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Adenine phosphoribosyltransferase

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Template:PBB Adenine phosphoribosyltransferase (APRTase) is an enzyme encoded by the APRT gene, found in humans on chromosome 16.[1] It is part of the Type I PRTase family and is involved in the nucleotide salvage pathway, which provides an alternative to nucleotide biosynthesis de novo in humans and most other animals.[2] In parasitic protozoa such as giardia, APRTase provides the sole mechanism by which adenine can be produced. [3] APRTase deficiency contributes to the formation of kidney stones (urolithiasis) and to potential kidney failure.[4]

Biological Function

APRTase catalyzes the following reaction in the purine nucleotide salvage pathway:

Adenine + Phosphoribosyl Pyrophosphate (PRPP) → Adenylate (AMP) + Pyrophosphate (PPi)

ARPTase catalyzes a phosphoribosyl transfer from PRPP to adenine, forming AMP and releasing pyrophosphate (PPi).

In organisms that can synthesize purines de novo, the nucleotide salvage pathway provides an alternative that is energetically more efficient. It can salvage adenine from the polyamine biosynthetic pathway or from dietary sources of purines.[2] Although APRTase is functionally redundant in these organisms, it becomes more important during periods of rapid growth, such as embryogenesis and tumor growth.[5] It is constitutively expressed in all mammalian tissue.[6]

In protozoan parasites, the nucleotide salvage pathway provides the sole means for nucleotide synthesis. Since the consequences of APRTase deficiency in humans is comparatively mild and treatable, it may be possible to treat certain parasitic infections by targeting APRTase function.[7]

In plants, as in other organisms, ARPTase functions primarily for the synthesis of adenylate. It has the unique ability to metabolize cytokinins -- a plant hormone that can exist as a base, nucleotide, or nucleoside -- into adenylate nucleotides.[8]

APRT is functionally related to hypoxanthine-guanine phosphoribosyltransferase (HPRT).

Structure

APRTase is a homodimer, with 179 amino acid residues per monomer. Each monomer contains the following regions:

Catalytic site of APRTase with reactants adenine and PRPP resolved. The Hood is believed to be important for purine specificity, while the flexible loop is thought to contain the molecules within the active site.
  • "Core" domain (residues 33-169) with five parallel βべーた-sheets
  • "Hood" domain (residues 5-34) with 2 αあるふぁ-helices and 2 βべーた-sheets
  • "Flexible loop" domain (residues 95-113) with 2 antiparallel βべーた-sheets [6]
Residues A131, L159, V25, and R27 are important for purine specificity in human APRTase.

The core is highly conserved across many PRTases. The hood, which contains the adenine binding site, has more variability within the family of enzymes. A 13-residue motif comprises the PRPP binding region and involves two adjacent acidic residues and at least one surrounding hydrophobic residue. [9]

The enzyme's specificity for adenine involves hydrophobic residues Ala131 and Leu159 in the core domain. In humans specifically, two residues in the hood domain hydrogen bond with the purine for further specificity: Val25 with the hydrogens on N6, and Arg27 with N1. Although the flexible loop does not interact with the hood during purine recognition, it is thought to close over the active site and sequester the reaction from solvents. [6]

Most research on APRTase reports that Mg2+ is essential for phosphoribosyl transfer, and this is conserved across Type I PRTases. [8] However, a recent effort to resolve the structure of human APRTase was unable to locate a single site for Mg2+, but did find evidence to suggest a Cl- atom near [[Tryptophan|Trp98}. Despite the difficulty of placing Mg2+, it is generally accepted that the catalytic mechanism is dependent on this ion. [2]

Mechanism

APRTase proceeds via a bi bi ordered sequential mechanism, involving the formation of a ternary complex. The enzyme first binds PRPP, followed by adenine. After the phosphoribosyl transfer occurs, pyrophosphate leaves first, followed by AMP. Kinetic studies indicate that the phosphoribosyl transfer is relatively fast, while the product release (particularly the release of AMP) is rate-limiting.[10]

In human APRTase, it is thought that adenine's N9 proton is abstracted by Glu104 to form an oxacarbenium transition state. This functions as the nucleophile to attack the anomeric carbon of PRPP, forming AMP and displacing pyrophosphate from PRPP. The mechanism of APRTase is generally consistent with that of other PRTases, which conserve the function of displacing PRPP's αあるふぁ-1-pyrophosphate using a nitrogen nucleophile, in either an SN1 or SN2 attack.[2]

Deficiency

2,8-Dihydroxy-adenine urolithiasis is also known as "adenine phosphoribosyltransferase deficiency". When APRTase has reduced or nonexistent activity, adenine accumulates from other pathways. It is degraded by xanthine dehydrogenase to 2,8-dihydroxyadenine (DHA). Although DHA is protein-bound in plasma, it has poor solubility in urine and gradually precipitates in kidney tubules, leading to the formation of kidney stones (urolithiasis). If left untreated, the condition can eventually produce kidney failure. Cite error: The opening <ref> tag is malformed or has a bad name (see the help page).

