecular function of CDK5RAP3; multiple independent studies converge on it. Supporting Evidence: PMID:38383789 UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:36543799 The UFM1 system regulates ER-phagy through the ufmylation of... | ACCEPT | Summary: IDA: CDK5RAP3 is active at the ER membrane (UFMylation/ER-phagy context). Reason: ER membrane is the site of CDK5RAP3 function within the UREL complex; is_active_in is well supported. Supporting Evidence: PMID:36543799 The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3 |
| GO:0071569 protein ufmylation | IDA PMID:36543799 The UFM1 system regulates ER-phagy through the ufmylation of... | ACCEPT | Summary: IDA annotation to protein ufmylation (CYB5R3 ufmylation / ER-phagy study). Reason: Directly supports the core ufmylation role of CDK5RAP3 as part of the E3 complex. Supporting Evidence: PMID:36543799 ufmylation of CYB5R3 |
| GO:0071569 protein ufmylation | IDA PMID:37595036 Mechanistic insights into the roles of the UFM1 E3 ligase co... | ACCEPT | Summary: IDA annotation to protein ufmylation (mechanistic ER-RQC study). Reason: Core ufmylation function directly supported; CDK5RAP3 is the adaptor for RPL26 ufmylation. Supporting Evidence: PMID:37595036 CDK5RAP3, an adaptor for ufmylation of ribosomal subunit RPL26 |
| GO:0072344 rescue of stalled cytosolic ribosome | IDA PMID:37595036 Mechanistic insights into the roles of the UFM1 E3 ligase co... | ACCEPT | Summary: IDA annotation to rescue of stalled cytosolic ribosome (ER-RQC). UREL ufmylates RPL26 on stalled-disome 60S subunits. Reason: Directly supported core function in ER ribosome-associated quality control. Supporting Evidence: PMID:37595036 Upon disome formation, the E3 complex associated with ufmylated RPL26 on the 60S subunit... Loss of E3 components... attenuated ER-RQC |
| GO:0140501 positive regulation of reticulophagy | IDA PMID:36543799 The UFM1 system regulates ER-phagy through the ufmylation of... | ACCEPT | Summary: IDA annotation to positive regulation of reticulophagy via ufmylation of CYB5R3. Reason: Reticulophagy promotion is directly evidenced for the UFM1 system including CDK5RAP3. Supporting Evidence: PMID:36543799 The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3 |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:38383785 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits ... | ACCEPT | Summary: IDA: CDK5RAP3 is active at the ER membrane as part of the UREL complex engaging 60S ribosomes. Reason: ER membrane is the validated site of action of the UREL complex (cryo-EM structures); is_active_in appropriate. Supporting Evidence: PMID:38383785 UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:38383789 The UFM1 E3 ligase recognizes and releases 60S ribosomes fro... | ACCEPT | Summary: IDA: CDK5RAP3 is active at the ER membrane as part of the UREL complex engaging 60S ribosomes. Reason: ER membrane is the validated site of action of the UREL complex (cryo-EM structures); is_active_in appropriate. Supporting Evidence: PMID:38383789 UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other |
| GO:0032790 ribosome disassembly | IDA PMID:38383785 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits ... | ACCEPT | Summary: IDA annotation to ribosome disassembly. UREL releases 60S subunits from the SEC61 translocon, dissociating 60S-SEC61 complexes. Reason: Directly supported by cryo-EM/biochemical evidence that UREL/CDK5RAP3 mediates release of 60S from SEC61 translocons. Supporting Evidence: PMID:38383785 UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes |
| GO:0032790 ribosome disassembly | IDA PMID:38383789 The UFM1 E3 ligase recognizes and releases 60S ribosomes fro... | ACCEPT | Summary: IDA annotation to ribosome disassembly. UREL releases 60S subunits from the SEC61 translocon, dissociating 60S-SEC61 complexes. Reason: Directly supported by cryo-EM/biochemical evidence that UREL/CDK5RAP3 mediates release of 60S from SEC61 translocons. Supporting Evidence: PMID:38383789 UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other |
