URT1_ARATH
ID URT1_ARATH Reviewed; 764 AA.
AC O64642; Q9C5K9;
DT 14-OCT-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=UTP:RNA uridylyltransferase 1 {ECO:0000303|PubMed:23748567};
DE EC=2.7.7.52 {ECO:0000269|PubMed:23748567};
GN Name=URT1 {ECO:0000303|PubMed:23748567};
GN OrderedLocusNames=At2g45620 {ECO:0000312|Araport:AT2G45620};
GN ORFNames=F17K2.15 {ECO:0000312|EMBL:AAC06161.2};
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 {ECO:0000312|Proteomes:UP000006548};
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=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 FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-491 AND ASP-493, AND
RP SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=23748567; DOI=10.1093/nar/gkt465;
RA Sement F.M., Ferrier E., Zuber H., Merret R., Alioua M., Deragon J.M.,
RA Bousquet-Antonelli C., Lange H., Gagliardi D.;
RT "Uridylation prevents 3' trimming of oligoadenylated mRNAs.";
RL Nucleic Acids Res. 41:7115-7127(2013).
RN [5]
RP FUNCTION, MUTAGENESIS OF PRO-618, SUBCELLULAR LOCATION, AND INTERACTION
RP WITH AGO1.
RX PubMed=25928341; DOI=10.1371/journal.pgen.1005091;
RA Wang X., Zhang S., Dou Y., Zhang C., Chen X., Yu B., Ren G.;
RT "Synergistic and independent actions of multiple terminal nucleotidyl
RT transferases in the 3' tailing of small RNAs in Arabidopsis.";
RL PLoS Genet. 11:E1005091-E1005091(2015).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, AND ACTIVITY REGULATION.
RX PubMed=25928405; DOI=10.1371/journal.pgen.1005119;
RA Tu B., Liu L., Xu C., Zhai J., Li S., Lopez M.A., Zhao Y., Yu Y.,
RA Ramachandran V., Ren G., Yu B., Li S., Meyers B.C., Mo B., Chen X.;
RT "Distinct and cooperative activities of HESO1 and URT1 nucleotidyl
RT transferases in microRNA turnover in Arabidopsis.";
RL PLoS Genet. 11:E1005119-E1005119(2015).
RN [7]
RP FUNCTION.
RX PubMed=26972004; DOI=10.1016/j.celrep.2016.02.060;
RA Zuber H., Scheer H., Ferrier E., Sement F.M., Mercier P., Stupfler B.,
RA Gagliardi D.;
RT "Uridylation and PABP cooperate to repair mRNA deadenylated ends in
RT Arabidopsis.";
RL Cell Rep. 14:2707-2717(2016).
RN [8]
RP FUNCTION.
RX PubMed=30364210; DOI=10.3389/fpls.2018.01438;
RA Zuber H., Scheer H., Joly A.C., Gagliardi D.;
RT "Respective contributions of URT1 and HESO1 to the uridylation of 5'
RT fragments produced from RISC-cleaved mRNAs.";
RL Front. Plant Sci. 9:1438-1438(2018).
RN [9]
RP FUNCTION.
RX PubMed=31076735; DOI=10.1038/s41477-019-0419-7;
RA Li T., Natran A., Chen Y., Vercruysse J., Wang K., Gonzalez N., Dubois M.,
RA Inze D.;
RT "A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA
RT metabolism and silencing.";
RL Nat. Plants 5:539-550(2019).
RN [10]
RP FUNCTION.
RX PubMed=33637717; DOI=10.1038/s41467-021-21382-2;
RA Scheer H., de Almeida C., Ferrier E., Simonnot Q., Poirier L., Pflieger D.,
RA Sement F.M., Koechler S., Piermaria C., Krawczyk P., Mroczek S.,
RA Chicher J., Kuhn L., Dziembowski A., Hammann P., Zuber H., Gagliardi D.;
RT "The TUTase URT1 connects decapping activators and prevents the
RT accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis.";
RL Nat. Commun. 12:1298-1298(2021).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS) OF 410-764 IN COMPLEX WITH UTP.
RX PubMed=32008746; DOI=10.1016/j.bbrc.2020.01.124;
RA Zhu L., Hu Q., Cheng L., Jiang Y., Lv M., Liu Y., Li F., Shi Y., Gong Q.;
RT "Crystal structure of Arabidopsis terminal uridylyl transferase URT1.";
RL Biochem. Biophys. Res. Commun. 524:490-496(2020).
