PUS5_ARATH
ID PUS5_ARATH Reviewed; 369 AA.
AC Q5M721; Q8VYW0; Q9FT56;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 05-MAY-2009, sequence version 2.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=RNA pseudouridine synthase 5;
DE EC=5.4.99.-;
DE AltName: Full=RNA pseudouridylate synthase 5;
DE AltName: Full=RNA-uridine isomerase 5;
GN OrderedLocusNames=At3g52260; ORFNames=T25B15.30;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q5M721-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q5M721-2; Sequence=VSP_037036;
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing donor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the pseudouridine synthase RluA family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAC07917.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL132972; CAC07917.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78921.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78922.1; -; Genomic_DNA.
DR EMBL; AY069882; AAL47436.1; -; mRNA.
DR EMBL; BX823148; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; BT020427; AAW28554.1; -; mRNA.
DR PIR; T46096; T46096.
DR RefSeq; NP_190794.2; NM_115086.3. [Q5M721-2]
DR RefSeq; NP_974416.1; NM_202687.3. [Q5M721-1]
DR AlphaFoldDB; Q5M721; -.
DR SMR; Q5M721; -.
DR ProteomicsDB; 236545; -. [Q5M721-1]
DR EnsemblPlants; AT3G52260.1; AT3G52260.1; AT3G52260. [Q5M721-2]
DR EnsemblPlants; AT3G52260.2; AT3G52260.2; AT3G52260. [Q5M721-1]
DR GeneID; 824391; -.
DR Gramene; AT3G52260.1; AT3G52260.1; AT3G52260. [Q5M721-2]
DR Gramene; AT3G52260.2; AT3G52260.2; AT3G52260. [Q5M721-1]
DR KEGG; ath:AT3G52260; -.
DR Araport; AT3G52260; -.
DR InParanoid; Q5M721; -.
DR OMA; TTYMHIG; -.
DR PhylomeDB; Q5M721; -.
DR PRO; PR:Q5M721; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q5M721; baseline and differential.
DR Genevisible; Q5M721; AT.
DR GO; GO:0009982; F:pseudouridine synthase activity; IEA:InterPro.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0001522; P:pseudouridine synthesis; IEA:InterPro.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProt.
DR CDD; cd02869; PseudoU_synth_RluA_like; 1.
DR CDD; cd00165; S4; 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 InterPro; IPR002942; S4_RNA-bd.
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; Reference proteome; RNA-binding.
FT CHAIN 1..369
FT /note="RNA pseudouridine synthase 5"
FT /id="PRO_0000371425"
FT DOMAIN 47..104
FT /note="S4 RNA-binding"
FT VAR_SEQ 290..369
FT /note="VGDPLYVAGGQPKCFDPDLVDDAAAFAEDGGYRRPNQAVPGDCGYHLHAHQV
FT ELPNLLNTHKVVKIVAPLPPILQTRCET -> GTLFM (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172, ECO:0000303|Ref.5"
FT /id="VSP_037036"
FT CONFLICT 245
FT /note="G -> W (in Ref. 3; AAL47436)"
FT /evidence="ECO:0000305"
FT CONFLICT 352
FT /note="V -> I (in Ref. 4; BX823148)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 369 AA; 40562 MW; 2D69A67CDF364C58 CRC64;
MSPPPQRIGL PWPELNDGLA YKDAISSSES ELTTVSEFYF TKYKSSAPLL GWIQRIQNGQ
IQIDGEVVKD PNTLLRSGSK LVYSRLPWKE PDTPYSLEVL YEDDDLIALN KPSGLQVLPG
GLFQQRTVLT QLQWCFGKND SYIGSRESPH PVPVHRLGRG TSGILLCAKT KLAKTKLAAY
FAEGTSLVGS GNLDQECGTG RKLSKIYRAL ADGIVEEDEV VIKQPIGVVR YPGVAQGLYV
ASPEGKPAFS KVFVLERDRE KNCSLVKVEI QSGRPHQIRI HLAYMGHPLV GDPLYVAGGQ
PKCFDPDLVD DAAAFAEDGG YRRPNQAVPG DCGYHLHAHQ VELPNLLNTH KVVKIVAPLP
PILQTRCET