| GO:0071569 protein ufmylation | IDA PMID:38383785 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits ... | ACCEPT | Summary: IDA annotation to protein ufmylation; structural studies of UREL ufmylating RPL26/uL24 on the 60S ribosome. Reason: Core ufmylation function directly and structurally evidenced. Supporting Evidence: PMID:38383785 UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes |
| GO:0071569 protein ufmylation | IDA PMID:38383789 The UFM1 E3 ligase recognizes and releases 60S ribosomes fro... | ACCEPT | Summary: IDA annotation to protein ufmylation; structural studies of UREL ufmylating RPL26/uL24 on the 60S ribosome. Reason: Core ufmylation function directly and structurally evidenced. Supporting Evidence: PMID:38383789 UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other |
| GO:0072344 rescue of stalled cytosolic ribosome | IDA PMID:38383785 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits ... | ACCEPT | Summary: IDA annotation to rescue of stalled cytosolic ribosome; UREL promotes recycling/release of 60S subunits from the ER translocon. Reason: Directly evidenced core function in ER ribosome rescue/recycling. Supporting Evidence: PMID:38383785 UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes |
| GO:0072344 rescue of stalled cytosolic ribosome | IDA PMID:38383789 The UFM1 E3 ligase recognizes and releases 60S ribosomes fro... | ACCEPT | Summary: IDA annotation to rescue of stalled cytosolic ribosome; UREL promotes recycling/release of 60S subunits from the ER translocon. Reason: Directly evidenced core function in ER ribosome rescue/recycling. Supporting Evidence: PMID:38383789 UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other |
| GO:0001889 liver development | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS annotation to liver development (from mouse ortholog Q99LM2). Duplicate of the IEA liver development call. Reason: Downstream physiological role of the UFMylation pathway; non-core. Supporting Evidence: PMID:30635284 a crucial role of CDK5RAP3 in liver development and hepatic functions |
| GO:0034976 response to endoplasmic reticulum stress | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS annotation to response to ER stress (from mouse ortholog). Duplicate of IEA call. Reason: Contextual/downstream process of the UFM1 system; non-core. Supporting Evidence: PMID:23152784 the Ufm1 system was transcriptionally up-regulated by disturbance of the ER homeostasis |
| GO:0060318 definitive erythrocyte differentiation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS annotation to definitive erythrocyte differentiation (from mouse ortholog). Duplicate of IEA call. Reason: Downstream physiological role of the UFMylation pathway; non-core. Supporting Evidence: PMID:23152784 the Ufm1-activating enzyme Uba5 is indispensible for erythroid differentiation in mice |
| GO:0071569 protein ufmylation | IMP PMID:30635284 CDK5RAP3, a UFL1 substrate adaptor, is crucial for liver dev... | ACCEPT | Summary: IMP annotation to protein ufmylation. CDK5RAP3 is described as a UFL1 substrate adaptor required for the ufmylation pathway in vivo. Reason: Loss-of-function (knockout) evidence supports CDK5RAP3 involvement in protein ufmylation; core function. Supporting Evidence: PMID:30635284 CDK5RAP3, a UFL1 substrate adaptor, is crucial for liver development |
| GO:0032991 protein-containing complex | IDA PMID:20531390 Suppression of the novel ER protein Maxer by mutant ataxin-1... | MARK AS OVER ANNOTATED | Summary: IDA annotation: CDK5RAP3 is part of a protein-containing complex (Maxer/DDRGK1-CDK5RAP3 at the ER). Reason: Generic 'protein-containing complex' is uninformative; the specific UREL transferase complex is captured by GO:1990234. Retain the more specific complex annotation instead. Supporting Evidence: PMID:20531390 Maxer is an endoplasmic reticulum (ER) membrane protein interacting with CDK5RAP3 |
