NUDT1_ARATH
ID NUDT1_ARATH Reviewed; 147 AA.
AC Q9CA40;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Nudix hydrolase 1;
DE Short=AtNUDT1;
DE AltName: Full=7,8-dihydro-8-oxoguanine-triphosphatase;
DE AltName: Full=8-oxo-dGTP diphosphatase;
DE Short=8-oxo-dGTPase;
DE EC=3.6.1.55;
DE AltName: Full=Dihydroneopterin triphosphate diphosphatase;
DE EC=3.6.1.67 {ECO:0000269|PubMed:15611104};
DE AltName: Full=Dihydroneopterin triphosphate pyrophosphohydrolase;
DE Short=DHNTP pyrophosphohydrolase;
DE AltName: Full=NADH pyrophosphatase;
DE EC=3.6.1.22;
GN Name=NUDT1; Synonyms=NUDX1; OrderedLocusNames=At1g68760;
GN ORFNames=F14K14.13;
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].
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].
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 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 (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NADH PYROPHOSPHATASE ACTIVITY, SUBUNIT, COFACTOR, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=12399474; DOI=10.1074/jbc.m205207200;
RA Dobrzanska M., Szurmak B., Wyslouch-Cieszynska A., Kraszewska E.;
RT "Cloning and characterization of the first member of the Nudix family from
RT Arabidopsis thaliana.";
RL J. Biol. Chem. 277:50482-50486(2002).
RN [8]
RP FUNCTION, AND CATALYTIC ACTIVITY AS DIHYDRONEOPTERIN PYROPHOSPHATASE.
RX PubMed=15611104; DOI=10.1074/jbc.m413759200;
RA Klaus S.M.J., Wegkamp A., Sybesma W., Hugenholtz J., Gregory J.F. III,
RA Hanson A.D.;
RT "A nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in
RT the folate synthesis pathway of bacteria and plants.";
RL J. Biol. Chem. 280:5274-5280(2005).
RN [9]
RP FUNCTION IN VITRO, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND TISSUE
RP SPECIFICITY.
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 [10]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR
RP LOCATION, INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17804481; DOI=10.1093/pcp/pcm112;
RA Yoshimura K., Ogawa T., Ueda Y., Shigeoka S.;
RT "AtNUDX1, an 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate
RT pyrophosphohydrolase, is responsible for eliminating oxidized nucleotides
RT in Arabidopsis.";
RL Plant Cell Physiol. 48:1438-1449(2007).
RN [11]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [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: Mediates the hydrolysis of some nucleoside diphosphate
CC derivatives. Its substrate specificity is unclear. In vitro, it can use
CC NTP, dNTP, 8-oxo-GTP, 8-oxo-dGTP, dGTP, dATP, dTTP or dihydroneopterin
CC triphosphate (DHNTP) as substrate. Has some NADH pyrophosphatase
CC activity in vitro; however, such activity may not be relevant in vivo
CC due to the high concentration of manganese used during the experiments.
CC Plays an important role in protection against oxidative DNA and RNA
CC damage by removing oxidatively damaged form of guanine.
CC {ECO:0000269|PubMed:15611104, ECO:0000269|PubMed:15878881,
CC ECO:0000269|PubMed:17804481}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7,8-dihydroneopterin 3'-triphosphate + H2O = 7,8-
CC dihydroneopterin 3'-phosphate + diphosphate + H(+);
CC Xref=Rhea:RHEA:25302, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:58462, ChEBI:CHEBI:58762; EC=3.6.1.67;
CC Evidence={ECO:0000269|PubMed:15611104};
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:17804481};
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:17804481};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate + H(+);
CC Xref=Rhea:RHEA:31575, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:63224, ChEBI:CHEBI:77896; EC=3.6.1.55;
CC Evidence={ECO:0000269|PubMed:17804481};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881};
CC Note=Magnesium may be the real cofactor in vivo.
