id: Q9UHC7 gene_symbol: MKRN1 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: >- MKRN1 (makorin RING finger protein 1; RNF61) is a cytoplasmic RNA-binding RING-type E3 ubiquitin ligase of the makorin family. It combines a C3HC4 RING domain, which confers ubiquitin-protein ligase activity, with multiple CCCH/C3H zinc-finger motifs that mediate RNA binding. MKRN1 ubiquitinates several substrate proteins - including p53/TP53 (which it suppresses under normal conditions to keep cells alive), the CDK inhibitor CDKN1A/p21 (which it degrades under stress to promote apoptosis), the telomerase catalytic subunit TERT (acting as a negative regulator of telomerase), and FILIP1 - thereby influencing cell-cycle arrest, apoptosis and telomere maintenance. In addition, MKRN1 acts in ribosome-associated quality control of poly(A) translation: by binding the poly(A)-binding protein PABPC1 and associating with polysomes just upstream of poly(A) tails, it promotes ribosome stalling on prematurely polyadenylated (A-rich) messages and ubiquitinates the 40S ribosomal protein RPS10 and PABPC1, positioning it upstream of ZNF598/LTN1 in clearing aberrant nascent chains and preventing production of erroneous proteins. existing_annotations: - term: id: GO:0016567 label: protein ubiquitination evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: >- MKRN1 ubiquitinates substrate proteins; protein ubiquitination is a core process for this RING E3 ligase. Well supported. action: ACCEPT reason: >- MKRN1 has demonstrated E3 ligase activity (EC 2.3.2.27) and ubiquitinates p53, p21, TERT and ribosome-associated substrates. supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - term: id: GO:0061630 label: ubiquitin protein ligase activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: >- Core molecular function: MKRN1 is a RING-type ubiquitin-protein ligase. action: ACCEPT reason: >- The RING domain confers E3 ligase activity, demonstrated biochemically. supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - term: id: GO:0000209 label: protein polyubiquitination evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: summary: >- MKRN1 catalyzes polyubiquitination of substrates targeting them for proteasomal degradation. Supported. action: ACCEPT reason: >- MKRN1 mediates proteasome-dependent degradation of p53/p21 via polyubiquitination. supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - term: id: GO:0046872 label: metal ion binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: >- MKRN1 contains a C3HC4 RING domain and CCCH zinc fingers that coordinate zinc ions. Generic metal-ion binding underlies these structural features. action: KEEP_AS_NON_CORE reason: >- Zinc coordination by the RING and zinc-finger motifs is structurally required, but the informative functions are E3 ligase activity and RNA binding. supported_by: - reference_id: file:human/MKRN1/MKRN1-uniprot.txt supporting_text: E3 ubiquitin-protein ligase makorin-1 - term: id: GO:0061630 label: ubiquitin protein ligase activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables review: summary: >- Duplicate (electronic) annotation of the core E3 ligase MF. Supported. action: ACCEPT reason: >- Consistent with experimental and phylogenetic evidence for RING E3 ligase activity. supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:19536131 qualifier: enables review: summary: >- IPI protein-binding annotation from the p53/p21 study. Records substrate interactions but the generic term is uninformative; the E3 ligase MF captures the function. action: KEEP_AS_NON_CORE reason: >- Substrate binding (p53, p21) is part of E3 ligase function; the generic term is not elevated to core. supported_by: - reference_id: PMID:19536131 supporting_text: negative regulator of p53 and p21. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:32296183 qualifier: enables review: summary: >- Generic protein-binding annotation from a large-scale binary interactome (HuRI). Uninformative as a molecular function. action: KEEP_AS_NON_CORE reason: >- High-throughput Y2H interactome; no specific functional insight. supported_by: - reference_id: PMID:32296183 supporting_text: A reference map of the human binary protein interactome. - term: id: GO:0016567 label: protein ubiquitination evidence_type: IEA original_reference_id: GO_REF:0000041 qualifier: involved_in review: summary: >- Electronic annotation of protein ubiquitination (UniProt keyword mapping). Supported. action: ACCEPT reason: >- Consistent with MKRN1's E3 ligase activity. supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - term: id: GO:0061630 label: ubiquitin protein ligase activity evidence_type: TAS original_reference_id: Reactome:R-HSA-8948775 qualifier: enables review: summary: >- Reactome TAS annotation of the core E3 ligase MF. Supported. action: ACCEPT reason: >- Consistent with established RING E3 ligase activity. supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - term: id: GO:0061630 label: ubiquitin protein ligase activity evidence_type: IDA original_reference_id: PMID:19536131 qualifier: enables review: summary: >- Direct demonstration of MKRN1 ubiquitin-protein ligase activity (in vitro ubiquitination of p53 and p21). Core MF. action: ACCEPT reason: >- Direct biochemical evidence of E3 ligase activity, also reflected in the UniProt catalytic activity (EC 2.3.2.27). supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-8948757 qualifier: located_in review: summary: >- Cytosol localization. Consistent with MKRN1's cytoplasmic E3 ligase and ribosome- associated functions. action: ACCEPT reason: >- MKRN1 acts in the cytoplasm on cytosolic substrates and polysomes. supported_by: - reference_id: PMID:31640799 supporting_text: MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-8948775 qualifier: located_in review: summary: >- Duplicate cytosol localization (Reactome TAS). Supported. action: ACCEPT