| GO:0010921 regulation of phosphatase activity | IMP PMID:21283629 LZAP inhibits p38 MAPK (p38) phosphorylation and activity by... | KEEP AS NON CORE | Summary: IMP annotation to regulation of phosphatase activity. LZAP increases Wip1/PPM1D phosphatase association with p38 MAPK. Reason: Part of the older LZAP p38/Wip1 regulatory literature; non-core relative to the UFMylation function. Supporting Evidence: PMID:21283629 the ability of LZAP to alter p38 phosphorylation depended, at least partially, on the p38 phosphatase, Wip1 |
| GO:0030968 endoplasmic reticulum unfolded protein response | IMP PMID:23152784 Transcriptional regulation of the Ufm1 conjugation system in... | KEEP AS NON CORE | Summary: IMP annotation to ER unfolded protein response. The Ufm1 system (including C53/CDK5RAP3) is linked to UPR and ER homeostasis. Reason: UPR involvement is contextual/downstream of the UFMylation pathway; non-core. Supporting Evidence: PMID:23152784 knockdown of the Ufm1 system in U2OS cells triggered UPR and amplification of the ER network |
| GO:0005874 microtubule | IDA PMID:23478299 Caspase-mediated cleavage of C53/LZAP protein causes abnorma... | KEEP AS NON CORE | Summary: IDA: colocalizes with microtubules. CDK5RAP3 binds microtubules indirectly; caspase-cleaved product causes abnormal MT bundling. Reason: Microtubule association is documented (apoptosis context) but non-core; colocalizes_with qualifier is appropriately weak. Supporting Evidence: PMID:23478299 expression of the C53/LZAP cleavage product caused abnormal MT bundling and NE rupture |
| GO:0030262 apoptotic nuclear changes | IMP PMID:23478299 Caspase-mediated cleavage of C53/LZAP protein causes abnorma... | KEEP AS NON CORE | Summary: IMP annotation to apoptotic nuclear changes. Caspase-cleaved C53/LZAP causes rupture of the nuclear envelope during apoptosis. Reason: A specialized apoptosis-associated role of the caspase-cleavage product; non-core relative to the main function. Supporting Evidence: PMID:23478299 expression of the C53/LZAP cleavage product caused abnormal MT bundling and NE rupture |
| GO:0043407 negative regulation of MAP kinase activity | IMP PMID:21283629 LZAP inhibits p38 MAPK (p38) phosphorylation and activity by... | KEEP AS NON CORE | Summary: IMP annotation to negative regulation of MAP kinase activity. LZAP inhibits p38 MAPK phosphorylation/activation. Reason: Older LZAP/p38 literature; non-core relative to the UFMylation adaptor function. Supporting Evidence: PMID:21283629 LZAP binds p38, alters p38 cellular localization, and inhibits basal and cytokine-stimulated p38 activity |
| GO:0044387 negative regulation of protein kinase activity by regulation of protein phosphorylation | IMP PMID:21283629 LZAP inhibits p38 MAPK (p38) phosphorylation and activity by... | KEEP AS NON CORE | Summary: IMP annotation to negative regulation of protein kinase activity by regulation of protein phosphorylation (p38 MAPK via Wip1). Reason: Older LZAP/p38/Wip1 literature; non-core. Supporting Evidence: PMID:21283629 Expression of LZAP inhibits p38 phosphorylation in a dose-dependent fashion |
| GO:0051019 mitogen-activated protein kinase binding | IPI PMID:21283629 LZAP inhibits p38 MAPK (p38) phosphorylation and activity by... | KEEP AS NON CORE | Summary: IPI annotation: mitogen-activated protein kinase binding (p38/MAPK14). LZAP binds p38. Reason: A specific but non-core interaction from the LZAP/p38 literature; more informative than bare protein binding so retained as non-core. Supporting Evidence: PMID:21283629 the LZAP binds p38 |
| GO:0005737 cytoplasm | IDA PMID:19223857 Tumor suppressor protein C53 antagonizes checkpoint kinases ... | ACCEPT | Summary: IDA localization to cytoplasm (C53/Chk1 study). Reason: Cytoplasmic localization directly supported. Supporting Evidence: PMID:19223857 a portion of C53 protein is localized at the centrosome |
