Catalyzes uridine to pseudouridine isomerization (pseudouridylation) of different mitochondrial RNA substrates (, ). Acts on position 1397 in 16S mitochondrial ribosomal RNA (16S mt-rRNA) . This modification is required for the assembly of 16S mt-rRNA into a functional mitochondrial ribosome . As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mt-rRNA, controls 16S mt-rRNA abundance and is required for intra-mitochondrial translation . Acts on position 39 in mitochondrial tRNA(Phe) . Also catalyzes pseudouridylation of mRNAs in nucleus: acts as a regulator of pre-mRNA splicing by mediating pseudouridylation of pre-mRNAs at locations associated with alternatively spliced regions . Pseudouridylation of pre-mRNAs near splice sites directly regulates mRNA splicing and mRNA 3'-end processing .
Subcellular locations: Mitochondrion matrix, Nucleus, Cytoplasm
Mainly localizes to mitochondrion ( ). Localizes to mitochondrial RNA granules, platforms for post-transcriptional RNA modification and ribosome assembly (, ). Also found in nucleus and cytoplasm .