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5'(3')-deoxyribonucleotidase, mitochondrial (5',3'-nucleotidase, mitochondrial) (EC 3.1.3.-) (Deoxy-5'-nucleotidase 2) (dNT-2)

 NT5M_HUMAN              Reviewed;         228 AA.
Q9NPB1;
31-OCT-2003, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
28-FEB-2018, entry version 133.
RecName: Full=5'(3')-deoxyribonucleotidase, mitochondrial;
Short=5',3'-nucleotidase, mitochondrial;
EC=3.1.3.-;
AltName: Full=Deoxy-5'-nucleotidase 2;
Short=dNT-2;
Flags: Precursor;
Name=NT5M; Synonyms=DNT2;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, SUBCELLULAR
LOCATION, AND TISSUE SPECIFICITY.
TISSUE=Muscle;
PubMed=10899995; DOI=10.1073/pnas.97.15.8239;
Rampazzo C., Gallinaro L., Milanesi E., Frigimelica E., Reichard P.,
Bianchi V.;
"A deoxyribonucleotidase in mitochondria: involvement in regulation of
dNTP pools and possible link to genetic disease.";
Proc. Natl. Acad. Sci. U.S.A. 97:8239-8244(2000).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Hippocampus;
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).
[3]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 34-227 IN COMPLEX WITH
MAGNESIUM AND A SUBSTRATE ANALOG.
PubMed=12352955; DOI=10.1038/nsb846;
Rinaldo-Matthis A., Rampazzo C., Reichard P., Bianchi V., Nordlund P.;
"Crystal structure of a human mitochondrial deoxyribonucleotidase.";
Nat. Struct. Biol. 9:779-787(2002).
-!- FUNCTION: Dephosphorylates specifically the 5' and 2'(3')-
phosphates of uracil and thymine deoxyribonucleotides, and so
protects mitochondrial DNA replication from excess dTTP. Has only
marginal activity towards dIMP and dGMP.
{ECO:0000269|PubMed:10899995}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
-!- SUBUNIT: Homodimer. {ECO:0000305|PubMed:12352955}.
-!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:10899995}.
-!- TISSUE SPECIFICITY: Highly expressed in heart, brain and skeletal
muscle. Detected at very low levels in kidney and pancreas.
{ECO:0000269|PubMed:10899995}.
-!- SIMILARITY: Belongs to the 5'(3')-deoxyribonucleotidase family.
{ECO:0000305}.
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EMBL; AJ277557; CAB99251.1; -; Genomic_DNA.
EMBL; AF210652; AAF87076.1; -; mRNA.
EMBL; BC035838; AAH35838.1; -; mRNA.
CCDS; CCDS32581.1; -.
RefSeq; NP_064586.1; NM_020201.3.
UniGene; Hs.513977; -.
PDB; 1MH9; X-ray; 1.80 A; A=32-228.
PDB; 1Q91; X-ray; 1.60 A; A=32-228.
PDB; 1Q92; X-ray; 1.40 A; A=32-228.
PDB; 1Z4I; X-ray; 1.98 A; A=32-228.
PDB; 1Z4J; X-ray; 1.80 A; A=32-228.
PDB; 1Z4K; X-ray; 1.75 A; A=32-228.
PDB; 1Z4L; X-ray; 1.80 A; A=32-228.
PDB; 1Z4M; X-ray; 1.70 A; A=32-228.
PDB; 1Z4P; X-ray; 2.00 A; X=32-228.
PDB; 1Z4Q; X-ray; 2.05 A; A=32-228.
PDB; 2JAU; X-ray; 1.80 A; A=32-228.
PDB; 2JAW; X-ray; 1.95 A; A=32-228.
PDB; 4L6A; X-ray; 1.40 A; A=32-228.
PDB; 4L6C; X-ray; 1.80 A; A=32-228.
PDB; 4MUM; X-ray; 1.27 A; A=32-227.
PDB; 4MWO; X-ray; 1.67 A; A=32-227.
PDB; 4NFL; X-ray; 1.38 A; A=32-227.
PDB; 4YIK; X-ray; 1.48 A; A=32-227.
PDBsum; 1MH9; -.
PDBsum; 1Q91; -.
PDBsum; 1Q92; -.
PDBsum; 1Z4I; -.
PDBsum; 1Z4J; -.
PDBsum; 1Z4K; -.
PDBsum; 1Z4L; -.
PDBsum; 1Z4M; -.
PDBsum; 1Z4P; -.
PDBsum; 1Z4Q; -.
PDBsum; 2JAU; -.
PDBsum; 2JAW; -.
PDBsum; 4L6A; -.
PDBsum; 4L6C; -.
PDBsum; 4MUM; -.
PDBsum; 4MWO; -.
PDBsum; 4NFL; -.
PDBsum; 4YIK; -.
ProteinModelPortal; Q9NPB1; -.
SMR; Q9NPB1; -.
BioGrid; 121277; 1.
IntAct; Q9NPB1; 1.
STRING; 9606.ENSP00000373674; -.
ChEMBL; CHEMBL3751654; -.
DrugBank; DB02217; Dpb-T.
DEPOD; Q9NPB1; -.
iPTMnet; Q9NPB1; -.
PhosphoSitePlus; Q9NPB1; -.
BioMuta; NT5M; -.
DMDM; 38258255; -.
PaxDb; Q9NPB1; -.
PeptideAtlas; Q9NPB1; -.
PRIDE; Q9NPB1; -.
Ensembl; ENST00000389022; ENSP00000373674; ENSG00000205309.
