Thymidine phosphorylase

Last updated
Thymidine phosphorylase
Thymidine phosphorylase dimer.png
Thymidine phosphorylase protein structure
Identifiers
EC number 2.4.2.4
CAS number 9030-23-3
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO

Thymidine phosphorylase (EC 2.4.2.4) is an enzyme that is encoded by the TYMP gene and catalyzes the reaction:

Contents

thymidine + phosphate thymine + 2-deoxy-alpha-D-ribose 1-phosphate

Thymidine phosphorylase is involved in purine metabolism, pyrimidine metabolism, and other metabolic pathways. Variations in thymidine phosphorylase and the TYMP gene that encode it are associated with mitochondrial neurogastrointestinal encephalopathy (MNGIE) syndrome and bladder cancer.

Nomenclature

This enzyme belongs to the family of glycosyltransferases, specifically the pentosyltransferases. The systematic name of this enzyme class is thymidine:phosphate deoxy-alpha-D-ribosyltransferase. Other names in common use include pyrimidine phosphorylase, thymidine-orthophosphate deoxyribosyltransferase, animal growth regulators, blood platelet-derived endothelial cell, growth factors, blood platelet-derived endothelial cell growth factor, deoxythymidine phosphorylase, gliostatins, pyrimidine deoxynucleoside phosphorylase, and thymidine:phosphate deoxy-D-ribosyltransferase.

Mechanism

Thymidine phosphorylase catalyzes the reversible phosphorylation of thymidine, deoxyuridine, and their analogs (except deoxycytidine) to their respective bases (thymine/uracil) and 2-deoxyribose 1-phosphate. The enzyme follows a sequential mechanism, where phosphate binds before thymidine (or deoxyuridine, etc.) and 2-deoxyribose 1-phosphate leaves after the nitrogenous base. The thymidine is bound in a high-energy conformation, in which the glycosidic bond weakens as the phosphate attacks the C1 position of the ribose ring, as shown below. The enzyme can then transfer deoxyribose 1-phosphate to other nitrogenous bases. [1]

Thymidine phosphorylase mechanism Enzymeproject mechanism.png
Thymidine phosphorylase mechanism

Further experiments have shown that thymine inhibits the enzyme via both substrate inhibition and nonlinear product inhibition. This suggests that thymine can inhibit the enzyme via multiple sites. The enzyme also displays cooperativity with respect to both thymidine and phosphate in the presence of thymine, which suggests that thymidine phosphorylase has several allosteric and/or catalytic sites as well. [2]

Structure

Arg-171, Ser-186, and Lys-190 interactions with thymine in ligand site of thymidine phosphorylase Thymidine phosphorylase ligand binding site.png
Arg-171, Ser-186, and Lys-190 interactions with thymine in ligand site of thymidine phosphorylase

Thymidine phosphorylase is a protein dimer with identical subunits – with a reported molecular weight of 90,000 daltons in Escherichia coli. It has an S-shape with a length of 110 Å and a width of 60 Å. Each monomer is composed of 440 amino acids and is composed of a small α-helical domain and a large α/β domain. The surface of the enzyme is smooth except for a 10 Å deep and 8 Å wide cavity between the two domains that contains the thymine, thymidine, and phosphate binding sites. [3] Detailed analysis of the binding sites shows that Arg-171, Ser-186, and Lys-190 are the important residues in binding the pyrimidine base. The residues Arg-171 and Lys-190 are close to O4 and O2 of the thymine ring, respectively, and can help stabilize the intermediate state. The terminal amino group of Lys-190, which forms a hydrogen bond with the 3′-hydroxyl of the thymidine ribose moiety is also in place to donate a proton to thymine N1 during the intermediate state. [4] As of late 2007, 6 structures have been solved for this class of enzymes, with PDB accession codes 1AZY, 1OTP, 1TPT, 1UOU, 2J0F, and 2TPT.

