NUD16_ARATH
ID NUD16_ARATH Reviewed; 180 AA.
AC Q9LHK1; A8MR20;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Nudix hydrolase 16, mitochondrial;
DE Short=AtNUDT16;
DE EC=3.6.1.-;
DE Flags: Precursor;
GN Name=NUDT16; Synonyms=NUDX16; OrderedLocusNames=At3g12600;
GN ORFNames=T2E22.9;
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=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
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] (ISOFORM 1).
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 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 TISSUE SPECIFICITY.
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: Probably mediates the hydrolysis of some nucleoside
CC diphosphate derivatives. {ECO:0000250}.
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 -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LHK1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LHK1-2; Sequence=VSP_037561;
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and
CC inflorescences. {ECO:0000269|PubMed:18815383}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
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DR EMBL; AP002044; BAB02251.1; -; Genomic_DNA.
DR EMBL; AC069474; AAG51020.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75221.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75222.1; -; Genomic_DNA.
DR EMBL; AF325001; AAG40353.1; -; mRNA.
DR EMBL; AF372914; AAK49630.1; -; mRNA.
DR EMBL; BT002659; AAO11575.1; -; mRNA.
DR RefSeq; NP_001078142.1; NM_001084673.1. [Q9LHK1-2]
DR RefSeq; NP_566428.1; NM_112095.4. [Q9LHK1-1]
DR AlphaFoldDB; Q9LHK1; -.
DR SMR; Q9LHK1; -.
DR STRING; 3702.AT3G12600.1; -.
DR PaxDb; Q9LHK1; -.
DR PRIDE; Q9LHK1; -.
DR ProteomicsDB; 250586; -. [Q9LHK1-1]
DR EnsemblPlants; AT3G12600.1; AT3G12600.1; AT3G12600. [Q9LHK1-1]
DR EnsemblPlants; AT3G12600.2; AT3G12600.2; AT3G12600. [Q9LHK1-2]
DR GeneID; 820440; -.
DR Gramene; AT3G12600.1; AT3G12600.1; AT3G12600. [Q9LHK1-1]
DR Gramene; AT3G12600.2; AT3G12600.2; AT3G12600. [Q9LHK1-2]
DR KEGG; ath:AT3G12600; -.
DR Araport; AT3G12600; -.
DR TAIR; locus:2091275; AT3G12600.
DR eggNOG; KOG2839; Eukaryota.
DR HOGENOM; CLU_037162_5_2_1; -.
DR InParanoid; Q9LHK1; -.
DR OMA; VKVLQYH; -.
DR PhylomeDB; Q9LHK1; -.
DR BioCyc; ARA:AT3G12600-MON; -.
DR PRO; PR:Q9LHK1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LHK1; baseline and differential.
DR Genevisible; Q9LHK1; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Hydrolase; Magnesium; Manganese; Metal-binding;
KW Mitochondrion; Reference proteome; Transit peptide.
FT TRANSIT 1..?
FT /note="Mitochondrion"
FT CHAIN ?..180
FT /note="Nudix hydrolase 16, mitochondrial"
FT /id="PRO_0000019959"
FT DOMAIN 18..162
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 63..84
FT /note="Nudix box"
FT BINDING 60
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q96DE0"
FT BINDING 63
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 78
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 78
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 82
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 82
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 144
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 144
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT VAR_SEQ 1..12
FT /note="MCDLVARTGRLQ -> MVE (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_037561"
SQ SEQUENCE 180 AA; 20392 MW; 7C628F7BD69B8DE6 CRC64;
MCDLVARTGR LQQRYEDGSR LVAGCIPFRY VNSDKDGNSE SGKVIQVLMI SSSSGPGLLF
PKGGWENDET VREAAAREAV EEAGVRGILM DFLGNYEFKS KSHQDEFSPE GLCKAAMYAL
YVKEELATWP EHETRTRKWL TIEEAVESCR HPWMKDALVE GFCKWHKEKM VKGEEITGEH