GeneID; 56953; -.
KEGG; hsa:56953; -.
UCSC; uc002grf.4; human.
CTD; 56953; -.
DisGeNET; 56953; -.
EuPathDB; HostDB:ENSG00000205309.13; -.
GeneCards; NT5M; -.
HGNC; HGNC:15769; NT5M.
HPA; HPA043777; -.
MIM; 605292; gene.
neXtProt; NX_Q9NPB1; -.
OpenTargets; ENSG00000205309; -.
PharmGKB; PA31805; -.
eggNOG; ENOG410IHG0; Eukaryota.
eggNOG; ENOG410XQYS; LUCA.
GeneTree; ENSGT00390000011596; -.
HOGENOM; HOG000236944; -.
HOVERGEN; HBG045599; -.
KO; K01081; -.
PhylomeDB; Q9NPB1; -.
TreeFam; TF331117; -.
Reactome; R-HSA-73621; Pyrimidine catabolism.
SABIO-RK; Q9NPB1; -.
EvolutionaryTrace; Q9NPB1; -.
GenomeRNAi; 56953; -.
PRO; PR:Q9NPB1; -.
Proteomes; UP000005640; Chromosome 17.
Bgee; ENSG00000205309; -.
CleanEx; HS_NT5M; -.
ExpressionAtlas; Q9NPB1; baseline and differential.
Genevisible; Q9NPB1; HS.
GO; GO:0005759; C:mitochondrial matrix; TAS:Reactome.
GO; GO:0005739; C:mitochondrion; TAS:ProtInc.
GO; GO:0008253; F:5'-nucleotidase activity; EXP:Reactome.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008252; F:nucleotidase activity; TAS:ProtInc.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
GO; GO:0006260; P:DNA replication; TAS:ProtInc.
GO; GO:0046079; P:dUMP catabolic process; IEA:Ensembl.
GO; GO:0009223; P:pyrimidine deoxyribonucleotide catabolic process; TAS:ProtInc.
GO; GO:0046135; P:pyrimidine nucleoside catabolic process; TAS:Reactome.
Gene3D; 3.40.50.1000; -; 2.
InterPro; IPR010708; 5'(3')-deoxyribonucleotidase.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR023214; HAD_sf.
Pfam; PF06941; NT5C; 1.
SUPFAM; SSF56784; SSF56784; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Hydrolase; Magnesium; Metal-binding;
Mitochondrion; Nucleotide metabolism; Nucleotide-binding;
Reference proteome; Transit peptide.
TRANSIT 1 31 Mitochondrion. {ECO:0000255}.
CHAIN 32 228 5'(3')-deoxyribonucleotidase,
mitochondrial.
/FTId=PRO_0000000011.
ACT_SITE 41 41 Nucleophile.
ACT_SITE 43 43 Proton donor. {ECO:0000305}.
METAL 41 41 Magnesium. {ECO:0000269|PubMed:12352955}.
METAL 43 43 Magnesium; via carbonyl oxygen.
{ECO:0000269|PubMed:12352955}.
METAL 176 176 Magnesium. {ECO:0000269|PubMed:12352955}.
BINDING 43 43 Substrate.
BINDING 49 49 Substrate.
BINDING 75 75 Substrate.
BINDING 76 76 Substrate.
BINDING 77 77 Substrate; via amide nitrogen.
BINDING 96 96 Substrate.
BINDING 130 130 Substrate.
BINDING 165 165 Substrate.
STRAND 36 40 {ECO:0000244|PDB:4MUM}.
TURN 44 46 {ECO:0000244|PDB:4MUM}.
HELIX 49 60 {ECO:0000244|PDB:4MUM}.
HELIX 69 71 {ECO:0000244|PDB:4MUM}.
HELIX 77 84 {ECO:0000244|PDB:4MUM}.
HELIX 88 96 {ECO:0000244|PDB:4MUM}.
TURN 99 104 {ECO:0000244|PDB:4MUM}.
HELIX 111 120 {ECO:0000244|PDB:4MUM}.
STRAND 124 130 {ECO:0000244|PDB:4MUM}.
TURN 136 138 {ECO:0000244|PDB:4NFL}.
HELIX 139 151 {ECO:0000244|PDB:4MUM}.
HELIX 153 158 {ECO:0000244|PDB:4MUM}.
STRAND 159 161 {ECO:0000244|PDB:4MUM}.
HELIX 165 167 {ECO:0000244|PDB:4MUM}.
STRAND 171 176 {ECO:0000244|PDB:4MUM}.
STRAND 188 194 {ECO:0000244|PDB:4MUM}.
TURN 197 201 {ECO:0000244|PDB:4MUM}.
STRAND 209 211 {ECO:0000244|PDB:4MUM}.
HELIX 218 223 {ECO:0000244|PDB:4MUM}.
SEQUENCE 228 AA; 25862 MW; 9AE6F57B16977F0F CRC64;
MIRLGGWCAR RLCSAAVPAG RRGAAGGLGL AGGRALRVLV DMDGVLADFE GGFLRKFRAR
FPDQPFIALE DRRGFWVSEQ YGRLRPGLSE KAISIWESKN FFFELEPLPG AVEAVKEMAS
LQNTDVFICT SPIKMFKYCP YEKYAWVEKY FGPDFLEQIV LTRDKTVVSA DLLIDDRPDI
TGAEPTPSWE HVLFTACHNQ HLQLQPPRRR LHSWADDWKA ILDSKRPC


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