CC {ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.36 mM for NADH (in the presence of 5 mM of manganese)
CC {ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881,
CC ECO:0000269|PubMed:17804481};
CC KM=0.48 mM for NAD (in the presence of 5 mM of manganese)
CC {ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881,
CC ECO:0000269|PubMed:17804481};
CC KM=6.8 uM for 8-oxo-dGTP {ECO:0000269|PubMed:12399474,
CC ECO:0000269|PubMed:15878881, ECO:0000269|PubMed:17804481};
CC KM=28.1 uM for 8-oxo-GTP {ECO:0000269|PubMed:12399474,
CC ECO:0000269|PubMed:15878881, ECO:0000269|PubMed:17804481};
CC KM=58.3 uM for dGTP {ECO:0000269|PubMed:12399474,
CC ECO:0000269|PubMed:15878881, ECO:0000269|PubMed:17804481};
CC KM=16.1 uM for dATP {ECO:0000269|PubMed:12399474,
CC ECO:0000269|PubMed:15878881, ECO:0000269|PubMed:17804481};
CC KM=15.6 uM for dTTP {ECO:0000269|PubMed:12399474,
CC ECO:0000269|PubMed:15878881, ECO:0000269|PubMed:17804481};
CC Vmax=12.7 umol/min/mg enzyme toward NADH (in the presence of 5 mM of
CC manganese) {ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881,
CC ECO:0000269|PubMed:17804481};
CC Vmax=0.62 umol/min/mg enzyme toward NAD (in the presence of 5 mM of
CC manganese) {ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881,
CC ECO:0000269|PubMed:17804481};
CC Vmax=0.8 umol/min/mg enzyme toward 8-oxo-dGTP
CC {ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881,
CC ECO:0000269|PubMed:17804481};
CC Vmax=1.7 umol/min/mg enzyme toward 8-oxo-GTP
CC {ECO:0000269|PubMed:12399474, ECO:0000269|PubMed:15878881,
CC ECO:0000269|PubMed:17804481};
CC Vmax=2.7 umol/min/mg enzyme toward dGTP {ECO:0000269|PubMed:12399474,
CC ECO:0000269|PubMed:15878881, ECO:0000269|PubMed:17804481};
CC Vmax=5.8 umol/min/mg enzyme toward dATP {ECO:0000269|PubMed:12399474,
CC ECO:0000269|PubMed:15878881, ECO:0000269|PubMed:17804481};
CC Vmax=0.8 umol/min/mg enzyme toward dTTP {ECO:0000269|PubMed:12399474,
CC ECO:0000269|PubMed:15878881, ECO:0000269|PubMed:17804481};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:12399474}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:17804481}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, stems and leaves.
CC {ECO:0000269|PubMed:15878881}.
CC -!- INDUCTION: Not induced by paraquat, salinity, high light and drought.
CC {ECO:0000269|PubMed:17804481}.
CC -!- DISRUPTION PHENOTYPE: Increased level of 8-oxo-G in genomic DNA.
CC {ECO:0000269|PubMed:17804481}.
CC -!- MISCELLANEOUS: Has the ability to complement a mutation of mutT in
CC E.coli and thereby completely suppress the increased frequency of
CC spontaneous mutations.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
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DR EMBL; AC011914; AAG52038.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE34836.1; -; Genomic_DNA.
DR EMBL; AK117564; BAC42225.1; -; mRNA.
DR EMBL; BT005039; AAO50572.1; -; mRNA.
DR EMBL; AK176885; BAD44648.1; -; mRNA.
DR EMBL; AY088162; AAM65706.1; -; mRNA.
DR PIR; D96712; D96712.
DR RefSeq; NP_177044.1; NM_105549.4.
DR PDB; 5GP0; X-ray; 1.70 A; A/E/F/I=1-147.
DR PDB; 5WWD; X-ray; 1.39 A; A/B=1-147.
DR PDB; 5WY6; X-ray; 1.78 A; A/E=1-147.
DR PDB; 6DBY; X-ray; 2.00 A; A/B=1-147.
DR PDB; 6DBZ; X-ray; 1.90 A; A/B=1-147.
DR PDB; 6FL4; X-ray; 1.60 A; A/B=1-147.
DR PDBsum; 5GP0; -.
