NT5C

5', 3'-nucleotidase, cytosolic, also known as 5'(3')-deoxyribonucleotidase, cytosolic type (cdN) or deoxy-5'-nucleotidase 1 (dNT-1), is an enzyme that in humans is encoded by the NT5C gene on chromosome 17.[5][6][7]

NT5C
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2I7D, 4L57, 4YIH
Identifiers
Aliases	NT5C, DNT, DNT1, HEL74, P5N2, PN-I, PN-II, UMPH2, cdN, dNT-1, 5', 3'-nucleotidase, cytosolic
External IDs	OMIM: 191720 MGI: 1354954 HomoloGene: 8745 GeneCards: NT5C
Gene location (Human) Chr. Chromosome 17 (human)[1] Band 17q25.1 Start 75,130,225 bp[1] End 75,131,757 bp[1]
Gene location (Mouse) Chr. Chromosome 11 (mouse)[2] Band 11|11 E2 Start 115,490,420 bp[2] End 115,491,862 bp[2]
RNA expression pattern More reference expression data
Gene ontology Molecular function • nucleotide binding • 5'-nucleotidase activity • pyrimidine nucleotide binding • phosphatase activity • metal ion binding • nucleotidase activity • hydrolase activity Cellular component • cytoplasm • mitochondrion • extracellular exosome • cell nucleus • cytosol Biological process • pyrimidine deoxyribonucleotide catabolic process • purine nucleotide catabolic process • nucleotide metabolic process • pyrimidine nucleoside catabolic process • deoxyribonucleotide catabolic process • dephosphorylation Sources:Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	30833	50773
Ensembl	ENSG00000125458	ENSMUSG00000020736
UniProt	Q8TCD5	Q9JM14
RefSeq (mRNA)	NM_001252377 NM_014595	NM_015807
RefSeq (protein)	NP_001239306 NP_055410	NP_056622
Location (UCSC)	Chr 17: 75.13 – 75.13 Mb	Chr 11: 115.49 – 115.49 Mb
PubMed search	[3]	[4]
Wikidata
View/Edit Human View/Edit Mouse

This gene encodes a nucleotidase that catalyzes the dephosphorylation of the 5' deoxyribonucleotides (dNTP) and 2'(3')-dNTP and ribonucleotides, but not 5' ribonucleotides. Of the different forms of nucleotidases characterized, this enzyme is unique in its preference for 5'-dNTP. It may be one of the enzymes involved in regulating the size of dNTP pools in cells. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2011][6]

Structure

cdN is one of seven 5' nucleotidases identified in humans, all of which differ in tissue specificity, subcellular location, primary structure and substrate specificity.[8][9] Of the seven, the mitochondrial counterpart of cdN, mdN, is the most closely related to cdN. Their genes, NT5M and NT5C, share the same exon/intron organization, and their amino acid sequences are 52% identical.[5][8][9] Both cdN and mdN share nearly identical catalytic phosphate binding sites with most members of the haloacid dehalogenase (HAD) superfamily.[9]

This enzyme forms a 45-kDa homodimer of two 22-kDa subunits composed of a core domain and cap domain.[9][10] The core domain is an α/β Rossmann-like fold containing six antiparallel β-strands surrounded by α-helixes, and it spans residues 1-17 and 77-201 of the amino acid sequence. The cap domain is a 4-helix bundle spanning residues 18-76. The cleft formed by the core and cap domains acts as the enzyme's active site, where three conserved motifs in the core domain plus the cofactor Mg2+ serve as the substrate binding site. Meanwhile, the residues Phe18, Phe44, Leu45, and Tyr65 in the cap domain form an aromatic, hydrophobic pocket that coordinates with the base of the nucleotide substrate and, thus, influences the enzyme's substrate specificity. Its two main chain amides form hydrogen bonds with the 4-carbonyl group of dUMP and dTMP and with the 6-carbonyl group of dGMP and dIMP, while repelling the 4-amino group of dCMP and dAMP. The residue Asp43 is responsible for donating a proton to O5’ of the nucleotide during catalysis.[9]

Function

This enzyme functions in dephosphorylating nucleoside triphosphates, especially the 5′- and 2′(3′)-phosphates of uracil and thymine, as well as inosine and guanine, dNTPs (dUMPs, dTMPs, dIMPs, and dGMPs, respectively).[5][8][9][11] Due to this function, cdN regulates the size of dNTP pools in cells, in conjunction with the cytosolic thymidine kinases, as part of the dNTP substrate cycle.[9][10][11][12]

The enzyme is ubiquitously expressed, though lymphoid cells display particularly high cdN activity.[12]

Clinical Significance

The protein cdN is essential to counteract accumulation of cellular dNTPs, as excess dNTPs have been linked to genetic disease.[10] In addition, this enzyme's dephosphorylation function could be applied to anticancer and antiviral treatments which use nucleoside analogs. These treatments rely on the kinase activation of the analogs, which then are incorporated into the DNA of the tumor cell or virus to act as DNA chain terminators.[12][13] cdN can be used to maintain the concentrations of nucleoside analogs at low levels to avoid cytotoxicity.[12]

Moreover, cdN may affect the sensitivity of acute myeloid leukemia (AML) patients to treatment with ara-C. as low cdN mRNA levels in leukemic blasts have been correlated with a worse clinical outcome.[14]

Interactions

cdN binds and dephosphorylates deoxyribonucleotides such as uracil, thymine, inosine, and guanine.[9]

