SVR1_ARATH
ID SVR1_ARATH Reviewed; 410 AA.
AC Q8L960; O80966; O80967;
DT 12-APR-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Putative ribosomal large subunit pseudouridine synthase SVR1, chloroplastic {ECO:0000305};
DE EC=5.4.99.- {ECO:0000305};
DE AltName: Full=Protein PIGMENT DEFECTIVE 328 {ECO:0000305};
DE AltName: Full=Protein SUPPRESSOR OF VARIEGATION 1 {ECO:0000303|PubMed:18599582};
DE Flags: Precursor;
GN Name=SVR1; Synonyms=PDE328 {ECO:0000305};
GN OrderedLocusNames=At2g39140 {ECO:0000312|Araport:AT2G39140};
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE,
RP AND MUTAGENESIS OF ASP-274.
RX PubMed=18599582; DOI=10.1105/tpc.107.054965;
RA Yu F., Liu X., Alsheikh M., Park S., Rodermel S.;
RT "Mutations in SUPPRESSOR OF VARIEGATION1, a factor required for normal
RT chloroplast translation, suppress var2-mediated leaf variegation in
RT Arabidopsis.";
RL Plant Cell 20:1786-1804(2008).
CC -!- FUNCTION: Responsible for synthesis of pseudouridine in chloroplastic
CC 23S ribosomal RNA (Probable). Necessary for normal chloroplast rRNA
CC processing and translation. Required for normal chloroplast development
CC and maintenance. May function in other plastids, such as root
CC amyloplasts (PubMed:18599582). {ECO:0000269|PubMed:18599582,
CC ECO:0000305|PubMed:18599582}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:18599582}.
CC -!- TISSUE SPECIFICITY: Highly expressed in young seedlings. Expressed in
CC roots, rosette leaves, cauline leaves, stems and flowers.
CC {ECO:0000269|PubMed:18599582}.
CC -!- DISRUPTION PHENOTYPE: Yellow-green leaves and significantly reduced
CC plant size. Impaired rRNA processing and translation in chloroplasts.
CC {ECO:0000269|PubMed:18599582}.
CC -!- SIMILARITY: Belongs to the pseudouridine synthase RsuA family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC28992.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes.; Evidence={ECO:0000305};
CC Sequence=AAC28994.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes.; Evidence={ECO:0000305};
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DR EMBL; AC004697; AAC28992.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC004697; AAC28994.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC09639.1; -; Genomic_DNA.
DR EMBL; AK117682; BAC42334.1; -; mRNA.
DR EMBL; AY088622; AAM66944.1; -; mRNA.
DR PIR; T02587; T02587.
DR PIR; T02588; T02588.
DR RefSeq; NP_181447.2; NM_129471.3.
DR AlphaFoldDB; Q8L960; -.
DR SMR; Q8L960; -.
DR STRING; 3702.AT2G39140.1; -.
DR PaxDb; Q8L960; -.
DR PRIDE; Q8L960; -.
DR ProteomicsDB; 226787; -.
DR EnsemblPlants; AT2G39140.1; AT2G39140.1; AT2G39140.
DR GeneID; 818500; -.
DR Gramene; AT2G39140.1; AT2G39140.1; AT2G39140.
DR KEGG; ath:AT2G39140; -.
DR Araport; AT2G39140; -.
DR TAIR; locus:2056108; AT2G39140.
DR eggNOG; ENOG502QT4T; Eukaryota.
DR HOGENOM; CLU_056831_0_0_1; -.
DR InParanoid; Q8L960; -.
DR OMA; GRDIIYV; -.
DR OrthoDB; 1501638at2759; -.
DR PhylomeDB; Q8L960; -.
DR BioCyc; ARA:AT2G39140-MON; -.
DR BRENDA; 5.4.99.B22; 399.
DR PRO; PR:Q8L960; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q8L960; baseline and differential.
DR GO; GO:0009501; C:amyloplast; TAS:TAIR.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0009982; F:pseudouridine synthase activity; TAS:TAIR.
DR GO; GO:0000488; P:maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA); IMP:TAIR.
DR GO; GO:0000489; P:maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA); IMP:TAIR.
DR GO; GO:0032544; P:plastid translation; IMP:TAIR.
DR GO; GO:0001522; P:pseudouridine synthesis; IEA:InterPro.
DR CDD; cd00165; S4; 1.
DR Gene3D; 3.10.290.10; -; 1.
DR Gene3D; 3.30.70.1560; -; 1.
DR Gene3D; 3.30.70.580; -; 1.
DR InterPro; IPR042092; PsdUridine_s_RsuA/RluB/E/F_cat.
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR InterPro; IPR018496; PsdUridine_synth_RsuA/RluB_CS.
DR InterPro; IPR002942; S4_RNA-bd.
DR InterPro; IPR036986; S4_RNA-bd_sf.
DR InterPro; IPR020094; TruA/RsuA/RluB/E/F_N.
DR Pfam; PF00849; PseudoU_synth_2; 1.
DR Pfam; PF01479; S4; 1.
DR SMART; SM00363; S4; 1.
DR SUPFAM; SSF55120; SSF55120; 1.
DR PROSITE; PS01149; PSI_RSU; 1.
DR PROSITE; PS50889; S4; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Isomerase; Plastid; Reference proteome; RNA-binding;
KW rRNA processing; Transit peptide.
FT TRANSIT 1..35
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 36..410
FT /note="Putative ribosomal large subunit pseudouridine
FT synthase SVR1, chloroplastic"
FT /evidence="ECO:0000255"
FT /id="PRO_0000439378"
FT DOMAIN 160..229
FT /note="S4 RNA-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00182"
FT REGION 96..143
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 118..138
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 274
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P37765"
FT MUTAGEN 274
FT /note="D->N: No effect on the function in rRNA processing."
FT /evidence="ECO:0000269|PubMed:18599582"
SQ SEQUENCE 410 AA; 45108 MW; 5B8B83E531272B9F CRC64;
MASVAASSSI SFAASFLKIK AFPLSPRFFP IRTLRCSVSS SSSEPIEFDI SFAPPKPKPS
STHGGVTPQQ LFIPWIVRSD DGTLKLQSQP PARLIHNLAI DATTQNPKKK DKSKKKQPQA
TSSSSATTTA SSPASHSEVK PKLSKAARRF YNENFKEQPQ RLSKVLAAAG VASRRTSEEL
IFDGKVTVNG ILCNTPQTRV DPSRDIIYVN GNRIPKKLPP KVYFALNKPK GYICSSGEKE
IKSAISLFDE YLSSWDKRNP GTPKPRLFTV GRLDVATTGL IVVTNDGDFA QKLSHPSSSL
PKEYITTVVG DIHKRHLMAI SEGTMVEGVH CVPDSVELMP KQHDIPRARL RIVVHEGRNH
EVRELVKNAG LEVHSLKRVR IGGFRLPSDL GLGKHVELKQ SELKALGWKN