Function

Thymidine phosphorylase plays a key role in pyrimidine salvage to recover nucleosides after DNA/RNA degradation. [5] Although the reaction it catalyzes between thymidine/deoxyuridine and their respective bases is reversible, the enzyme's function is primarily catabolic. [6]

Recent research has found that thymidine phosphorylase is also involved in angiogenesis. Experiments show inhibition of angiogenic effect by thymidine phosphorylase in the presence of 6-amino-5-chlorouracil, an inhibitor of thymidine phosphorylase, suggesting that the enzymatic activity of thymidine phosphorylase is required for its angiogenic activity. [7] Thymidine phosphorylase has been determined to be almost identical to the platelet-derived endothelial cell growth factor (PD-ECGF). Although the mechanism of angiogenesis by thymidine phosphorylase is not yet known, reports show that the enzyme itself is not a growth factor but indirectly causes angiogenesis by stimulating chemotaxis of endothelial and other cells. [8] Some reports suggest that thymidine phosphorylase promotes endothelial cell growth by reducing levels of thymidine that would otherwise inhibit endothelial cell growth. [9] An alternative explanation is that the enzyme’s products induce angiogenesis. Experiments have found that 2-deoxyribose is an endothelial-cell chemoattractant and angiogenesis-inducing factor, which supports this explanation. [10] Research has found thymidine phosphorylase is involved in angiogenesis during the menstrual cycle. The enzyme's expression in the endometrium is raised by a combination of progesterone and transforming growth factor-β1 and varies over the course of the menstrual cycle. [11]

Disease relevance

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an autosomal recessive disorder caused by mutations in the thymidine phosphorylase (TP) gene. [12] Because mitochondrial DNA (mtDNA) depends strongly on thymidine salvage (more so than nuclear DNA), it suffers damage from thymidine phosphorylase deficiency. In MNGIE disease, multiple deletions and depletion of mtDNA accumulate over time, leading to mitochondrial dysfunction. [13] Symptoms of MNGIE disease include diarrhea and abdominal pain as a result of dysmotility, caused by neuromuscular dysfunction, as well as ptosis, ophthalmoparesis, peripheral neuropathy, and hearing loss. [14]

Thymidine phosphorylase has also been found to play a dual role in both cancer development and therapy. [15] The enzyme's angiogenic activity promotes tumor growth, as supported by research showing much higher expression and activity of thymidine phosphorylase in malignant tumors (including carcinomas in the esophagus, stomach, colorectum, pancreas, and lung) than in adjacent non-neoplastic tissues [16] Thymidine phosphorylase in these carcinomas is up-regulated by cytokines interferon-γ and TNF-α, which are released by inflammatory cells during wound healing. The enzyme is also up-regulated by low oxygen levels and low pH environments in order to control vascularization of hypoxic regions. [17]

However, thymidine phosphorylase has also been found to play an essential role in the activation of the anti-cancer drug capecitabine. Specifically, it converts the intermediate metabolite 5’-deoxy-5-fluorocytidine in tumors to 5-fluorouracil, which acts as a thymidylate synthase inhibitor. [18]

Related Research Articles

Angiogenesis blood vessel formation when new vessels emerge from existing vessels

Angiogenesis is the physiological process through which new blood vessels form from pre-existing vessels, formed in the earlier stage of vasculogenesis. Angiogenesis continues the growth of the vasculature by processes of sprouting and splitting. Vasculogenesis is the embryonic formation of endothelial cells from mesoderm cell precursors, and from neovascularization, although discussions are not always precise. The first vessels in the developing embryo form through vasculogenesis, after which angiogenesis is responsible for most, if not all, blood vessel growth during development and in disease.

Thymidine Chemical compound

Thymidine is a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used to synchronize the cells in G1/early S phase.

Ribonucleotide chemical compound

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. The monomer itself from ribonucleotides forms the basic building blocks for RNA. However, the reduction of ribonucleotide, by enzyme ribonucleotide reductase (RNR), forms deoxyribonucleotide, which is the essential building block for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds by 3'-5'.

