DXO_ARATH
ID DXO_ARATH Reviewed; 544 AA.
AC Q8RY73; O23603;
DT 21-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=NAD-capped RNA hydrolase DXO1 {ECO:0000305};
DE Short=DeNADding enzyme DXO1 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000269|PubMed:30949699};
GN Name=DXO1 {ECO:0000303|PubMed:30949699}; OrderedLocusNames=At4g17620;
GN ORFNames=dl4845w, FCAALL.74;
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=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
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 [4]
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 [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-119, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [6] {ECO:0007744|PDB:6DKN}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 196-544, FUNCTION, CATALYTIC
RP ACTIVITY, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP 394-GLU--ASP-396.
RX PubMed=30949699; DOI=10.1093/nar/gkz100;
RA Kwasnik A., Wang V.Y., Krzyszton M., Gozdek A., Zakrzewska-Placzek M.,
RA Stepniak K., Poznanski J., Tong L., Kufel J.;
RT "Arabidopsis DXO1 links RNA turnover and chloroplast function independently
RT of its enzymatic activity.";
RL Nucleic Acids Res. 47:4751-4764(2019).
CC -!- FUNCTION: Decapping enzyme for NAD-capped RNAs: specifically hydrolyzes
CC the nicotinamide adenine dinucleotide (NAD) cap from a subset of RNAs
CC by removing the entire NAD moiety from the 5'-end of an NAD-capped RNA
CC (PubMed:30949699). The NAD-cap is present at the 5'-end of some RNAs
CC and promotes mRNA decay (By similarity). Its precise role is unclear:
CC may be involved in the connection between RNA turnover and retrograde
CC chloroplast-to-nucleus signaling independently of its deNADding
CC activity (PubMed:30949699). {ECO:0000250|UniProtKB:O70348,
CC ECO:0000269|PubMed:30949699}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-
CC end phospho-ribonucleoside in mRNA + H(+) + NAD(+);
CC Xref=Rhea:RHEA:60880, Rhea:RHEA-COMP:15692, Rhea:RHEA-COMP:15698,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:138282, ChEBI:CHEBI:144029;
CC Evidence={ECO:0000269|PubMed:30949699};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60881;
CC Evidence={ECO:0000269|PubMed:30949699};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC Note=Binds 2 magnesium ions. {ECO:0000250|UniProtKB:O70348};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:30949699}. Nucleus
CC {ECO:0000269|PubMed:30949699}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q8RY73-1; Sequence=Displayed;
CC -!- DISRUPTION PHENOTYPE: Growth and pigmentation defects associated with
CC global transcriptomic changes and accumulation of RNA quality control
CC siRNAs. {ECO:0000269|PubMed:30949699}.
CC -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
CC -!- CAUTION: In contrast to other members of the family, shows reduced
CC activity toward of m7G capped or incompletely capped RNAs, probably
CC caused by the presence of an Asn residue in position 298 instead of a
CC Gly (PubMed:30949699). The presence of an Asn-298 does not affect the
CC decapping activity on NAD-cap RNAs (PubMed:30949699).
CC {ECO:0000269|PubMed:30949699}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB10542.1; Type=Erroneous gene model prediction; Note=The predicted gene At4g17620 has been split into 3 genes: At4g17615, At4g17616 and At4g17620.; Evidence={ECO:0000305};
CC Sequence=CAB78765.1; Type=Erroneous gene model prediction; Note=The predicted gene At4g17620 has been split into 3 genes: At4g17615, At4g17616 and At4g17620.; Evidence={ECO:0000305};
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DR EMBL; Z97343; CAB10542.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161546; CAB78765.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83924.1; -; Genomic_DNA.
DR EMBL; AY074548; AAL69514.1; -; mRNA.
DR EMBL; AY133815; AAM91749.1; -; mRNA.
DR PIR; A71446; A71446.
DR RefSeq; NP_193498.2; NM_117871.5. [Q8RY73-1]
DR PDB; 6DKN; X-ray; 1.80 A; A/B=196-544.
DR PDBsum; 6DKN; -.
DR AlphaFoldDB; Q8RY73; -.
DR SMR; Q8RY73; -.
DR STRING; 3702.AT4G17620.1; -.
DR iPTMnet; Q8RY73; -.
DR PaxDb; Q8RY73; -.
DR ProteomicsDB; 222039; -. [Q8RY73-1]
DR EnsemblPlants; AT4G17620.1; AT4G17620.1; AT4G17620. [Q8RY73-1]
DR GeneID; 827482; -.
