Three-Dimensional Structure of Human Adenine Phosphoribosyltransferase and Its Relation to DHA-Urolithiasis^,

Abstract

In mammals, adenine phosphoribosyltransferase (APRT, EC 2.4.2.7) is present in all tissues and provides the only known mechanism for the metabolic salvage of adenine resulting from the polyamine biosynthesis pathway or from dietary sources. In humans, APRT deficiency results in serious kidney illness such as nephrolithiasis, interstitial nephritis, and chronic renal failure as a result of 2,8-dihydroxyadenine (DHA) precipitation in the renal interstitium. To address the molecular basis of DHA-urolithiasis, the recombinant human APRT was crystallized in complex with adenosine 5'-monophosphate (AMP). Refinement of X-ray diffraction data extended to 2.1 A resolution led to a final crystallographic R(factor) of 13.3% and an R(free) of 17.6%. This structure is composed of nine beta-strands and six alpha-helices, and the active site pocket opens slightly to accommodate the AMP product. The core of APRT is similar to that of other phosphoribosyltransferases (PRTases), although the adenine-binding domain is quite different. Structural comparisons between the human APRT and other "type I" PRTases of known structure revealed several important features of the biochemistry of PRTases. We propose that the residues located at positions corresponding to Leu159 and Ala131 in hAPRT are responsible for the base specificities of type I PRTases. The comparative analysis shown here also provides structural information for the mechanism by which mutations in the human APRT lead to DHA-urolithiasis.

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

“…Such interactions are common to nucleotide-binding proteins; anionic interaction with a nucleotide hydroxyl group, [30][31][32] and aromatic stacking against a nucleotide base occur in the DNA repair enzymes, 33,34 γ-tubulin, 35 the U1A spliceosomal protein, 36 the purine and pyrimidine phosphoribosyltransferases 32,37 and aspartyl-tRNA synthetase. 38 Indeed, the binding configuration at the SRP GTPase external nucleotide site is specifically reminiscent of similar arrangements in crystal structures of the editing complex of Klenow fragment 34,39 and AMP-bound adenine phosphoribosyltransferase (APRT) 40 ( Figure 6). In the 3′ to 5′ exonuclease active site of the Klenow fragment, the 3′-terminal base of the single-stranded DNA is positioned between Leu361 and Phe473, and the 2′-OH interacts with Glu357 ( Figure 6(b)).…”

“…33 In APRT (as in other purine and pyrimidine phosphoribosyltransferases), the base of the nucleoside monophosphate reaction product is sandwiched between an aromatic residue providing π-π stacking on one face and a leucine (or isoleucine) residue on the other, with a hydroxyl group coordinated via a carboxylate side-chain ( Figure 6(c)). 32,40 In all three systems, the residues that contribute to these sites are highly conserved; however, their sequence contexts are distinct. Thus, in APRT, the Glu/Leu pair are neighbors in the highly conserved PRT signature motif, 41 while the aromatic residue (here Phe26) is from a separate domain.…”

Hereditary causes of kidney stones and chronic kidney disease

“… 7 APRT activity in red blood cell lysates ranges from 16-32 nmol/h/mg hemoglobin in healthy subjects [118]; homozygotes and compound heterozygotes have no measurable enzyme activity and in heterozygotes the activity is approximately 25%. Recent blood transfusion may falsely elevate APRT activity.…”

The biosynthetic pathway of 2-azahypoxanthine in fairy-ring forming fungus

“…In the flowering plant, Arabidopsis, mutations in APRT affected pollen development causing male sterile21. APRT protein and its crystal structure from animals, bacteria, protista, fungi and archaea have been determined until now has been well-studied9222324252627. By contrast, there is still no knowledge on APRT in fairy ring-forming fungi.…”