Endothelium Cells that line the Inner surface of blood vessels

Endothelium refers to cells that line the interior surface of blood vessels and lymphatic vessels, forming an interface between circulating blood or lymph in the lumen and the rest of the vessel wall. It is a thin layer of simple, or single-layered, squamous cells called endothelial cells. Endothelial cells in direct contact with blood are called vascular endothelial cells, whereas those in direct contact with lymph are known as lymphatic endothelial cells.

A salvage pathway is a pathway in which a biological product is produced from intermediates in the degradative pathway of its own or a similar substance. The term often refers to nucleotide salvage in particular, in which nucleotides are synthesized from intermediates in their degradative pathway.

A nucleoside triphosphate is a molecule containing a nitrogenous base bound to a 5-carbon sugar, with three phosphate groups bound to the sugar. It is an example of a Nucleotide. They are the building blocks of both DNA and RNA, which are chains of nucleotides made through the processes of DNA replication and transcription. Nucleoside triphosphates also serve as a source of energy for cellular reactions and are involved in signalling pathways.

Vascular endothelial growth factor (VEGF), originally known as vascular permeability factor (VPF), is a signal protein produced by cells that stimulates the formation of blood vessels. To be specific, VEGF is a sub-family of growth factors, the platelet-derived growth factor family of cystine-knot growth factors. They are important signaling proteins involved in both vasculogenesis and angiogenesis.

An angiogenesis inhibitor is a substance that inhibits the growth of new blood vessels (angiogenesis). Some angiogenesis inhibitors are endogenous and a normal part of the body's control and others are obtained exogenously through pharmaceutical drugs or diet.

Endostatin chemical compound

Endostatin is a naturally occurring, 20-kDa C-terminal fragment derived from type XVIII collagen. It is reported to serve as an anti-angiogenic agent, similar to angiostatin and thrombospondin.

Angiogenin protein-coding gene in the species Homo sapiens

Angiogenin (Ang) also known as ribonuclease 5 is a small 123 amino acid protein that in humans is encoded by the ANG gene. Angiogenin is a potent stimulator of new blood vessels through the process of angiogenesis. Ang hydrolyzes cellular RNA, resulting in modulated levels of protein synthesis and interacts with DNA causing a promoter-like increase in the expression of rRNA. Ang is associated with cancer and neurological disease through angiogenesis and through activating gene expression that suppresses apoptosis.

Floxuridine chemical compound

Floxuridine is an oncology drug that belongs to the class known as antimetabolites. Specifically, floxuridine is a pyrimidine analog, classified as a deoxyuridine. The drug is usually administered via an artery, and most often used in the treatment of colorectal cancer. The quality of life and survival rates of individuals that receive continuous hepatic artery infusion of floxuridine for colorectal cancer metastases is significantly higher than control groups. Floxuridine can also be prescribed for the treatment of kidney and stomach cancers. In vitro uses of floxuridine include 5-minute treatments of fluorouracil, floxuridine, and mitomycin to increase cell proliferation in Tenon's capsule fibroblasts.

Purine nucleoside phosphorylase InterPro Family

Purine nucleoside phosphorylase (PNP) also known as PNPase and inosine phosphorylase is an enzyme that in humans is encoded by the NP gene.

Nucleic acid metabolism

Nucleic acid metabolism is the process by which nucleic acids are synthesized and degraded. Nucleic acids are polymers of nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. Destruction of nucleic acid is a catabolic reaction. Additionally, parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases.

Thrombospondin 1 protein-coding gene in the species Homo sapiens

Thrombospondin 1, abbreviated as THBS1, is a protein that in humans is encoded by the THBS1 gene.

Mitochondrial neurogastrointestinal encephalopathy syndrome Human disease

Mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE) is a rare autosomal recessive mitochondrial disease. It has been previously referred to as polyneuropathy, ophthalmoplegia, leukoencephalopathy, and POLIP syndrome. The disease presents in childhood, but often goes unnoticed for decades. Unlike typical mitochondrial diseases caused by mitochondrial DNA (mtDNA) mutations, MNGIE is caused by mutations in the TYMP gene, which encodes the enzyme thymidine phosphorylase. Mutations in this gene result in impaired mitochondrial function, leading to intestinal symptoms as well as neuro-ophthalmologic abnormalities. A secondary form of MNGIE, called MNGIE without leukoencephalopathy, can be caused by mutations in the POLG gene.