CC -!- FUNCTION: UTP:RNA uridylyltransferase with a marked preference for
CC uridine polymerization and a distributive activity for the first added
CC nucleotides (PubMed:23748567, PubMed:25928405). Uridylates oligo(A)-
CC tailed mRNAs to prevent 3' to 5' ribonucleotytic attacks
CC (PubMed:23748567). Reduces the accumulation of oligo(A)-tailed mRNAs
CC (PubMed:33637717). Prevents the accumulation of excessively
CC deadenylated mRNAs to avoid siRNA biogenesis (PubMed:26972004,
CC PubMed:33637717). Uridylation repairs deadenylated extremities to
CC restore the size distribution observed for non-uridylated oligo(A)
CC tails (PubMed:26972004). Can prevent the 3' trimming of mRNAs still
CC engaged on polysomes (PubMed:23748567). Acts synergistically with HESO1
CC in unmethylated miRNA uridylation, leading to their degradation
CC (PubMed:25928341). URT1 and HESO1 prefer substrates with different 3'
CC end nucleotides and act cooperatively to tail different forms of the
CC same miRNAs (PubMed:25928405). URT1 and HESO1 act sequentially, with
CC URT1 mono-uridylating the miRNAs followed by their further uridylation
CC by HESO1 (PubMed:25928405). URT1 and HESO1 are involved in the
CC uridylation and clearance of RISC-generated 5' mRNA fragments
CC (PubMed:30364210). Has no effect on uridylation of heterochromatic
CC siRNAs (PubMed:25928341). Able to act on AGO1-bound miRNAs and the
CC uridylated species stay associated with AGO1 (PubMed:25928405). Acts as
CC post-transcriptional gene silencing (PTGS) suppressor
CC (PubMed:31076735). {ECO:0000269|PubMed:23748567,
CC ECO:0000269|PubMed:25928341, ECO:0000269|PubMed:25928405,
CC ECO:0000269|PubMed:26972004, ECO:0000269|PubMed:30364210,
CC ECO:0000269|PubMed:31076735, ECO:0000269|PubMed:33637717}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=RNA(n) + UTP = diphosphate + RNA(n)-3'-uridine ribonucleotide;
CC Xref=Rhea:RHEA:14785, Rhea:RHEA-COMP:14527, Rhea:RHEA-COMP:17348,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:46398, ChEBI:CHEBI:140395,
CC ChEBI:CHEBI:173116; EC=2.7.7.52;
CC Evidence={ECO:0000269|PubMed:23748567, ECO:0000269|PubMed:25928405};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q9NVV4};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q9NVV4};
CC -!- ACTIVITY REGULATION: Completely inhibited by 2'-O-methylation on the
CC substrate RNA. {ECO:0000269|PubMed:25928405}.
CC -!- SUBUNIT: Interacts with AGO1. {ECO:0000269|PubMed:25928341}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:23748567}.
CC Cytoplasm, P-body {ECO:0000269|PubMed:23748567,
CC ECO:0000269|PubMed:25928341}. Note=The P618L single amino acid
CC substitutiontarget URT1 to the nucleoplasm.
CC {ECO:0000269|PubMed:25928341}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B-like family.
CC {ECO:0000305}.
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DR EMBL; AC003680; AAC06161.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC10577.1; -; Genomic_DNA.
DR EMBL; AF360181; AAK25891.1; -; mRNA.
DR EMBL; AY039997; AAK64074.1; -; mRNA.
DR PIR; T00875; T00875.
DR RefSeq; NP_566048.1; NM_130124.1.
DR PDB; 6L3F; X-ray; 1.98 A; A=410-764.
DR PDB; 6L8K; X-ray; 3.00 A; A=410-764.
DR PDBsum; 6L3F; -.
DR PDBsum; 6L8K; -.
DR AlphaFoldDB; O64642; -.
DR SMR; O64642; -.
DR STRING; 3702.AT2G45620.1; -.
DR iPTMnet; O64642; -.
DR PaxDb; O64642; -.
DR PRIDE; O64642; -.
DR ProteomicsDB; 228699; -.
DR EnsemblPlants; AT2G45620.1; AT2G45620.1; AT2G45620.
DR GeneID; 819170; -.
DR Gramene; AT2G45620.1; AT2G45620.1; AT2G45620.
DR KEGG; ath:AT2G45620; -.
DR Araport; AT2G45620; -.
DR TAIR; locus:2043669; AT2G45620.
DR eggNOG; KOG2277; Eukaryota.
DR HOGENOM; CLU_023274_0_0_1; -.
DR InParanoid; O64642; -.
DR OMA; NDIHRYD; -.
DR OrthoDB; 803033at2759; -.
DR PhylomeDB; O64642; -.
DR BRENDA; 2.7.7.52; 399.
DR PRO; PR:O64642; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; O64642; baseline and differential.
DR Genevisible; O64642; AT.
DR GO; GO:0000932; C:P-body; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; HDA:TAIR.
DR GO; GO:0016779; F:nucleotidyltransferase activity; IBA:GO_Central.
DR GO; GO:0050265; F:RNA uridylyltransferase activity; IDA:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IMP:TAIR.
DR GO; GO:0060965; P:negative regulation of miRNA-mediated gene silencing; IDA:GO_Central.
DR GO; GO:1900369; P:negative regulation of post-transcriptional gene silencing by RNA; IGI:TAIR.
DR GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; IDA:TAIR.
DR GO; GO:1903705; P:positive regulation of siRNA production; IDA:UniProtKB.
DR GO; GO:0071076; P:RNA 3' uridylation; IDA:UniProtKB.
