NUD19_ARATH
ID NUD19_ARATH Reviewed; 438 AA.
AC Q94A82; Q0WV54; Q0WVK5;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Nudix hydrolase 19, chloroplastic {ECO:0000305};
DE Short=AtNUDT19 {ECO:0000303|PubMed:15878881};
DE AltName: Full=NAD-capped RNA hydrolase NUDT19;
DE Short=DeNADding enzyme NUDT19;
DE EC=3.6.1.- {ECO:0000250|UniProtKB:Q9DCN1};
DE AltName: Full=NADH pyrophosphatase NUDT19;
DE EC=3.6.1.22 {ECO:0000269|PubMed:18815383};
DE Flags: Precursor;
GN Name=NUDT19; Synonyms=NUDX19 {ECO:0000303|PubMed:15878881};
GN OrderedLocusNames=At5g20070; ORFNames=F28I16.220;
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=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(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].
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].
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NOMENCLATURE.
RX PubMed=15878881; DOI=10.1074/jbc.m503536200;
RA Ogawa T., Ueda Y., Yoshimura K., Shigeoka S.;
RT "Comprehensive analysis of cytosolic nudix hydrolases in Arabidopsis
RT thaliana.";
RL J. Biol. Chem. 280:25277-25283(2005).
RN [6]
RP SUBCELLULAR LOCATION, FUNCTION, CATALYTIC ACTIVITY, TISSUE SPECIFICITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND DISRUPTION PHENOTYPE.
RX PubMed=18815383; DOI=10.1104/pp.108.128413;
RA Ogawa T., Yoshimura K., Miyake H., Ishikawa K., Ito D., Tanabe N.,
RA Shigeoka S.;
RT "Molecular characterization of organelle-type Nudix hydrolases in
RT Arabidopsis.";
RL Plant Physiol. 148:1412-1424(2008).
CC -!- FUNCTION: mRNA decapping enzyme that specifically removes the
CC nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by
CC hydrolyzing the diphosphate linkage to produce nicotinamide
CC mononucleotide (NMN) and 5' monophosphate mRNA. The NAD-cap is present
CC at the 5'-end of some RNAs; in contrast to the canonical N7
CC methylguanosine (m7G) cap, the NAD cap promotes mRNA decay (By
CC similarity). Mediates the hydrolysis of some nucleoside diphosphate
CC derivatives. Has a high affinity for NADPH compared with that for NADH
CC (PubMed:18815383). {ECO:0000250|UniProtKB:Q9DCN1,
CC ECO:0000269|PubMed:18815383}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-
CC end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-
CC nicotinamide D-ribonucleotide + 2 H(+); Xref=Rhea:RHEA:60876,
CC Rhea:RHEA-COMP:15698, Rhea:RHEA-COMP:15719, ChEBI:CHEBI:14649,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:144029,
CC ChEBI:CHEBI:144051; Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60877;
CC Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NAD(+) = AMP + beta-nicotinamide D-ribonucleotide + 2
CC H(+); Xref=Rhea:RHEA:11800, ChEBI:CHEBI:14649, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:456215;
CC EC=3.6.1.22; Evidence={ECO:0000269|PubMed:18815383};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NADH = AMP + 2 H(+) + reduced beta-nicotinamide D-
CC ribonucleotide; Xref=Rhea:RHEA:48868, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57945, ChEBI:CHEBI:90832,
CC ChEBI:CHEBI:456215; EC=3.6.1.22;
CC Evidence={ECO:0000269|PubMed:18815383};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000250|UniProtKB:Q9DCN1};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q9DCN1};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q9DCN1};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=335.3 uM for NADH {ECO:0000269|PubMed:18815383};
CC KM=36.9 uM for NADPH {ECO:0000269|PubMed:18815383};
CC Vmax=0.74 umol/min/mg enzyme with NADH as substrate
CC {ECO:0000269|PubMed:18815383};
CC Vmax=0.78 umol/min/mg enzyme with NADPH as substrate
CC {ECO:0000269|PubMed:18815383};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:18815383}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and
CC inflorescences. {ECO:0000269|PubMed:18815383}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:18815383}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NudC subfamily.
CC {ECO:0000305}.
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DR EMBL; AF296836; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED92790.1; -; Genomic_DNA.
DR EMBL; AY049280; AAK83622.1; -; mRNA.
