E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. Acts as a key developmental timer that helps ensure puberty begins at the appropriate age, by inhibiting premature activation of the reproductive hormone cascade. Epigenetically regulates GNRH1 transcription by disrupting the binding of methyl-DNA binding protein 3/MBD3 to the promoter of GNRH1. Mechanistically, mediates the non-proteolytic ubiquitination of MBD3 at multiple sites with 'Lys27' ubiquitin linkages and thereby regulates the methylation status of the genome, including GNRH1 promoter (PubMed:34692086). Modulates the stability and translation of GNRH1 mRNA by mediating the non-proteolytic ubiquitination of PABP family members PABPC1, PABPC3 and PABPC4 at multiple sites (PubMed:33744966). Also participates in the maintenance of genomic and epigenomic stability by regulating the abundance of APEX2 via 'Lys-48'-linked ubiquitination (PubMed:38705397). {ECO:0000250|UniProtKB:Q60764, ECO:0000269|PubMed:19066619, ECO:0000269|PubMed:34692086, ECO:0000269|PubMed:38705397}. This is the function of MKRN3 (makorin ring finger protein 3, ENSG00000179455).