ID   PUS3_ARATH              Reviewed;         478 AA.
AC   Q5XET6; Q67Z99; Q9ZVA9;
DT   05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   03-AUG-2022, entry version 110.
DE   RecName: Full=RNA pseudouridine synthase 3, mitochondrial;
DE            EC=5.4.99.-;
DE   AltName: Full=RNA pseudouridylate synthase 3;
DE   AltName: Full=RNA-uridine isomerase 3;
DE   Flags: Precursor;
GN   OrderedLocusNames=At1g78910; ORFNames=F9K20.4;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130712; DOI=10.1038/35048500;
RA   Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA   Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA   Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA   Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA   Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA   Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA   Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA   Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA   Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA   Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA   Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA   Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA   Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA   Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA   Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL   Nature 408:816-820(2000).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   STRAIN=cv. Columbia;
RA   Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA   Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA   Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA   Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA   Shinozaki K.;
RT   "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL   Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC   STRAIN=cv. Columbia;
RA   Shinn P., Chen H., Cheuk R.F., Kim C.J., Ecker J.R.;
RT   "Arabidopsis ORF clones.";
RL   Submitted (DEC-2004) to the EMBL/GenBank/DDBJ databases.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a uridine in RNA = a pseudouridine in RNA;
CC         Xref=Rhea:RHEA:48348, Rhea:RHEA-COMP:12068, Rhea:RHEA-COMP:12069,
CC         ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC   -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q5XET6-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q5XET6-2; Sequence=VSP_037035;
CC   -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC       site. {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the pseudouridine synthase RluA family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAC83020.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AC005679; AAC83020.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002684; AEE36173.1; -; Genomic_DNA.
DR   EMBL; AK176219; BAD43982.1; -; mRNA.
DR   EMBL; BT015880; AAU95416.1; -; mRNA.
DR   EMBL; BT020453; AAW30031.1; -; mRNA.
DR   PIR; F96818; F96818.
DR   RefSeq; NP_178012.2; NM_106540.3. [Q5XET6-1]
DR   AlphaFoldDB; Q5XET6; -.
DR   STRING; 3702.AT1G78910.1; -.
DR   PaxDb; Q5XET6; -.
DR   PRIDE; Q5XET6; -.
DR   ProteomicsDB; 226461; -. [Q5XET6-1]
DR   EnsemblPlants; AT1G78910.1; AT1G78910.1; AT1G78910. [Q5XET6-1]
DR   GeneID; 844229; -.
DR   Gramene; AT1G78910.1; AT1G78910.1; AT1G78910. [Q5XET6-1]
DR   KEGG; ath:AT1G78910; -.
DR   Araport; AT1G78910; -.
DR   TAIR; locus:2037593; AT1G78910.
DR   eggNOG; KOG1919; Eukaryota.
DR   HOGENOM; CLU_016902_13_0_1; -.
DR   InParanoid; Q5XET6; -.
DR   OrthoDB; 1378690at2759; -.
DR   PhylomeDB; Q5XET6; -.
DR   BioCyc; ARA:AT1G78910-MON; -.
DR   PRO; PR:Q5XET6; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q5XET6; baseline and differential.
DR   GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR   GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0000455; P:enzyme-directed rRNA pseudouridine synthesis; IBA:GO_Central.
DR   CDD; cd02869; PseudoU_synth_RluA_like; 1.
DR   InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR   InterPro; IPR006224; PsdUridine_synth_RluC/D_CS.
DR   InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR   Pfam; PF00849; PseudoU_synth_2; 1.
DR   SUPFAM; SSF55120; SSF55120; 1.
DR   PROSITE; PS01129; PSI_RLU; 1.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Isomerase; Mitochondrion; Reference proteome;
KW   RNA-binding; Transit peptide.
FT   TRANSIT         1..20
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           21..478
FT                   /note="RNA pseudouridine synthase 3, mitochondrial"
FT                   /id="PRO_0000371423"
FT   DOMAIN          92..162
FT                   /note="S4 RNA-binding"
FT   ACT_SITE        232
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         1..152
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000303|Ref.3"
FT                   /id="VSP_037035"
SQ   SEQUENCE   478 AA;  53801 MW;  85E4749371DA8353 CRC64;
     MWKAKTCFRQ IYLTVLIRRY SRVAPPPSSV IRVTNNVAHL GPPKQGPLPR QLISLPPFPG
     HPLPGKNAGA DGDDGDSGGH VTAISWVKYY FEEIYDKAIQ THFTKGLVQM EFRGRRDASR
     EKEDGAIPMR KIKHNEVMQI GDKIWLPVSI AEMRISKRYD TIPSGTLYPN ADEIAYLQRL
     VRFKDSAIIV LNKPPKLPVK GNVPIHNSMD ALAAAALSFG NDEGPRLVHR LDRETSGLLV
     MGRTKESIDY LHSVFSDYKG RNSSCKAWNK ACEAMYQQYW ALVIGSPKEK EGLISAPLSK
     VLLDDGKTDR VVLAQGSGFE ASQDAITEYK VLGPKINGCS WVELRPITSR KHQLRVHCAE
     ALGTPIVGDY KYGWFVHKRW KQMPQVDIEP TTGKPYKLRR PEGLDVQKGS VLSKVPLLHL
     HCREMVLPNI AKFLHVMNQQ ETEPLHTGII DKPDLLRFVA SMPSHMKISW NLMSSYLV