DR EMBL; AY090287; AAL90948.1; -; mRNA.
DR EMBL; AK226742; BAE98843.1; -; mRNA.
DR EMBL; AK226922; BAE98994.1; -; mRNA.
DR RefSeq; NP_197507.1; NM_122014.4.
DR AlphaFoldDB; Q94A82; -.
DR SMR; Q94A82; -.
DR STRING; 3702.AT5G20070.1; -.
DR iPTMnet; Q94A82; -.
DR PaxDb; Q94A82; -.
DR PRIDE; Q94A82; -.
DR ProteomicsDB; 226031; -.
DR EnsemblPlants; AT5G20070.1; AT5G20070.1; AT5G20070.
DR GeneID; 832129; -.
DR Gramene; AT5G20070.1; AT5G20070.1; AT5G20070.
DR KEGG; ath:AT5G20070; -.
DR Araport; AT5G20070; -.
DR TAIR; locus:2147665; AT5G20070.
DR eggNOG; KOG3084; Eukaryota.
DR HOGENOM; CLU_037162_0_2_1; -.
DR InParanoid; Q94A82; -.
DR OMA; DLVYWAV; -.
DR OrthoDB; 1436400at2759; -.
DR PhylomeDB; Q94A82; -.
DR BioCyc; ARA:AT5G20070-MON; -.
DR BRENDA; 3.6.1.22; 399.
DR SABIO-RK; Q94A82; -.
DR PRO; PR:Q94A82; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q94A82; baseline and differential.
DR Genevisible; Q94A82; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0005777; C:peroxisome; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000210; F:NAD+ diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0035529; F:NADH pyrophosphatase activity; IBA:GO_Central.
DR GO; GO:0110153; F:RNA NAD-cap (NMN-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0019677; P:NAD catabolic process; IBA:GO_Central.
DR GO; GO:0006734; P:NADH metabolic process; IBA:GO_Central.
DR GO; GO:0006742; P:NADP catabolic process; IBA:GO_Central.
DR InterPro; IPR015375; NADH_PPase-like_N.
DR InterPro; IPR020476; Nudix_hydrolase.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR InterPro; IPR015376; Znr_NADH_PPase.
DR Pfam; PF00293; NUDIX; 1.
DR Pfam; PF09296; NUDIX-like; 1.
DR Pfam; PF09297; zf-NADH-PPase; 1.
DR PRINTS; PR00502; NUDIXFAMILY.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Hydrolase; Magnesium; Metal-binding; NAD; Plastid;
KW Reference proteome; Transit peptide; Zinc.
FT TRANSIT 1..36
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 37..438
FT /note="Nudix hydrolase 19, chloroplastic"
FT /id="PRO_0000019943"
FT DOMAIN 241..371
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 277..298
FT /note="Nudix box"
FT MOTIF 422..424
FT /note="Microbody targeting signal"
FT /evidence="ECO:0000250|UniProtKB:Q9BQG2"
FT BINDING 212
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 215
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 230
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 235
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 240
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 276..278
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 276
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 292
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 292
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 292
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 296
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 296
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 296
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 342
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 342
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT BINDING 342
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9DCN1"
FT CONFLICT 125
FT /note="L -> M (in Ref. 4; BAE98843)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 438 AA; 48347 MW; BE99D765E6B8C15F CRC64;
MLALFLSSSS YPTLSFLSRS VTLNLARTTT LSALTMSMNL KTHAFAGNPL KSKTPKSTDP
FSPTSAFESL KTLIPVIPNH STPSPDFKVL PFSKGRPLVF SSGGDANTTP IWHLGWVSLA
DCKVLLASCG VDLNEDSLVY LGPKLEEDLV YWAVDLAEDG FVSELGGRKL CFVELRTLMV
AADWADQRAM DELAIAGNAR ALLEWHNVSQ FCGSCGSKTF PKEAGRRKQC SDETCRKRVY
PRVDPVVIML VIDRENDRAL LSRQSRYVPR MWSCLAGFIE PGESLEEAVR RETWEETGIE
VGDVVYHSSQ PWPVGPSSMP CQLMLGFFAF AKTLDINVDK EELEDAQWHS REEVKKALAV
AEYRKAQRTA AAKVEQICKG VERSQSLSTD FNLESGELAP MFIPGPFAIA HHLISAWVNQ
APDDVHSKQQ AGVSLSSL