| GO:0005813 centrosome | IDA PMID:19223857 Tumor suppressor protein C53 antagonizes checkpoint kinases ... | KEEP AS NON CORE | Summary: IDA localization to centrosome; centrosome-targeted C53 promotes local Cdk1 activation. Reason: Centrosomal pool is experimentally supported but reflects a non-core cell-cycle role. Supporting Evidence: PMID:19223857 a portion of C53 protein is localized at the centrosome, and centrosome-targeting C53 potently promotes local Cdk1 activation |
| GO:0007095 mitotic G2 DNA damage checkpoint signaling | IMP PMID:15790566 Cdk5 activator-binding protein C53 regulates apoptosis induc... | KEEP AS NON CORE | Summary: IMP annotation to mitotic G2 DNA damage checkpoint signaling. C53 modulates the G2/M DNA damage checkpoint via Cdk1-cyclin B1. Reason: Older C53 checkpoint literature; non-core relative to the UFMylation function. Supporting Evidence: PMID:15790566 C53 acts as a pivotal player in modulating the G(2)/M DNA damage checkpoint |
| GO:0019901 protein kinase binding | IPI PMID:19223857 Tumor suppressor protein C53 antagonizes checkpoint kinases ... | KEEP AS NON CORE | Summary: IPI annotation: protein kinase binding (CHEK1/Chk1). C53 interacts with and antagonizes Chk1. Reason: Specific CHEK1 interaction from the checkpoint literature; informative but non-core. Retained as non-core. Supporting Evidence: PMID:19223857 C53 interacts with Chk1 and antagonizes its function |
| GO:0044818 mitotic G2/M transition checkpoint | IMP PMID:19223857 Tumor suppressor protein C53 antagonizes checkpoint kinases ... | KEEP AS NON CORE | Summary: IMP annotation to mitotic G2/M transition checkpoint. C53 antagonizes Chk1 to promote Cdk1 activation and mitotic entry. Reason: Older C53 checkpoint literature; non-core. Supporting Evidence: PMID:19223857 By counteracting Chk1, C53 promotes Cdk1 activation and mitotic entry |
| GO:0071901 negative regulation of protein serine/threonine kinase activity | IMP PMID:19223857 Tumor suppressor protein C53 antagonizes checkpoint kinases ... | KEEP AS NON CORE | Summary: IMP annotation to negative regulation of protein serine/threonine kinase activity (Chk1 antagonism). Reason: Checkpoint-kinase regulation from older C53 literature; non-core. Supporting Evidence: PMID:19223857 activation of checkpoint kinase 1 and 2 (Chk1 and Chk2) is partially inhibited by C53 overexpression |
| GO:0001933 negative regulation of protein phosphorylation | IMP PMID:17785205 LZAP, a putative tumor suppressor, selectively inhibits NF-k... | KEEP AS NON CORE | Summary: IMP annotation to negative regulation of protein phosphorylation. LZAP impairs RelA Ser536 phosphorylation. Reason: Part of the LZAP/NF-kB tumor-suppressor literature; non-core. Supporting Evidence: PMID:17785205 LZAP directly bound to RelA, impaired serine 536 phosphorylation of RelA |
| GO:0005515 protein binding | IPI PMID:20228063 A novel C53/LZAP-interacting protein regulates stability of ... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' IPI from the RCAD/DDRGK1 study (interactions with UFL1 and DDRGK1). Reason: Bare protein binding is uninformative; the underlying UFL1/DDRGK1 interactions are captured by ubiquitin-like protein ligase binding and the UREL complex annotations. Supporting Evidence: PMID:20228063 C53/LZAP and RCAD may form a large protein complex |
| GO:0051059 NF-kappaB binding | IPI PMID:17785205 LZAP, a putative tumor suppressor, selectively inhibits NF-k... | KEEP AS NON CORE | Summary: IPI annotation: NF-kappaB binding (RelA). LZAP directly binds RelA and inhibits NF-kB transcriptional activity. Reason: Specific RelA/NF-kB binding from the LZAP tumor-suppressor literature; informative but non-core relative to the UFMylation function. Supporting Evidence: PMID:17785205 LZAP directly bound to RelA, impaired serine 536 phosphorylation of RelA |
