ID   RUSD4_DANRE             Reviewed;         358 AA.
AC   Q6DBR0;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   16-AUG-2004, sequence version 1.
DT   03-AUG-2022, entry version 86.
DE   RecName: Full=Pseudouridylate synthase RPUSD4, mitochondrial {ECO:0000305};
DE            EC=5.4.99.- {ECO:0000250|UniProtKB:Q96CM3};
DE   AltName: Full=RNA pseudouridylate synthase domain-containing protein 4 {ECO:0000305};
DE   Flags: Precursor;
GN   Name=rpusd4 {ECO:0000250|UniProtKB:Q96CM3};
GN   ORFNames=zgc:92006 {ECO:0000303|Ref.1};
OS   Danio rerio (Zebrafish) (Brachydanio rerio).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC   Danionidae; Danioninae; Danio.
OX   NCBI_TaxID=7955;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Catalyzes uridine to pseudouridine isomerization
CC       (pseudouridylation) of different mitochondrial RNA substrates. Acts on
CC       position 1397 in 16S mitochondrial ribosomal RNA (16S mt-rRNA). This
CC       modification is required for the assembly of 16S mt-rRNA into a
CC       functional mitochondrial ribosome. Acts on position 39 in mitochondrial
CC       tRNA(Phe). Also catalyzes pseudouridylation of mRNAs in nucleus: acts
CC       as a regulator of pre-mRNA splicing by mediating pseudouridylation of
CC       pre-mRNAs at locations associated with alternatively spliced regions.
CC       Pseudouridylation of pre-mRNAs near splice sites directly regulates
CC       mRNA splicing and mRNA 3'-end processing.
CC       {ECO:0000250|UniProtKB:Q96CM3}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=uridine in 5S rRNA = pseudouridine in 5S rRNA;
CC         Xref=Rhea:RHEA:47036, Rhea:RHEA-COMP:11730, Rhea:RHEA-COMP:11731,
CC         ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC         Evidence={ECO:0000250|UniProtKB:Q96CM3};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a uridine in tRNA = a pseudouridine in tRNA;
CC         Xref=Rhea:RHEA:54572, Rhea:RHEA-COMP:13339, Rhea:RHEA-COMP:13934,
CC         ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC         Evidence={ECO:0000250|UniProtKB:Q96CM3};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a uridine in mRNA = a pseudouridine in mRNA;
CC         Xref=Rhea:RHEA:56644, Rhea:RHEA-COMP:14658, Rhea:RHEA-COMP:14659,
CC         ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC         Evidence={ECO:0000250|UniProtKB:Q96CM3};
CC   -!- SUBCELLULAR LOCATION: Mitochondrion matrix
CC       {ECO:0000250|UniProtKB:Q96CM3}. Nucleus {ECO:0000250|UniProtKB:Q96CM3}.
CC       Cytoplasm {ECO:0000250|UniProtKB:Q96CM3}. Note=Mainly localizes to
CC       mitochondrion. Localizes to mitochondrial RNA granules, platforms for
CC       post-transcriptional RNA modification and ribosome assembly. Also found
CC       in nucleus and cytoplasm. {ECO:0000250|UniProtKB:Q96CM3}.
CC   -!- SIMILARITY: Belongs to the pseudouridine synthase RluA family.
CC       {ECO:0000305}.
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DR   EMBL; BC078405; AAH78405.1; -; mRNA.
DR   RefSeq; NP_001003495.1; NM_001003495.1.
DR   AlphaFoldDB; Q6DBR0; -.
DR   SMR; Q6DBR0; -.
DR   STRING; 7955.ENSDARP00000011603; -.
DR   PaxDb; Q6DBR0; -.
DR   PRIDE; Q6DBR0; -.
DR   Ensembl; ENSDART00000020283; ENSDARP00000011603; ENSDARG00000012674.
DR   Ensembl; ENSDART00000179986; ENSDARP00000152597; ENSDARG00000012674.
DR   Ensembl; ENSDART00000188329; ENSDARP00000144970; ENSDARG00000012674.
DR   GeneID; 445101; -.
DR   KEGG; dre:445101; -.
DR   CTD; 84881; -.
DR   ZFIN; ZDB-GENE-040801-238; rpusd4.
DR   eggNOG; KOG1919; Eukaryota.
DR   GeneTree; ENSGT00940000158436; -.
DR   HOGENOM; CLU_016902_2_1_1; -.
DR   InParanoid; Q6DBR0; -.
DR   OMA; RMRIAKH; -.
DR   OrthoDB; 1378690at2759; -.
DR   PhylomeDB; Q6DBR0; -.
DR   TreeFam; TF337899; -.
DR   PRO; PR:Q6DBR0; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 11.
DR   Bgee; ENSDARG00000012674; Expressed in ovary and 22 other tissues.
DR   GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0000455; P:enzyme-directed rRNA pseudouridine synthesis; IBA:GO_Central.
DR   GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR   GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR   GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR   CDD; cd02869; PseudoU_synth_RluA_like; 1.
DR   InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR   InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR   Pfam; PF00849; PseudoU_synth_2; 1.
DR   SUPFAM; SSF55120; SSF55120; 1.
PE   2: Evidence at transcript level;
KW   Cytoplasm; Isomerase; Mitochondrion; mRNA processing; mRNA splicing;
KW   Nucleus; Reference proteome; rRNA processing; Transit peptide;
KW   tRNA processing.
FT   TRANSIT         1..12
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           13..358
FT                   /note="Pseudouridylate synthase RPUSD4, mitochondrial"
FT                   /id="PRO_0000300828"
SQ   SEQUENCE   358 AA;  40133 MW;  3043EAF7192FBDBA CRC64;
     MRHAREVTFA RLMRTFAAVS DTQTVASKHK TAPKAADIAN RLRKEKEKEK DDKNEVPVSP
     LQSRVNELKQ FSQQLQSVHP SVFAKALYRS SLYEDQNIIA INKPYDVPLH NINGIRNSIA
     ECLPLLAKIT DNMRPGSQLH LCHKLEKETT GVLILAKTEE AAEHVQTLIQ SHKVEMKYLA
     ITVGVPVPSE GVIDIPVIER AVVGPQPHFK MALSPLFKVN EDGDGVTRVR AHRQAHAAVT
     RYQVLDNTSG CSLVELQPLT GVKNQLRVHM ALALTCPILG DHKYSHWSKL APQKLPEGTL
     RRLGLVQSKT RYLPLHLHSR RIVLPGFKGH RDITVSCPLP KYFINALKRL EIPLPAKE