ARPTase deficiency was first diagnosed in the UK in 1976. Since then, two categories of APRTase deficiency have been defined in humans.[11]

Type I deficiency results in a complete loss of APRTase activity and can occur in patients that are homozygous or compound heterozygous for various mutations.[12] Sequencing has revealed many different mutations that can account for Type 1, including missense mutations, nonsense mutations, a duplicated set of 4 base pairs in exon 3, [13] and a single thymine insertion in intron 4.[14] These mutations cause effects that are clustered into three main areas: in the binding of PRPP's βべーた-phosphate, in the binding of PRPP's 5'-phosphate, and in the segment of the flexible loop that closes over the active site during catalysis [6] Type I deficiency has been observed in various ethnic groups but studied predominately among White populations. [14]

Type II deficiency causes APRTase to have a reduced affinity for PRPP, resulting in a tenfold increase in the KM value. [2] It has been observed and studied primarily in Japan. [14]

A diagnosis of APRTase deficiency can be made by analyzing kidney stones, measuring DHA concentrations in urine, or analyzing APRTase activity in erythrocytes. It is treatable with regular doses of allopurinol or febuxostat, which inhibit xanthine dehydrogenase activity to prevent the accumulation and precipitation of DHA. [15] The condition can also be attenuated with a low-purine diet and high fluid intake. [11]

References

  1. ^ Valaperta, R; Rizzo, V; Lombardi, F; Verdelli, C; Piccoli, M; Ghiroldi, A; Creo, P; Colombo, A; Valisi, M; Margiotta, E; Panella, R; Costa, E (1 July 2014). "Adenine phosphoribosyltransferase (APRT) deficiency: identification of a novel nonsense mutation". BMC nephrology. 15: 102. PMID 24986359.
  2. ^ a b c d e Silva, CH; Silva, M; Iulek, J; Thiemann, OH (June 2008). "Structural complexes of human adenine phosphoribosyltransferase reveal novel features of the APRT catalytic mechanism". Journal of biomolecular structure & dynamics. 25 (6): 589–97. PMID 18399692.
  3. ^ Sarver, AE; Wang, CC (18 October 2002). "The adenine phosphoribosyltransferase from Giardia lamblia has a unique reaction mechanism and unusual substrate binding properties". The Journal of biological chemistry. 277 (42): 39973–80. PMID 12171924.
  4. ^ Shi, Wuxian; Tanaka, Kelly; Crother, Timothy; Taylor, Milton; Almo, Steven; Schramm, Vern (2001). "Structural Analysis of Adenine Phosphoribosyltransferase from Saccharomyces cerevisiae". Biochemistry. 40 (36): 10800–10809.
  5. ^ Bashor, C; Denu, JM; Brennan, RG; Ullman, B (26 March 2002). "Kinetic mechanism of adenine phosphoribosyltransferase from Leishmania donovani". Biochemistry. 41 (12): 4020–31. PMID 11900545.
  6. ^ a b c d Silva, M; Silva, CH; Iulek, J; Thiemann, OH (22 June 2004). "Three-dimensional structure of human adenine phosphoribosyltransferase and its relation to DHA-urolithiasis". Biochemistry. 43 (24): 7663–71. PMID 15196008.
  7. ^ Shi, W; Sarver, AE; Wang, CC; Tanaka, KS; Almo, SC; Schramm, VL (18 October 2002). "Closed site complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration". The Journal of biological chemistry. 277 (42): 39981–8. PMID 12171925.
  8. ^ a b Allen, M; Qin, W; Moreau, F; Moffatt, B (May 2002). "Adenine phosphoribosyltransferase isoforms of Arabidopsis and their potential contributions to adenine and cytokinin metabolism". Physiologia plantarum. 115 (1): 56–68. PMID 12010467.
  9. ^ Kukimoto-Niino, Mutsuko; et al. (March 2005). "Crystal structure of a predicted phosphoribosyltransferase (TT1426) from Thermus thermophilus HB8 at 2.01 Å resolution". Protein Science. 14 (3): 823–7. PMID 2279281. {{cite journal}}: Explicit use of et al. in: |last2= (help)
  10. ^ Bashor, C; Denu, JM; Brennan, RG; Ullman, B (26 March 2002). "Kinetic mechanism of adenine phosphoribosyltransferase from Leishmania donovani". Biochemistry. 41 (12): 4020–31. PMID 11900545.
  11. ^ a b Cassidy, MJ; McCulloch, T; Fairbanks, LD; Simmonds, HA (March 2004). "Diagnosis of adenine phosphoribosyltransferase deficiency as the underlying cause of renal failure in a renal transplant recipient". Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. 19 (3): 736–8. PMID 14767036.
  12. ^ Bollée, G; Harambat, J; Bensman, A; Knebelmann, B; Daudon, M; Ceballos-Picot, I (September 2012). "Adenine phosphoribosyltransferase deficiency". Clinical journal of the American Society of Nephrology : CJASN. 7 (9): 1521–7. PMID 22700886.
  13. ^ Kamatani, N; Hakoda, M; Otsuka, S; Yoshikawa, H; Kashiwazaki, S (July 1992). "Only three mutations account for almost all defective alleles causing adenine phosphoribosyltransferase deficiency in Japanese patients". The Journal of clinical investigation. 90 (1): 130–5. PMID 1353080.
  14. ^ a b c Bollée, G; Dollinger, C; Boutaud, L; Guillemot, D; Bensman, A; Harambat, J; Deteix, P; Daudon, M; Knebelmann, B; Ceballos-Picot, I (April 2010). "Phenotype and genotype characterization of adenine phosphoribosyltransferase deficiency". Journal of the American Society of Nephrology : JASN. 21 (4): 679–88. PMID 20150536.
  15. ^ Edvardsson, VO; Palsson, R; Sahota, A; Pagon, RA; Adam, MP; Ardinger, HH; Wallace, SE; Amemiya, A; Bean, LJH; Bird, TD; Fong, CT; Mefford, HC; Smith, RJH; Stephens, K (1993). "Adenine Phosphoribosyltransferase Deficiency". PMID 22934314. {{cite journal}}: Cite journal requires |journal= (help)

Further reading

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