| GO:0005737 cytoplasm | IDA PMID:15790566 Cdk5 activator-binding protein C53 regulates apoptosis induc... | ACCEPT | Summary: IDA localization to cytoplasm (C53/cyclin B1 study). Reason: Cytoplasmic localization directly supported. Supporting Evidence: PMID:15790566 C53 and cyclin B1 co-localize and associate in vivo |
| GO:0030332 cyclin binding | IPI PMID:15790566 Cdk5 activator-binding protein C53 regulates apoptosis induc... | KEEP AS NON CORE | Summary: IPI annotation: cyclin binding (cyclin B1/CCNB1). C53 associates with cyclin B1. Reason: Specific cyclin B1 interaction from the checkpoint literature; informative but non-core. Supporting Evidence: PMID:15790566 C53 and cyclin B1 co-localize and associate in vivo, indicating a direct role of C53 in regulating the Cdk1-cyclin B1 complex |
| GO:0031398 positive regulation of protein ubiquitination | IDA PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | KEEP AS NON CORE | Summary: IDA annotation to positive regulation of protein ubiquitination. LZAP affects ARF/HDM2-mediated p53 ubiquitination. Reason: Part of the LZAP/ARF/MDM2/p53 literature; non-core relative to the UFMylation function. Supporting Evidence: PMID:16173922 LZAP reversed the ability of ARF to inhibit HDM2's ubiquitin ligase activity towards p53 |
| GO:0042177 negative regulation of protein catabolic process | IDA PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | KEEP AS NON CORE | Summary: IDA annotation to negative regulation of protein catabolic process. LZAP co-operates with ARF to maintain p53 stability (reduce p53 degradation). Reason: Part of the LZAP/p53-stability literature; non-core. Supporting Evidence: PMID:16173922 co-operated with ARF, maintaining p53 stability and increasing p53 transcriptional activity |
| GO:1900182 positive regulation of protein localization to nucleus | IDA PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | KEEP AS NON CORE | Summary: IDA annotation to positive regulation of protein localization to nucleus (p53-related). Reason: Part of the LZAP/p53 literature; non-core. Supporting Evidence: PMID:16173922 maintaining p53 stability and increasing p53 transcriptional activity |
| GO:1901798 positive regulation of signal transduction by p53 class mediator | IDA PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | KEEP AS NON CORE | Summary: IDA annotation to positive regulation of signal transduction by p53 class mediator. LZAP activates p53 and causes p53-dependent G1 arrest. Reason: Part of the LZAP/p53 tumor-suppressor literature; non-core. Supporting Evidence: PMID:16173922 Expression of LZAP also caused activation of p53 and a p53-dependent G1 cell-cycle arrest |
| GO:2000060 positive regulation of ubiquitin-dependent protein catabolic process | IDA NOT PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | ACCEPT | Summary: Negated (NOT) IDA annotation: CDK5RAP3/LZAP does NOT positively regulate ubiquitin-dependent protein catabolic process. Consistent with LZAP reversing ARF inhibition of HDM2 and maintaining p53 stability rather than promoting its degradation. Reason: The informative negative annotation is supported: LZAP maintains rather than degrades p53, so it does not positively regulate ubiquitin-dependent catabolism here. Retain as a curated negative. Supporting Evidence: PMID:16173922 co-operated with ARF, maintaining p53 stability and increasing p53 transcriptional activity |
| GO:0097371 MDM2/MDM4 family protein binding | IPI PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | KEEP AS NON CORE | Summary: IPI annotation: MDM2/MDM4 family protein binding (MDM2/HDM2). LZAP interacts with MDM2 in an ARF-containing complex. Reason: Specific MDM2 interaction from the LZAP/ARF/p53 literature; informative but non-core. Supporting Evidence: PMID:16173922 LZAP reversed the ability of ARF to inhibit HDM2's ubiquitin ligase activity towards p53 |
