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8-oxo-dGDP phosphatase NUDT18 (EC 3.6.1.58) (2-hydroxy-dADP phosphatase) (7,8-dihydro-8-oxoguanine phosphatase) (MutT homolog 3) (Nucleoside diphosphate-linked moiety X motif 18) (Nudix motif 18)

 NUD18_HUMAN             Reviewed;         323 AA.
Q6ZVK8; Q8IZ75; Q9H687;
18-MAR-2008, integrated into UniProtKB/Swiss-Prot.
06-MAR-2013, sequence version 3.
12-SEP-2018, entry version 120.
RecName: Full=8-oxo-dGDP phosphatase NUDT18;
EC=3.6.1.58;
AltName: Full=2-hydroxy-dADP phosphatase;
AltName: Full=7,8-dihydro-8-oxoguanine phosphatase;
AltName: Full=MutT homolog 3;
AltName: Full=Nucleoside diphosphate-linked moiety X motif 18;
Short=Nudix motif 18;
Name=NUDT18; Synonyms=MTH3;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
TISSUE=Cerebellum;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16421571; DOI=10.1038/nature04406;
Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S.,
Garber M., Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A.,
Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Yang X.,
Allen N.R., Anderson S., Asakawa T., Blechschmidt K., Bloom T.,
Borowsky M.L., Butler J., Cook A., Corum B., DeArellano K.,
DeCaprio D., Dooley K.T., Dorris L. III, Engels R., Gloeckner G.,
Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K., Jaffe D.B.,
Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P.,
Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H.,
Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C.,
O'Leary S.B., O'Neill K., Parker S.C.J., Polley A., Raymond C.K.,
Reichwald K., Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R.,
Smith C.L., Sneddon T.P., Talamas J.A., Tenzin P., Topham K.,
Venkataraman V., Wen G., Yamazaki S., Young S.K., Zeng Q.,
Zimmer A.R., Rosenthal A., Birren B.W., Platzer M., Shimizu N.,
Lander E.S.;
"DNA sequence and analysis of human chromosome 8.";
Nature 439:331-335(2006).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Uterus;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND
FUNCTION.
PubMed=22556419; DOI=10.1074/jbc.M112.363010;
Takagi Y., Setoyama D., Ito R., Kamiya H., Yamagata Y., Sekiguchi M.;
"Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine
and deoxyguanosine diphosphates: comparison with MTH1 and MTH2.";
J. Biol. Chem. 287:21541-21549(2012).
[5]
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 26-179.
Structural genomics consortium (SGC);
"Crystal structure of the nudix domain of human nudt18.";
Submitted (MAR-2009) to the PDB data bank.
-!- FUNCTION: Mediates the hydrolyzis of oxidized nucleoside
diphosphate derivatives. Hydrolyzes 8-oxo-7,8-dihydroguanine (8-
oxo-Gua)-containing deoxyribo- and ribonucleoside diphosphates to
the monophosphates. Hydrolyzes 8-oxo-dGDP and 8-oxo-GDP with the
same efficiencies. Hydrolyzes also 8-OH-dADP and 2-OH-dADP.
Exhibited no or minimal hydrolyzis activity against 8-oxo-dGTP, 8-
oxo-GTP, dGTP, GTP, dGDP and GDP. Probably removes oxidized
guanine nucleotides from both the DNA and RNA precursor pools.
{ECO:0000269|PubMed:22556419}.
-!- CATALYTIC ACTIVITY: 8-oxo-dGDP + H(2)O = 8-oxo-dGMP + phosphate.
{ECO:0000269|PubMed:22556419}.
