ID NUD15_ARATH Reviewed; 285 AA.
AC Q8GYB1; Q0WKX6; Q3E701; Q3E702; Q67YK3; Q9SHQ7;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2005, sequence version 2.
DT 27-MAR-2024, entry version 130.
DE RecName: Full=Nudix hydrolase 15, mitochondrial;
DE Short=AtNUDT15;
DE EC=3.6.1.-;
DE AltName: Full=Coenzyme A diphosphatase NUDT15;
DE Flags: Precursor;
GN Name=NUDT15; Synonyms=NUDX15; OrderedLocusNames=At1g28960;
GN ORFNames=F1K23.16, F1K23.5;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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] (ISOFORMS 1 AND 3).
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] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [6]
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 [7]
RP SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
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).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-24, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER SER-23, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Coenzyme A diphosphatase which mediates the cleavage of
CC oxidized CoA. Can use malonyl-CoA, hexanoyl-CoA, lauroyl-CoA,
CC myristoyl-CoA and palmitoyl-CoA as substrates, but not isobutyryl-CoA
CC or propionyl-CoA.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=118.7 uM for CoA {ECO:0000269|PubMed:18815383};
CC Vmax=1.40 umol/min/mg enzyme with CoA as substrate
CC {ECO:0000269|PubMed:18815383};
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:18815383}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q8GYB1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8GYB1-2; Sequence=VSP_015093;
CC Name=3;
CC IsoId=Q8GYB1-3; Sequence=VSP_037560;
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 -!- MISCELLANEOUS: [Isoform 2]: May be due to an intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF24540.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC007508; AAF24540.2; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE31022.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31024.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31026.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58454.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58455.1; -; Genomic_DNA.
DR EMBL; AK117752; BAC42400.1; -; mRNA.
DR EMBL; AK175332; BAD43095.1; -; mRNA.
DR EMBL; AK176465; BAD44228.1; -; mRNA.
DR EMBL; AK221329; BAD94135.1; -; mRNA.
DR EMBL; AK228486; BAF00412.1; -; mRNA.
DR EMBL; AK230433; BAF02231.1; -; mRNA.
DR EMBL; AK317052; BAH19745.1; -; mRNA.
DR RefSeq; NP_001031104.1; NM_001036027.2. [Q8GYB1-3]
DR RefSeq; NP_001320887.1; NM_001332826.1. [Q8GYB1-1]
DR RefSeq; NP_564316.1; NM_102640.3. [Q8GYB1-3]
DR RefSeq; NP_849724.1; NM_179393.4. [Q8GYB1-1]
DR RefSeq; NP_849725.2; NM_179394.3. [Q8GYB1-3]
DR AlphaFoldDB; Q8GYB1; -.
DR SMR; Q8GYB1; -.
DR BioGRID; 25008; 1.
DR STRING; 3702.Q8GYB1; -.
DR iPTMnet; Q8GYB1; -.
DR PaxDb; 3702-AT1G28960-1; -.
DR ProteomicsDB; 250525; -. [Q8GYB1-1]
DR EnsemblPlants; AT1G28960.1; AT1G28960.1; AT1G28960. [Q8GYB1-3]
DR EnsemblPlants; AT1G28960.3; AT1G28960.3; AT1G28960. [Q8GYB1-3]
DR EnsemblPlants; AT1G28960.5; AT1G28960.5; AT1G28960. [Q8GYB1-3]
DR EnsemblPlants; AT1G28960.6; AT1G28960.6; AT1G28960. [Q8GYB1-1]
DR EnsemblPlants; AT1G28960.7; AT1G28960.7; AT1G28960. [Q8GYB1-1]
DR GeneID; 839773; -.
DR Gramene; AT1G28960.1; AT1G28960.1; AT1G28960. [Q8GYB1-3]
DR Gramene; AT1G28960.3; AT1G28960.3; AT1G28960. [Q8GYB1-3]
DR Gramene; AT1G28960.5; AT1G28960.5; AT1G28960. [Q8GYB1-3]
DR Gramene; AT1G28960.6; AT1G28960.6; AT1G28960. [Q8GYB1-1]
DR Gramene; AT1G28960.7; AT1G28960.7; AT1G28960. [Q8GYB1-1]
DR KEGG; ath:AT1G28960; -.
DR Araport; AT1G28960; -.
DR TAIR; AT1G28960; NUDX15.
DR eggNOG; KOG3069; Eukaryota.
DR HOGENOM; CLU_040940_8_0_1; -.
DR InParanoid; Q8GYB1; -.
DR OMA; VGAKYSH; -.
DR OrthoDB; 399667at2759; -.
DR PhylomeDB; Q8GYB1; -.
DR SABIO-RK; Q8GYB1; -.
DR PRO; PR:Q8GYB1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8GYB1; baseline and differential.
DR Genevisible; Q8GYB1; AT.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0010945; F:coenzyme A diphosphatase activity; IDA:TAIR.
DR GO; GO:0008893; F:guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0015937; P:coenzyme A biosynthetic process; IDA:TAIR.
DR GO; GO:0006753; P:nucleoside phosphate metabolic process; IDA:TAIR.
DR GO; GO:0006104; P:succinyl-CoA metabolic process; IDA:TAIR.
DR CDD; cd03426; CoAse; 1.
DR Gene3D; 3.90.79.10; Nucleoside Triphosphate Pyrophosphohydrolase; 1.
DR InterPro; IPR045121; CoAse.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR030674; Nudix_hydrolase_AtNUDT22.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR PANTHER; PTHR12992; NUDIX HYDROLASE; 1.
DR PANTHER; PTHR12992:SF24; PEROXISOMAL COENZYME A DIPHOSPHATASE NUDT7; 1.
DR Pfam; PF00293; NUDIX; 1.
DR PIRSF; PIRSF038132; Nudix_hydrolase_AtNUDT22; 1.
DR SUPFAM; SSF55811; Nudix; 1.
DR PROSITE; PS51462; NUDIX; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Hydrolase; Magnesium; Manganese;
KW Metal-binding; Mitochondrion; Reference proteome; Transit peptide.
FT TRANSIT 1..23
FT /note="Mitochondrion"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 24..285
FT /note="Nudix hydrolase 15, mitochondrial"
FT /id="PRO_0000019958"
FT DOMAIN 99..255
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT REGION 51..72
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 129..152
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 140..161
FT /note="Nudix box"
FT COMPBIAS 137..152
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 155
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 159
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT MOD_RES 24
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT VAR_SEQ 254..285
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_015093"
FT VAR_SEQ 285
FT /note="M -> MVEKHTCMP (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:11910074"
FT /id="VSP_037560"
FT CONFLICT 264
FT /note="S -> P (in Ref. 3; BAC42400)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 285 AA; 31898 MW; C790D52CA9DF2AB8 CRC64;
MFLLYRRLPS FARTTTTTLL CKSMEPAITA TSSSSFGGGS SRLAALAQQL RQYKPPPSSS
FDDSEEMQTD QETAGKVVSQ VGFQESIAPL SKDPDRFKPK RAAVLICLFE GDDGDLRVIL
TKRSSKLSTH SGEVSLPGGK AEEDDKDDGM TATREAEEEI GLDPSLVDVV TSLEPFLSKH
LLRVIPVIGI LRDKNKFNPI PNPGEVEAVF DAPLEMFLKD ENRRSEEREW MGEKYLIHYF
DYRTGDKDYM IWGLTAGILI RAASVTYERP PAFIEQCPKF KYPKM
//