See also

• NT5M

References

1. GRCh38: Ensembl release 89: ENSG00000125458 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000020736 - Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. Rampazzo C, Gallinaro L, Milanesi E, Frigimelica E, Reichard P, Bianchi V (Aug 2000). "A deoxyribonucleotidase in mitochondria: involvement in regulation of dNTP pools and possible link to genetic disease". Proc Natl Acad Sci U S A. 97 (15): 8239–44. doi:10.1073/pnas.97.15.8239. PMC 26931. PMID 10899995.
6. "Entrez Gene: NT5C 5', 3'-nucleotidase, cytosolic".
7. "UniProtKB: Q8TCD5 (NT5C_HUMAN)".
8. Rinaldo-Matthis, A; Rampazzo, C; Reichard, P; Bianchi, V; Nordlund, P (October 2002). "Crystal structure of a human mitochondrial deoxyribonucleotidase". Nature Structural Biology. 9 (10): 779–87. doi:10.1038/nsb846. PMID 12352955.
9. Walldén, K; Rinaldo-Matthis, A; Ruzzenente, B; Rampazzo, C; Bianchi, V; Nordlund, P (4 December 2007). "Crystal structures of human and murine deoxyribonucleotidases: insights into recognition of substrates and nucleotide analogues". Biochemistry. 46 (48): 13809–18. doi:10.1021/bi7014794. PMID 17985935.
10. Höglund, L; Reichard, P (25 April 1990). "Cytoplasmic 5'(3')-nucleotidase from human placenta". The Journal of Biological Chemistry. 265 (12): 6589–95. PMID 2157703.
11. Gallinaro, L; Crovatto, K; Rampazzo, C; Pontarin, G; Ferraro, P; Milanesi, E; Reichard, P; Bianchi, V (20 September 2002). "Human mitochondrial 5'-deoxyribonucleotidase. Overproduction in cultured cells and functional aspects". The Journal of Biological Chemistry. 277 (38): 35080–7. doi:10.1074/jbc.m203755200. PMID 12124385.
12. Rampazzo, C; Johansson, M; Gallinaro, L; Ferraro, P; Hellman, U; Karlsson, A; Reichard, P; Bianchi, V (25 February 2000). "Mammalian 5'(3')-deoxyribonucleotidase, cDNA cloning, and overexpression of the enzyme in Escherichia coli and mammalian cells". The Journal of Biological Chemistry. 275 (8): 5409–15. doi:10.1074/jbc.275.8.5409. PMID 10681516.
13. Walldén, K; Ruzzenente, B; Rinaldo-Matthis, A; Bianchi, V; Nordlund, P (July 2005). "Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase". Structure. 13 (7): 1081–8. doi:10.1016/j.str.2005.04.023. PMID 16004879.
14. Galmarini, CM; Cros, E; Graham, K; Thomas, X; Mackey, JR; Dumontet, C (May 2004). "5'-(3')-nucleotidase mRNA levels in blast cells are a prognostic factor in acute myeloid leukemia patients treated with cytarabine". Haematologica. 89 (5): 617–9. PMID 15136231.

Further reading

• Höglund L, Reichard P (1990). "Cytoplasmic 5'(3')-nucleotidase from human placenta". J. Biol. Chem. 265 (12): 6589–95. PMID 2157703.
• Wilson DE, Swallow DM, Povey S (1988). "Assignment of the human gene for uridine 5'-monophosphate phosphohydrolase (UMPH2) to the long arm of chromosome 17". Ann. Hum. Genet. 50 (Pt 3): 223–7. doi:10.1111/j.1469-1809.1986.tb01042.x. PMID 2833155.
• Xu WM, Gorman PA, Rider SH, et al. (1988). "Construction of a genetic map of human chromosome 17 by use of chromosome-mediated gene transfer". Proc. Natl. Acad. Sci. U.S.A. 85 (22): 8563–7. doi:10.1073/pnas.85.22.8563. PMC 282499. PMID 3186746.
• Rampazzo C, Johansson M, Gallinaro L, et al. (2000). "Mammalian 5'(3')-deoxyribonucleotidase, cDNA cloning, and overexpression of the enzyme in Escherichia coli and mammalian cells". J. Biol. Chem. 275 (8): 5409–15. doi:10.1074/jbc.275.8.5409. PMID 10681516.
• Rampazzo C, Kost-Alimova M, Ruzzenente B, et al. (2003). "Mouse cytosolic and mitochondrial deoxyribonucleotidases: cDNA cloning of the mitochondrial enzyme, gene structures, chromosomal mapping and comparison with the human orthologs". Gene. 294 (1–2): 109–17. doi:10.1016/S0378-1119(02)00651-0. PMID 12234672.
• Amici A, Emanuelli M, Ruggieri S, et al. (2003). "Kinetic evidence for covalent phosphoryl-enzyme intermediate in phosphotransferase activity of human red cell pyrimidine nucleotidases". Meth. Enzymol. Methods in Enzymology. 354: 149–59. doi:10.1016/S0076-6879(02)54011-8. ISBN 978-0-12-182257-6. PMID 12418222.
• Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
• Balta G, Gumruk F, Akarsu N, et al. (2003). "Molecular characterization of Turkish patients with pyrimidine 5' nucleotidase-I deficiency". Blood. 102 (5): 1900–3. doi:10.1182/blood-2003-02-0628. PMID 12714505.
• Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40–5. doi:10.1038/ng1285. PMID 14702039.
• Galmarini CM, Cros E, Graham K, et al. (2006). "5'-(3')-nucleotidase mRNA levels in blast cells are a prognostic factor in acute myeloid leukemia patients treated with cytarabine". Haematologica. 89 (5): 617–9. PMID 15136231.
• Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.