reason: >- MKRN1 is cytoplasmic. supported_by: - reference_id: PMID:31640799 supporting_text: MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) - term: id: GO:0000209 label: protein polyubiquitination evidence_type: IDA original_reference_id: PMID:19536131 qualifier: involved_in review: summary: >- Direct evidence for MKRN1-mediated polyubiquitination of p53/p21 leading to proteasomal degradation. Supported. action: ACCEPT reason: >- MKRN1 polyubiquitinates substrates for degradation. supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - term: id: GO:0003723 label: RNA binding evidence_type: HDA original_reference_id: PMID:22658674 qualifier: enables review: summary: >- RNA binding (mRNA interactome capture). MKRN1 contains CCCH zinc fingers and binds RNA; this underlies its poly(A)-tail recognition in RQC. Genuine and informative. action: ACCEPT reason: >- MKRN1 is an RNA-binding ubiquitin ligase; it binds RNA (including poly(A) regions) and PABPC1 to act co-translationally. supported_by: - reference_id: PMID:31640799 supporting_text: The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. - term: id: GO:1990116 label: ribosome-associated ubiquitin-dependent protein catabolic process evidence_type: IMP original_reference_id: PMID:31640799 qualifier: involved_in review: summary: >- NEW annotation capturing MKRN1's role in ribosome-associated quality control of poly(A) translation. MKRN1 promotes ribosome stalling at poly(A) and ubiquitinates RPS10 and PABPC1, positioning it upstream of ZNF598/LTN1-mediated clearance of aberrant nascent chains. action: NEW reason: >- Direct experimental evidence (iCLIP, ubiquitin-remnant profiling, in vitro ubiquitylation) establishes MKRN1 as an RQC factor for poly(A) translation; this is a core function not yet captured in the GOA set. supported_by: - reference_id: PMID:31640799 supporting_text: MKRN1 depletion abrogates ribosome stalling at A-rich sequences and results in reduced ubiquitylation of RPS10 and PABPC1. - reference_id: PMID:31640799 supporting_text: The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. core_functions: - description: >- MKRN1 is a RING-type E3 ubiquitin-protein ligase that catalyzes ubiquitin transfer onto substrate lysines, targeting substrates (p53, CDKN1A/p21, TERT, FILIP1, and ribosome- associated RPS10/PABPC1) for regulation or proteasomal degradation. molecular_function: id: GO:0061630 label: ubiquitin protein ligase activity locations: - id: GO:0005829 label: cytosol supported_by: - reference_id: PMID:19536131 supporting_text: both p53 and p21 through ubiquitination and proteasome-dependent degradation. - description: >- As an RNA-binding ubiquitin ligase, MKRN1 binds poly(A)/PABPC1 on polysomes, promotes ribosome stalling on prematurely polyadenylated mRNAs, and ubiquitinates the 40S protein RPS10 and PABPC1 to trigger ribosome-associated quality control of poly(A) translation. molecular_function: id: GO:0061630 label: ubiquitin protein ligase activity locations: - id: GO:0005829 label: cytosol supported_by: - reference_id: PMID:31640799 supporting_text: MKRN1 depletion abrogates ribosome stalling at A-rich sequences and results in reduced ubiquitylation of RPS10 and PABPC1. directly_involved_in: - id: GO:1990116 label: ribosome-associated ubiquitin-dependent protein catabolic process proposed_new_terms: [] suggested_questions: - question: How is MKRN1 substrate choice partitioned between its nucleocytoplasmic targets (p53, p21, TERT) and its ribosome-associated RQC substrates (RPS10, PABPC1)? - question: Is MKRN1's poly(A)-RQC role redundant with or distinct from that of its paralogs MKRN2/3, and how does it interface with ZNF598 and LTN1? suggested_experiments: - description: Ribosome profiling and ubiquitin-remnant proteomics in MKRN1-knockout versus rescue (RING-dead and RNA-binding-dead mutants) to separate catalytic from RNA-binding contributions to poly(A) stalling. - description: Reconstituted in vitro RQC assays with poly(A)-stalled ribosomes to test the order of MKRN1, ZNF598 and LTN1 ubiquitylation events. references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000041 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:19536131 title: Differential regulation of p53 and p21 by MKRN1 E3 ligase controls cell cycle arrest and apoptosis. findings: - statement: MKRN1 is an E3 ligase that ubiquitinates p53 and p21 for proteasomal degradation, suppressing p53 under normal conditions and degrading p21 under stress to promote apoptosis. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: Cached publication title matches the YAML title and GOA anchors this PMID to IDA for GO:0061630 (ubiquitin protein ligase activity) and GO:0000209; establishes MKRN1's core E3 ligase function on p53/p21. - id: PMID:22658674 title: Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. findings: [] - id: PMID:31640799 title: The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. findings: - statement: MKRN1 binds PABPC1 and polysomes upstream of poly(A) tails, promotes ribosome stalling at A-rich sequences, and ubiquitinates RPS10 and PABPC1, acting in ribosome-associated quality control of poly(A) translation. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: Cached publication title matches the YAML title and content describes MKRN1 binding PABPC1/polysomes and ubiquitinating RPS10/PABPC1; establishes the RNA-binding ubiquitin-ligase role in poly(A) RQC. - id: PMID:32296183 title: A reference map of the human binary protein interactome. findings: [] - id: Reactome:R-HSA-8948757 title: Reactome pathway annotation (cytosol localization) findings: [] - id: Reactome:R-HSA-8948775 title: Reactome pathway annotation (MKRN1 ubiquitin ligase activity) findings: [] - id: file:human/MKRN1/MKRN1-uniprot.txt title: UniProt entry Q9UHC7 (MKRN1_HUMAN) findings: [] - id: file:human/MKRN1/MKRN1-goa.tsv title: GOA annotations for MKRN1 findings: []