DR Gramene; AT4G17620.1; AT4G17620.1; AT4G17620. [Q8RY73-1]
DR KEGG; ath:AT4G17620; -.
DR Araport; AT4G17620; -.
DR TAIR; locus:2129311; AT4G17620.
DR eggNOG; KOG1982; Eukaryota.
DR HOGENOM; CLU_024877_3_0_1; -.
DR OMA; WIQSFIA; -.
DR PhylomeDB; Q8RY73; -.
DR PRO; PR:Q8RY73; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8RY73; baseline and differential.
DR Genevisible; Q8RY73; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:TAIR.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IDA:TAIR.
DR GO; GO:0016787; F:hydrolase activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IDA:TAIR.
DR GO; GO:0110152; F:RNA NAD-cap (NAD-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0034353; F:RNA pyrophosphohydrolase activity; IBA:GO_Central.
DR GO; GO:0110155; P:NAD-cap decapping; IBA:GO_Central.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IDA:TAIR.
DR GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; IDA:TAIR.
DR InterPro; IPR013961; RAI1.
DR InterPro; IPR039039; RAI1-like_fam.
DR PANTHER; PTHR12395; PTHR12395; 1.
DR Pfam; PF08652; RAI1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cytoplasm; Hydrolase; Magnesium;
KW Metal-binding; Nuclease; Nucleotide-binding; Nucleus; Phosphoprotein;
KW Reference proteome; RNA-binding.
FT CHAIN 1..544
FT /note="NAD-capped RNA hydrolase DXO1"
FT /id="PRO_0000013633"
FT REGION 1..121
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 136..188
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..24
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 25..53
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 77..92
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 100..118
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 272
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 296..298
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 352
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 352
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 377
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 394
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 394
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 396
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 396
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 410
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 411
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 412
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 436
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT MOD_RES 119
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MUTAGEN 394..396
FT /note="EMD->AMA: Abolishes the decapping activity on NAD-
FT cap RNAs."
FT /evidence="ECO:0000269|PubMed:30949699"
FT STRAND 197..202
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 207..211
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 221..228
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 248..251
FT /evidence="ECO:0007829|PDB:6DKN"
FT TURN 256..259
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 260..262
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 271..283
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 293..296
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 297..305
FT /evidence="ECO:0007829|PDB:6DKN"
FT TURN 306..308
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 314..321
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 324..329
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 339..354
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 375..384
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 387..394
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 397..400
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 406..415
FT /evidence="ECO:0007829|PDB:6DKN"
FT TURN 419..421
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 422..427
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 429..439
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 444..450
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 454..463
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 464..473
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 479..496
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 502..507
FT /evidence="ECO:0007829|PDB:6DKN"
FT STRAND 512..518
FT /evidence="ECO:0007829|PDB:6DKN"
FT HELIX 524..532
FT /evidence="ECO:0007829|PDB:6DKN"
SQ SEQUENCE 544 AA; 60381 MW; 4BBD27AC6E2D0853 CRC64;
MDSPPKKNPM DDLFGEDSDN DSRSSRSKSS SSGNASSSSS SSSSSSSSSS AAGGDGEGDG
GGADSGSASD SGSGSSGGKE EHGDDKVESY RSNDNGESGV YPYEEEEEEE EDEKDLFGSD
NEEYTKTPAI STYSIPVLPA GWSNDNHGGR GGMGRGRWSN GRGGPGLLPR PGPYPGRGGN
RGGFGGRYQN YQRDERFVSE LKLSKSKETL ARKQTNFQEP CELTCYSRVE GGEVIYDDQG
LRLFKRHIGE EIGADLNQGY DTFIEKKDLG SEGFGDLLGS IRAKNISLDN IHFVTFRNNL
NKILGAAYNR HEPWEMGVHK RNGTIYLDVH KLPERPQSDL DRRRCYWGYC FESLATEDPG
RAYGEEIHHV DANVEFCSVV RTKLGAHRVM MGAEMDCCDV SDKGKRFYVE LKTTRELDDR
TVDRFEREKL LKFWIQSFVA GVPYIVVGFR DDGGRLVRTE RLTTRDIAHR ARLKNYWQGG
VCLAFADEVL CWLYGTVKEN EDYILQFVHP FMRLELLQAQ SCPDAITNHV HLLQNPASPP
PPPQ