In enzymology, a deoxyribose-phosphate aldolase is an enzyme that catalyzes the reversible chemical reaction

TYMP (gene) protein-coding gene in the species Homo sapiens

TYMP is a gene that encodes for the enzyme thymidine phosphorylase. The TYMP gene is also known as ECGF1 and MNGIE due to its role in MNGIE syndrome.

In enzymology, a deoxyuridine phosphorylase is an enzyme that catalyzes the chemical reaction

Angiogenesis is the process of forming new blood vessels from existing blood vessels. It is a highly complex process involving extensive interplay between cells, soluble factors, and the extracellular matrix (ECM). Angiogenesis is critical during normal physiological development, but it also occurs in adults during inflammation, wound healing, ischemia, and in pathological conditions such as rheumatoid arthritis, hemangioma, and tumor growth. Proteolysis has been indicated as one of the first and most sustained activities involved in the formation of new blood vessels. Numerous proteases including matrix metalloproteases (MMPs), a disintegrin and metalloprotease domain (ADAM), a disintegrin and metalloprotease domain with throbospondin motifs (ADAMTS), and cysteine and serine proteases are involved in angiogenesis. This article focuses on the important and diverse roles that these proteases play in the regulation of angiogenesis.

Trifluridine/tipiracil chemical compound

Trifluridine/tipiracil is a combination drug that is used as a third- or fourth-line treatment of metastatic colorectal cancer, after chemotherapy and targeted therapeutics have failed. It is a combination of two active pharmaceutical ingredients: trifluridine, a nucleoside analog, and tipiracil, a thymidine phosphorylase inhibitor. Tipiracil prevents rapid metabolism of trifluridine, increasing the bioavailability of trifluridine.