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000250, ECO:0000269|PubMed:22556419};
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000250, ECO:0000269|PubMed:22556419};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=10.7 uM for 8-Oxo-dGDP {ECO:0000269|PubMed:22556419};
KM=11.7 uM for 8-Oxo-GDP {ECO:0000269|PubMed:22556419};
Vmax=212 pmol/min/ug enzyme toward 8-Oxo-dGDP (at 30 degrees
Celsius) {ECO:0000269|PubMed:22556419};
Vmax=246 pmol/min/ug enzyme toward 8-Oxo-GDP (at 30 degrees
Celsius) {ECO:0000269|PubMed:22556419};
pH dependence:
Optimum pH is 8.5. {ECO:0000269|PubMed:22556419};
-!- INTERACTION:
Q96GX9:APIP; NbExp=3; IntAct=EBI-740486, EBI-359248;
P49366:DHPS; NbExp=3; IntAct=EBI-740486, EBI-741925;
P33316:DUT; NbExp=3; IntAct=EBI-740486, EBI-353224;
Q96CN4:EVI5L; NbExp=3; IntAct=EBI-740486, EBI-749523;
Q9BPX1:HSD17B14; NbExp=3; IntAct=EBI-740486, EBI-742664;
P49902:NT5C2; NbExp=3; IntAct=EBI-740486, EBI-742084;
P22234:PAICS; NbExp=3; IntAct=EBI-740486, EBI-712261;
Q8TBN0:RAB3IL1; NbExp=3; IntAct=EBI-740486, EBI-743796;
Q9UI14:RABAC1; NbExp=3; IntAct=EBI-740486, EBI-712367;
P03410:tax (xeno); NbExp=4; IntAct=EBI-740486, EBI-9676218;
P14079:tax (xeno); NbExp=5; IntAct=EBI-740486, EBI-9675698;
Q9NYB0:TERF2IP; NbExp=2; IntAct=EBI-740486, EBI-750109;
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q6ZVK8-1; Sequence=Displayed;
Name=2;
IsoId=Q6ZVK8-2; Sequence=VSP_032276, VSP_032277;
Note=No experimental confirmation available.;
-!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAC85853.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AK026147; BAB15376.1; -; mRNA.
EMBL; AK124446; BAC85853.1; ALT_INIT; mRNA.
EMBL; BC016902; AAH16902.1; -; mRNA.
CCDS; CCDS75706.1; -. [Q6ZVK8-1]
RefSeq; NP_079091.3; NM_024815.3. [Q6ZVK8-1]
UniGene; Hs.527101; -.
UniGene; Hs.745387; -.
PDB; 3GG6; X-ray; 2.10 A; A=26-179.
PDB; 4HVY; X-ray; 1.46 A; A=26-179.
PDBsum; 3GG6; -.
PDBsum; 4HVY; -.
ProteinModelPortal; Q6ZVK8; -.
SMR; Q6ZVK8; -.
BioGrid; 122961; 42.
IntAct; Q6ZVK8; 43.
MINT; Q6ZVK8; -.
STRING; 9606.ENSP00000307852; -.
iPTMnet; Q6ZVK8; -.
PhosphoSitePlus; Q6ZVK8; -.
BioMuta; NUDT18; -.
DMDM; 460018323; -.
EPD; Q6ZVK8; -.
MaxQB; Q6ZVK8; -.
PaxDb; Q6ZVK8; -.
PeptideAtlas; Q6ZVK8; -.
PRIDE; Q6ZVK8; -.
ProteomicsDB; 68421; -.
ProteomicsDB; 68422; -. [Q6ZVK8-2]
DNASU; 79873; -.
Ensembl; ENST00000611621; ENSP00000480722; ENSG00000275074. [Q6ZVK8-1]
GeneID; 79873; -.
KEGG; hsa:79873; -.
UCSC; uc033beu.2; human. [Q6ZVK8-1]
CTD; 79873; -.
EuPathDB; HostDB:ENSG00000275074.1; -.
GeneCards; NUDT18; -.
HGNC; HGNC:26194; NUDT18.
HPA; HPA028581; -.
HPA; HPA030125; -.
MIM; 615791; gene.
neXtProt; NX_Q6ZVK8; -.
OpenTargets; ENSG00000275074; -.
PharmGKB; PA142671238; -.
eggNOG; ENOG410IN6N; Eukaryota.
eggNOG; ENOG41102IB; LUCA.
GeneTree; ENSGT00390000002931; -.
HOGENOM; HOG000035136; -.
HOVERGEN; HBG108203; -.
InParanoid; Q6ZVK8; -.
KO; K17817; -.
OMA; HLPITAC; -.
OrthoDB; EOG091G0XZN; -.
PhylomeDB; Q6ZVK8; -.
TreeFam; TF106355; -.
BioCyc; MetaCyc:ENSG00000173566-MONOMER; -.
Reactome; R-HSA-2393930; Phosphate bond hydrolysis by NUDT proteins.
SABIO-RK; Q6ZVK8; -.
EvolutionaryTrace; Q6ZVK8; -.
GenomeRNAi; 79873; -.
PRO; PR:Q6ZVK8; -.
