Biology:NT5C3

Generic protein structure example

Cytosolic 5'-nucleotidase 3 (NTC53), also known as cytosolic 5'-nucleotidase 3A, pyrimidine 5’-nucleotidase (PN-I or P5'NI), and p56, is an enzyme that in humans is encoded by the NT5C3, or NT5C3A, gene on chromosome 7.

This gene encodes a member of the 5'-nucleotidase family of enzymes that catalyze the dephosphorylation of nucleoside 5'-monophosphates. The encoded protein is the type 1 isozyme of pyrimidine 5' nucleotidase and catalyzes the dephosphorylation of pyrimidine 5' monophosphates. Mutations in this gene are a cause of hemolytic anemia due to uridine 5-prime monophosphate hydrolase deficiency. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and pseudogenes of this gene are located on the long arm of chromosomes 3 and 4. [provided by RefSeq, Mar 2012]

Structure

The NT5C3 gene consists of 10 exons and can be alternatively spliced at exon 2. Four possible isoforms have been identified, encoding proteins with lengths of 336 residues, 297 residues, 286 residues, and 285 residues. The 286-residue long isozyme is a monomeric protein containing 5 cysteine residues and no disulfide bridges or phosphate content. It has a predicted mass of 32.7 kDa and a predicted globular tertiary structure consisting of approximately 30% α-helices and 26% extended strands. This enzyme structurally resembles members of the haloacid dehalogenase (HAD) superfamily in regards to the shared α/β-Rossmann-like domain and a smaller 4-helix bundle domain. Three motifs in the α/β-Rossmann-like domain form the catalytic phosphate-binding site. Motif I is responsible for the 5′-nucleotidase activity: the first Asp makes a nucleophilic attack on the phosphate of the nucleoside monophosphate substrate, while the second Asp donates a proton to the leaving nucleoside. The active site is located in a cleft between the α/β-Rossmann-like domain and 4-helix bundle domain.

Function

NT5C3 is a member of the 5'-nucleotidase family and one of the five cytosolic members identified in humans. NTC53 catalyzes the dephosphorylation of the pyrimidine 5′ monophosphates UMP and CMP to the corresponding nucleosides. This function contributes to RNA degradation during the erythrocyte maturation process. As a result, NT5C3 regulates both the endogenous nucleoside and nucleotide pool balance, as well as that of pyrimidine analogs such as gemcitabine and AraC.

NT5C3 was first discovered in red blood cells, but its expression has been observed in multiple tumors (lung, ovary, colon, bladder), fetal tissues (lung, heart, spleen, liver), adult testis, and the brain. In particular, the 297-residue isoform of this enzyme is highly expressed in lymphoblastoid cells.

Clinical Significance

The loss of NT5C3 in pyrimidine 5' nucleotidase deficiency, an autosomal recessive condition, leads to the accumulation of high concentrations of pyrimidine nucleotides within erythrocytes. This deficiency is characterized by moderate hemolytic anemia, jaundice, splenomegaly, and marked basophilic stippling, and has been associated with learning difficulties. Two homozygous mutations identified in this gene produced large deletions that could cripple the enzyme’s structure and function, and are thus causally linked to pyrimidine 5' nucleotidase deficiency and hemolytic anemia. Heterozygous mutations in pyrimidine 5' nucleotidase deficiency may contribute to the large variability in thalassemia phenotypes. Pyrimidine 5' nucleotidase deficiency is also linked to the conversion of hemoglobin E disease into an unstable hemoglobinopathy-like disease. NT5C3 is identical to p36, a previously identified alpha-interferon-induced protein involved in forming lupus inclusions. Since NT5C3 can metabolize AraC, a nucleoside analog used in chemotherapy for acute myeloid leukemia patients, genotyping one of its polymorphisms may aid detection of patients who will respond favorably to this therapy.

Interactions

NTC53 is known to interact with pyrimidine nucleoside monophosphates, specifically UMP and CMP, as well as the anineoplastic agents 5’-AZTMP and 5’-Ara-CMP.

Further reading

• "Homogeneous pyrimidine nucleotidase from human erythrocytes: enzymic and molecular properties". Biochem. J. 304 (Pt 3): 987–92. 1995. doi:10.1042/bj3040987. PMID 7818506. 
• "Purification, microsequencing, and immunolocalization of p36, a new interferon-alpha-induced protein that is associated with human lupus inclusions". J. Biol. Chem. 271 (2): 1118–26. 1996. doi:10.1074/jbc.271.2.1118. PMID 8557639. 
• "Generation and analysis of 280,000 human expressed sequence tags". Genome Res. 6 (9): 807–28. 1997. doi:10.1101/gr.6.9.807. PMID 8889549. 
• "Pyrimidine nucleotidases from human erythrocyte possess phosphotransferase activities specific for pyrimidine nucleotides". FEBS Lett. 419 (2–3): 263–7. 1998. doi:10.1016/S0014-5793(97)01464-6. PMID 9428647. 
• "DNA Cloning Using In Vitro Site-Specific Recombination". Genome Res. 10 (11): 1788–95. 2001. doi:10.1101/gr.143000. PMID 11076863. 
• "Toward a Catalog of Human Genes and Proteins: Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs". Genome Res. 11 (3): 422–35. 2001. doi:10.1101/gr.GR1547R. PMID 11230166. 
• "Genetic basis of hemolytic anemia caused by pyrimidine 5' nucleotidase deficiency". Blood 97 (11): 3327–32. 2001. doi:10.1182/blood.V97.11.3327. PMID 11369620. 
• "Human erythrocyte pyrimidine 5'-nucleotidase, PN-I". Arch. Biochem. Biophys. 397 (2): 184–90. 2002. doi:10.1006/abbi.2001.2676. PMID 11795870. 
• "Kinetic evidence for covalent phosphoryl-enzyme intermediate in phosphotransferase activity of human red cell pyrimidine nucleotidases". Meth. Enzymol.. Methods in Enzymology 354: 149–59. 2003. doi:10.1016/S0076-6879(02)54011-8. ISBN 978-0-12-182257-6. PMID 12418222. 
• "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. 2003. doi:10.1073/pnas.242603899. PMID 12477932. Bibcode: 2002PNAS...9916899M. 
• "Molecular characterization of Turkish patients with pyrimidine 5' nucleotidase-I deficiency". Blood 102 (5): 1900–3. 2003. doi:10.1182/blood-2003-02-0628. PMID 12714505. 
• "Molecular characterization of six unrelated Italian patients affected by pyrimidine 5'-nucleotidase deficiency". Br. J. Haematol. 122 (5): 847–51. 2003. doi:10.1046/j.1365-2141.2003.04532.x. PMID 12930399. 
• "Molecular basis of Japanese variants of pyrimidine 5'-nucleotidase deficiency". Br. J. Haematol. 126 (2): 265–71. 2004. doi:10.1111/j.1365-2141.2004.05029.x. PMID 15238149. 
• "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. 2004. doi:10.1101/gr.2596504. PMID 15489334. 
• "From ORFeome to Biology: A Functional Genomics Pipeline". Genome Res. 14 (10B): 2136–44. 2004. doi:10.1101/gr.2576704. PMID 15489336. 
• "Functional analysis of pyrimidine 5'-nucleotidase mutants causing nonspherocytic hemolytic anemia". Blood 105 (8): 3340–5. 2005. doi:10.1182/blood-2004-10-3895. PMID 15604219. 
• "The LIFEdb database in 2006". Nucleic Acids Res. 34 (Database issue): D415–8. 2006. doi:10.1093/nar/gkj139. PMID 16381901.