DR GO; GO:0031123; P:RNA 3'-end processing; IBA:GO_Central.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR002058; PAP_assoc.
DR InterPro; IPR045100; TUTase_dom.
DR Pfam; PF03828; PAP_assoc; 1.
DR Pfam; PF19088; TUTase; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Magnesium; Metal-binding; mRNA processing;
KW Reference proteome; Transferase.
FT CHAIN 1..764
FT /note="UTP:RNA uridylyltransferase 1"
FT /id="PRO_0000434142"
FT DOMAIN 656..714
FT /note="PAP-associated"
FT /evidence="ECO:0000255"
FT REGION 1..79
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 185..271
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 339..367
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 381..412
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 26..40
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 56..74
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 185..202
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 203..219
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 255..271
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 480
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:32008746,
FT ECO:0007744|PDB:6L8K"
FT BINDING 491
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q9NVV4"
FT BINDING 493
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q9NVV4"
FT BINDING 555..559
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:32008746,
FT ECO:0007744|PDB:6L8K"
FT BINDING 580
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:32008746,
FT ECO:0007744|PDB:6L8K"
FT BINDING 584
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:32008746,
FT ECO:0007744|PDB:6L8K"
FT BINDING 598..599
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:32008746,
FT ECO:0007744|PDB:6L8K"
FT BINDING 708
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:32008746,
FT ECO:0007744|PDB:6L8K"
FT BINDING 714
FT /ligand="UTP"
FT /ligand_id="ChEBI:CHEBI:46398"
FT /evidence="ECO:0000269|PubMed:32008746,
FT ECO:0007744|PDB:6L8K"
FT MUTAGEN 491
FT /note="D->A: Loss of catalytic activity; when associated
FT with A-493."
FT /evidence="ECO:0000269|PubMed:23748567"
FT MUTAGEN 493
FT /note="D->A: Loss of catalytic activity; when associated
FT with A-491."
FT /evidence="ECO:0000269|PubMed:23748567"
FT MUTAGEN 618
FT /note="P->L: In urt1-3; Decreased catalytic activity and
FT relocalization to the nucleoplasm."
FT /evidence="ECO:0000269|PubMed:25928341"
FT HELIX 431..434
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 435..445
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 449..469
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 474..478
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 479..481
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 490..497
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 505..518
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 522..529
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 532..538
FT /evidence="ECO:0007829|PDB:6L3F"
FT TURN 540..542
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 545..550
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 553..566
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 571..585
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 591..593
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 598..611
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 612..614
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 620..622
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 626..631
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 634..638
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 642..645
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 648..651
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 656..669
FT /evidence="ECO:0007829|PDB:6L3F"
FT TURN 673..675
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 676..679
FT /evidence="ECO:0007829|PDB:6L3F"
FT TURN 680..683
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 684..688
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 703..707
FT /evidence="ECO:0007829|PDB:6L3F"
FT STRAND 709..711
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 716..719
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 724..741
FT /evidence="ECO:0007829|PDB:6L3F"
FT HELIX 745..749
FT /evidence="ECO:0007829|PDB:6L3F"
SQ SEQUENCE 764 AA; 85764 MW; 33757363CD158B9C CRC64;
MADGGAEPPA PPSSINAGEF LLSILHGSPS PSSQGPQHHQ SFALDPAIAA IGPTVNNPFP
PSNWQSNGHR PSNHNPPSWP LAFSPPHNLS PNFLGFPQFP PSPFTTNQFD GNQRVSPEDA
YRLGFPGTTN PAIQSMVQQQ QQQQLPPPQS ETRKLVFGSF SGDATQSLNG LHNGNLKYDS
NQHEQLMRHP QSTLSNSNMD PNLSHHRNHD LHEQRGGHSG RGNWGHIGNN GRGLKSTPPP
PPPGFSSNQR GWDMSLGSKD DDRGMGRNHD QAMGEHSKVW NQSVDFSAEA NRLRGLSIQN
ESKFNLSQQI DHPGPPKGAS LHSVSAADAA DSFSMLNKEA RRGGERREEL GQLSKAKREG
NANSDEIEDF GEDIVKSLLL EDETGEKDAN DGKKDSKTSR EKESRVDNRG QRLLGQKARM
VKMYMACRND IHRYDATFIA IYKSLIPAEE ELEKQRQLMA HLENLVAKEW PHAKLYLYGS
CANSFGFPKS DIDVCLAIEG DDINKSEMLL KLAEILESDN LQNVQALTRA RVPIVKLMDP
VTGISCDICI NNVLAVVNTK LLRDYAQIDV RLRQLAFIVK HWAKSRRVNE TYQGTLSSYA
YVLMCIHFLQ QRRPPILPCL QEMEPTYSVR VDNIRCTYFD NVDRLRNFGS NNRETIAELV
WGFFNYWAYA HDYAYNVVSV RTGSILGKRE KDWTRRVGND RHLICIEDPF ETSHDLGRVV
DKFSIRVLRE EFERAARIMH QDPNPCAKLL EPYIPEDNNG QGHN