DR PDBsum; 5WWD; -.
DR PDBsum; 5WY6; -.
DR PDBsum; 6DBY; -.
DR PDBsum; 6DBZ; -.
DR PDBsum; 6FL4; -.
DR AlphaFoldDB; Q9CA40; -.
DR SMR; Q9CA40; -.
DR STRING; 3702.AT1G68760.1; -.
DR iPTMnet; Q9CA40; -.
DR PaxDb; Q9CA40; -.
DR PRIDE; Q9CA40; -.
DR ProteomicsDB; 249351; -.
DR EnsemblPlants; AT1G68760.1; AT1G68760.1; AT1G68760.
DR GeneID; 843207; -.
DR Gramene; AT1G68760.1; AT1G68760.1; AT1G68760.
DR KEGG; ath:AT1G68760; -.
DR Araport; AT1G68760; -.
DR TAIR; locus:2012443; AT1G68760.
DR eggNOG; ENOG502S3YT; Eukaryota.
DR HOGENOM; CLU_037162_9_2_1; -.
DR InParanoid; Q9CA40; -.
DR OMA; HFEASRN; -.
DR OrthoDB; 1602447at2759; -.
DR PhylomeDB; Q9CA40; -.
DR BioCyc; ARA:AT1G68760-MON; -.
DR BioCyc; MetaCyc:AT1G68760-MON; -.
DR BRENDA; 3.6.1.55; 399.
DR BRENDA; 3.6.1.67; 399.
DR SABIO-RK; Q9CA40; -.
DR PRO; PR:Q9CA40; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9CA40; baseline and differential.
DR Genevisible; Q9CA40; AT.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0035539; F:8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity; IBA:GO_Central.
DR GO; GO:0008413; F:8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity; IDA:TAIR.
DR GO; GO:0019177; F:dihydroneopterin triphosphate pyrophosphohydrolase activity; IDA:TAIR.
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:0006974; P:cellular response to DNA damage stimulus; IMP:TAIR.
DR GO; GO:0006203; P:dGTP catabolic process; IBA:GO_Central.
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 Pfam; PF00293; NUDIX; 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 3D-structure; Acetylation; Cytoplasm; Hydrolase; Magnesium; Manganese;
KW Metal-binding; NAD; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..147
FT /note="Nudix hydrolase 1"
FT /id="PRO_0000057121"
FT DOMAIN 7..140
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 41..62
FT /note="Nudix box"
FT BINDING 56
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 60
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT STRAND 9..18
FT /evidence="ECO:0007829|PDB:5WWD"
FT STRAND 21..27
FT /evidence="ECO:0007829|PDB:5WWD"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:5WWD"
FT STRAND 39..42
FT /evidence="ECO:0007829|PDB:5WWD"
FT HELIX 49..61
FT /evidence="ECO:0007829|PDB:5WWD"
FT STRAND 65..78
FT /evidence="ECO:0007829|PDB:5WWD"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:5WWD"
FT STRAND 85..98
FT /evidence="ECO:0007829|PDB:5WWD"
FT TURN 108..110
FT /evidence="ECO:0007829|PDB:5WWD"
FT STRAND 111..118
FT /evidence="ECO:0007829|PDB:5WWD"
FT HELIX 119..121
FT /evidence="ECO:0007829|PDB:6FL4"
FT STRAND 124..126
FT /evidence="ECO:0007829|PDB:5WWD"
FT HELIX 128..135
FT /evidence="ECO:0007829|PDB:5WWD"
FT TURN 140..142
FT /evidence="ECO:0007829|PDB:5WWD"
SQ SEQUENCE 147 AA; 16357 MW; 84EDDAF6D65247C9 CRC64;
MSTGEAIPRV AVVVFILNGN SILLGRRRSS IGNSTFALPG GHLEFGESFE ECAAREVMEE
TGLKIEKMKL LTVTNNVFKE APTPSHYVSV SIRAVLVDPS QEPKNMEPEK CEGWDWYDWE
NLPKPLFWPL EKLFGSGFNP FTHGGGD