Proteomes; UP000005640; Chromosome 8.
Bgee; ENSG00000275074; Expressed in 148 organ(s), highest expression level in blood.
CleanEx; HS_NUDT18; -.
ExpressionAtlas; Q6ZVK8; baseline and differential.
Genevisible; Q6ZVK8; HS.
GO; GO:0005829; C:cytosol; TAS:Reactome.
GO; GO:0044717; F:8-hydroxy-dADP phosphatase activity; IDA:UniProtKB.
GO; GO:0044715; F:8-oxo-dGDP phosphatase activity; IDA:UniProtKB.
GO; GO:0044716; F:8-oxo-GDP phosphatase activity; IDA:UniProtKB.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0046057; P:dADP catabolic process; IDA:UniProtKB.
GO; GO:0046067; P:dGDP catabolic process; IDA:UniProtKB.
GO; GO:0046712; P:GDP catabolic process; IDA:UniProtKB.
GO; GO:0034656; P:nucleobase-containing small molecule catabolic process; TAS:Reactome.
InterPro; IPR020476; Nudix_hydrolase.
InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
InterPro; IPR020084; NUDIX_hydrolase_CS.
InterPro; IPR000086; NUDIX_hydrolase_dom.
Pfam; PF00293; NUDIX; 1.
PRINTS; PR00502; NUDIXFAMILY.
SUPFAM; SSF55811; SSF55811; 1.
PROSITE; PS51462; NUDIX; 1.
PROSITE; PS00893; NUDIX_BOX; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Complete proteome; Hydrolase;
Magnesium; Manganese; Metal-binding; Nucleotide metabolism;
Reference proteome.
CHAIN 1 323 8-oxo-dGDP phosphatase NUDT18.
/FTId=PRO_0000324567.
DOMAIN 37 167 Nudix hydrolase. {ECO:0000255|PROSITE-
ProRule:PRU00794}.
MOTIF 76 97 Nudix box.
METAL 91 91 Magnesium or manganese. {ECO:0000250}.
METAL 95 95 Magnesium or manganese. {ECO:0000250}.
VAR_SEQ 1 100 Missing (in isoform 2).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_032276.
VAR_SEQ 101 125 EPETLLSVEERGPSWVRFVFLARPT -> MSVDSARAALLS
TQTLPAPSPTSPP (in isoform 2).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_032277.
CONFLICT 177 177 L -> P (in Ref. 1; BAB15376).
{ECO:0000305}.
CONFLICT 224 224 M -> V (in Ref. 1; BAB15376/BAC85853).
{ECO:0000305}.
STRAND 43 49 {ECO:0000244|PDB:4HVY}.
STRAND 55 61 {ECO:0000244|PDB:4HVY}.
HELIX 65 67 {ECO:0000244|PDB:4HVY}.
STRAND 74 77 {ECO:0000244|PDB:4HVY}.
HELIX 84 96 {ECO:0000244|PDB:4HVY}.
STRAND 98 112 {ECO:0000244|PDB:4HVY}.
STRAND 115 127 {ECO:0000244|PDB:4HVY}.
HELIX 132 134 {ECO:0000244|PDB:4HVY}.
STRAND 136 138 {ECO:0000244|PDB:3GG6}.
STRAND 140 146 {ECO:0000244|PDB:4HVY}.
STRAND 152 155 {ECO:0000244|PDB:4HVY}.
HELIX 158 172 {ECO:0000244|PDB:4HVY}.
SEQUENCE 323 AA; 35501 MW; 8162BA4BDEC4374D CRC64;
MASEGLAGAL ASVLAGQGSS VHSCDSAPAG EPPAPVRLRK NVCYVVLAVF LSEQDEVLLI
QEAKRECRGS WYLPAGRMEP GETIVEALQR EVKEEAGLHC EPETLLSVEE RGPSWVRFVF
LARPTGGILK TSKEADAESL QAAWYPRTSL PTPLRAHDIL HLVELAAQYR QQARHPLILP
QELPCDLVCQ RLVATFTSAQ TVWVLVGTVG MPHLPVTACG LDPMEQRGGM KMAVLRLLQE
CLTLHHLVVE IKGLLGLQHL GRDHSDGICL NVLVTVAFRS PGIQDEPPKV RGENFSWWKV
MEEDLQSQLL QRLQGSSVVP VNR


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