| GO:0005515 protein binding | IPI PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' IPI (interaction with ARF/CDKN2A). Reason: Bare protein binding is uninformative; the ARF interaction is the basis of the LZAP non-core p53 role described elsewhere. Supporting Evidence: PMID:16173922 that interacts with endogenous ARF in mammalian cells |
| GO:0005634 nucleus | IDA PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | KEEP AS NON CORE | Summary: IDA localization to nucleus (LZAP/p53 study). Reason: Nuclear localization is supported but secondary to the ER/cytosolic core function. Supporting Evidence: PMID:16173922 Expression of LZAP also caused activation of p53 and a p53-dependent G1 cell-cycle arrest |
| GO:0005730 nucleolus | IDA NOT PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | ACCEPT | Summary: Negated (NOT) IDA annotation: CDK5RAP3/LZAP is NOT localized to the nucleolus (in this study). Reason: Informative curated negative localization; retain as-is. Supporting Evidence: PMID:16173922 that interacts with endogenous ARF in mammalian cells |
| GO:0005737 cytoplasm | IDA PMID:16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of ... | ACCEPT | Summary: IDA localization to cytoplasm (LZAP/p53 study). Reason: Cytoplasmic localization directly supported. Supporting Evidence: PMID:16173922 that interacts with endogenous ARF in mammalian cells |
| GO:0008283 cell population proliferation | IDA PMID:12054757 A novel gene IC53 stimulates ECV304 cell proliferation and i... | KEEP AS NON CORE | Summary: IDA annotation to cell population proliferation. IC53 (isoform 2) stimulates ECV304 cell proliferation. Reason: Proliferation effect from an early overexpression study; non-core and isoform-specific in origin. Supporting Evidence: PMID:12054757 IC53 stimulates ECV304 cell proliferation by 2.1-fold |
| GO:0005737 cytoplasm | IDA PMID:20531390 Suppression of the novel ER protein Maxer by mutant ataxin-1... | ACCEPT | Summary: IDA localization to cytoplasm (Maxer/DDRGK1 study). Reason: Cytoplasmic localization directly supported; Maxer/DDRGK1 anchors CDK5RAP3 at the ER. Supporting Evidence: PMID:20531390 Maxer anchors CDK5RAP3 to the ER |
| GO:0044389 ubiquitin-like protein ligase binding | IDA PMID:20531390 Suppression of the novel ER protein Maxer by mutant ataxin-1... | ACCEPT | Summary: IDA annotation: ubiquitin-like protein ligase binding. CDK5RAP3 binds the UFM1 ligase machinery (via DDRGK1/Maxer-UFL1 axis). Reason: Binding to the UFM1 E3 ligase components is a core, informative interaction underlying the UREL complex. Supporting Evidence: PMID:20531390 Maxer is an endoplasmic reticulum (ER) membrane protein interacting with CDK5RAP3 |
| GO:0016020 membrane | HDA PMID:19946888 Defining the membrane proteome of NK cells. | MARK AS OVER ANNOTATED | Summary: HDA annotation to membrane from an NK-cell membrane proteome study. Very general localization. Reason: Generic 'membrane' from a high-throughput proteomic survey is subsumed by the specific ER membrane localization; uninformative. Supporting Evidence: PMID:19946888 define the composition of the membrane proteome of the Natural Killer (NK) like cell line YTS |
| GO:0071569 protein ufmylation | IDA PMID:23152784 Transcriptional regulation of the Ufm1 conjugation system in... | ACCEPT | Summary: IDA annotation to protein ufmylation (acts_upstream_of_or_within). C53/LZAP, with RCAD/Ufl1, is involved in ufmylation of endogenous Ufm1 targets. Reason: Supports the core ufmylation involvement; consistent with the broader body of UFMylation evidence. Supporting Evidence: PMID:23152784 involvement of RCAD/Ufl1, a putative Ufm1-specific E3 ligase, and its binding partner C53/LZAP protein in ufmylation of endogenous Ufm1 targets |
| GO:0005515 protein binding | IPI PMID:20164180 A novel LZAP-binding protein, NLBP, inhibits cell invasion. | MARK AS OVER ANNOTATED | Summary: Bare 'protein binding' IPI (interaction with UFL1/NLBP study). Reason: Bare protein binding is uninformative; the UFL1 interaction is captured by ubiquitin-like protein ligase binding and the UREL complex annotations. Supporting Evidence: PMID:20164180 we identify NLBP as a novel LZAP-binding protein using tandem affinity purification |
| GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS annotation to regulation of cyclin-dependent protein serine/threonine kinase activity, transferred from rodent ortholog (Q9JLH7). Reflects the historical 'CDK5 activator-binding' name. Reason: There is no robust evidence that human CDK5RAP3 regulates CDK activity; the annotation derives from the misleading name and ortholog transfer. CDK5RAP3 has no catalytic activity and its established role is UFMylation. Supporting Evidence: PMID:21283629 LZAP has no known enzymatic activity, implying that its biological functions are likely mediated by its protein-protein interactions |
| GO:0007420 brain development | NAS PMID:10915792 Identification of a common protein association region in the... | KEEP AS NON CORE | Summary: NAS annotation to brain development from an early Cdk5-activator binding-protein cloning paper. Reason: Author-statement only, based on the Cdk5-activator association; speculative and non-core. Retained as non-core rather than removed. Supporting Evidence: PMID:10915792 Cyclin-dependent protein kinase 5 (Cdk5) depends on the association with neuronal Cdk5 activator (Nck5a) |
| GO:0045664 regulation of neuron differentiation | NAS PMID:10721722 Cloning of three novel neuronal Cdk5 activator binding prote... | KEEP AS NON CORE | Summary: NAS annotation to regulation of neuron differentiation from the original Cdk5-activator binding-protein cloning paper. Reason: Author-statement speculation tied to Cdk5/neuronal context; non-core relative to the established UFMylation function. Supporting Evidence: PMID:10721722 isolation of three other novel p35nck5a-associated proteins |
| GO:0019901 protein kinase binding | NAS PMID:10721722 Cloning of three novel neuronal Cdk5 activator binding prote... | KEEP AS NON CORE | Summary: NAS annotation: protein kinase binding, from the cloning of Cdk5-activator (p35) binding proteins. Note CDK5RAP3 binds the Cdk5 activator p35, not necessarily Cdk5 kinase itself. Reason: Historical NAS evidence underlying the gene name; the interaction is with the Cdk5 activator and there is no evidence CDK5RAP3 regulates Cdk5 kinase activity. Non-core. Supporting Evidence: PMID:10721722 novel p35nck5a-associated proteins |
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Download this section (compressed HTML)Q: Are the older LZAP/C53 NF-kB, ARF/MDM2/p53 and G2/M checkpoint activities mechanistically separable from the UFMylation adaptor function, or are they downstream/indirect consequences of perturbing the UFM1 system?
Q: Which CDK5RAP3 isoforms participate in the UREL complex versus the nuclear/cell-cycle roles, and do the N-terminally truncated isoforms (IC53, IC53-2) retain UFL1/ribosome binding?
Q: Is CDK5RAP3 itself UFMylated in human cells (as suggested for the mouse ortholog), and does this regulate UREL activity or stability?
Experiment: Separation-of-function mutants of CDK5RAP3 (e.g. RPL10a-binding domain or UFL1-binding residues E217/D355/E359/E373/R432) expressed in CDK5RAP3-knockout cells to test which phenotypes (ribosome recycling, ER-phagy, NF-kB, checkpoint) depend on UREL assembly versus UFMylation-independent moonlighting.
Experiment: Ribosome profiling and 60S-SEC61 release assays in CDK5RAP3-depleted human cells to quantify the contribution of CDK5RAP3 (versus UFL1/DDRGK1) to ER ribosome-associated quality control under stalling stress.
Experiment: Proximity labeling (BioID/TurboID) of CDK5RAP3 across ER, cytosol, nucleus and centrosome compartments to define compartment-specific interactomes and test whether the cell-cycle/NF-kB partners are engaged independently of the UREL complex.
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