References

  1. Norman RA, Barry ST, Bate M, Breed J, Colls JG, Ernill RJ, Luke RW, Minshull CA, McAlister MS, McCall EJ, McMiken HH, Paterson DS, Timms D, Tucker JA, Pauptit RA (January 2004). "Crystal structure of human thymidine phosphorylase in complex with a small molecule inhibitor". Structure. 12 (1): 75–84. doi:10.1016/j.str.2003.11.018. PMID   14725767.
  2. Iltzsch MH, el Kouni MH, Cha S (November 1985). "Kinetic studies of thymidine phosphorylase from mouse liver". Biochemistry. 24 (24): 6799–807. doi:10.1021/bi00345a011. PMID   4074727.
  3. Walter MR, Cook WJ, Cole LB, Short SA, Koszalka GW, Krenitsky TA, Ealick SE (August 1990). "Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution". The Journal of Biological Chemistry. 265 (23): 14016–22. PMID   2199449.
  4. Pugmire MJ, Cook WJ, Jasanoff A, Walter MR, Ealick SE (August 1998). "Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase". Journal of Molecular Biology. 281 (2): 285–99. doi:10.1006/jmbi.1998.1941. PMID   9698549.
  5. LaFon SW, Nelson DJ, Berens RL, Marr JJ (January 1982). "Purine and pyrimidine salvage pathways in Leishmania donovani". Biochemical Pharmacology. 31 (2): 231–8. doi:10.1016/0006-2952(82)90216-7. PMID   7059364.
  6. Desgranges C, Razaka G, Rabaud M, Bricaud H (July 1981). "Catabolism of thymidine in human blood platelets: purification and properties of thymidine phosphorylase". Biochimica et Biophysica Acta. 654 (2): 211–8. doi:10.1016/0005-2787(81)90174-x. PMID   7284378.
  7. Haraguchi M, Miyadera K, Uemura K, Sumizawa T, Furukawa T, Yamada K, Akiyama S, Yamada Y (March 1994). "Angiogenic activity of enzymes". Nature. 368 (6468): 198. doi:10.1038/368198a0. PMID   7511797.
  8. Miyadera K, Sumizawa T, Haraguchi M, Yoshida H, Konstanty W, Yamada Y, Akiyama S (April 1995). "Role of thymidine phosphorylase activity in the angiogenic effect of platelet derived endothelial cell growth factor/thymidine phosphorylase". Cancer Research. 55 (8): 1687–90. PMID   7536129.
  9. Finnis C, Dodsworth N, Pollitt CE, Carr G, Sleep D (February 1993). "Thymidine phosphorylase activity of platelet-derived endothelial cell growth factor is responsible for endothelial cell mitogenicity". European Journal of Biochemistry. 212 (1): 201–10. doi:10.1111/j.1432-1033.1993.tb17651.x. PMID   8444155.
  10. Li W, Chiba Y, Kimura T, Morioka K, Uesaka T, Ihaya A, Muraoka R (February 2001). "Transmyocardial laser revascularization induced angiogenesis correlated with the expression of matrix metalloproteinases and platelet-derived endothelial cell growth factor". European Journal of Cardio-Thoracic Surgery. 19 (2): 156–63. doi: 10.1016/s1010-7940(00)00649-7 . PMID   11167105.
  11. Hague S, Manek S, Oehler MK, MacKenzie IZ, Bicknell R, Rees MC (March 2002). "Tamoxifen induction of angiogenic factor expression in endometrium". British Journal of Cancer. 86 (5): 761–7. doi:10.1038/sj.bjc.6600157. PMC   2375303 . PMID   11875740.
  12. Nishino I, Spinazzola A, Hirano M (January 1999). "Thymidine phosphorylase gene mutations in MNGIE, a human mitochondrial disorder". Science. 283 (5402): 689–92. doi:10.1126/science.283.5402.689. PMID   9924029.
  13. Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJ, Bird TD, Fong CT, Mefford HC, Smith RJ, Stephens K, Hirano M (1993). "Mitochondrial Neurogastrointestinal Encephalopathy Disease". PMID   20301358.Cite journal requires |journal= (help)
  14. Nishino I, Spinazzola A, Papadimitriou A, Hammans S, Steiner I, Hahn CD, Connolly AM, Verloes A, Guimarães J, Maillard I, Hamano H, Donati MA, Semrad CE, Russell JA, Andreu AL, Hadjigeorgiou GM, Vu TH, Tadesse S, Nygaard TG, Nonaka I, Hirano I, Bonilla E, Rowland LP, DiMauro S, Hirano M (June 2000). "Mitochondrial neurogastrointestinal encephalomyopathy: an autosomal recessive disorder due to thymidine phosphorylase mutations". Annals of Neurology. 47 (6): 792–800. doi:10.1002/1531-8249(200006)47:6<792::aid-ana12>3.3.co;2-p. PMID   10852545.
  15. Bronckaers A, Gago F, Balzarini J, Liekens S (November 2009). "The dual role of thymidine phosphorylase in cancer development and chemotherapy". Medicinal Research Reviews. 29 (6): 903–53. doi:10.1002/med.20159. PMID   19434693.
  16. Takebayashi Y, Yamada K, Miyadera K, Sumizawa T, Furukawa T, Kinoshita F, Aoki D, Okumura H, Yamada Y, Akiyama S, Aikou T (June 1996). "The activity and expression of thymidine phosphorylase in human solid tumours". European Journal of Cancer. 32A (7): 1227–32. doi:10.1016/0959-8049(96)00061-5. PMID   8758258.
  17. Brown NS, Bicknell R (August 1998). "Thymidine phosphorylase, 2-deoxy-D-ribose and angiogenesis". The Biochemical Journal. 334 (1): 1–8. doi:10.1042/bj3340001. PMC   1219653 . PMID   9693094.
  18. Sawada N, Ishikawa T, Fukase Y, Nishida M, Yoshikubo T, Ishitsuka H (April 1998). "Induction of thymidine phosphorylase activity and enhancement of capecitabine efficacy by taxol/taxotere in human cancer xenografts". Clinical Cancer Research. 4 (4): 1013–9. PMID   9563897.

Further reading