Three-dimensional structure of N-5-carboxyaminoimidazole ribonucleotide synthetase: A member of the ATP grasp protein superfamily

Escherichia coli PurK, a dimeric N-5-carboxyaminoimidazole ribonucleotide ( N-5-CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucl eotide (AIR), ATP, and bicarbonate to N-5-CAIR, ADP, and Pi. Crystallizatio n of both a sulfate-liganded and the MgADP-liganded E. coli PurK has result ed in structures at 2.1 and 2.5 Angstrom resolution, respectively. PurK bel ongs to the ATP grasp superfamily of C-N ligase enzymes, Each subunit of Pu rK is composed of three domains (A, B, and C). The B domain contains a flex ible, glycine-rich loop (B loop, T-123-G(130)) that is disordered in the su lfate-PurK structure and becomes ordered in the MgADP-PurK structure. MgADP is wedged between the B and C domains, as with all members of the ATP gras p superfamily. Other enzymes in this superfamily contain a conserved Omega loop proposed to interact with the B loop, define the specificity of their nonnucleotide substrate, and protect the acyl phosphate intermediate formed from this substrate. PurK contains a minimal Omega loop without conserved residues. In the reaction catalyzed by PurK, carboxyphosphate is the putati ve acyl phosphate intermediate. The sulfate of the sulfate ion-liganded Pur K interacts electrostatically with Arg 242 and the backbone amide group of Asn 245, components of the J loop of the C domain. This sulfate may reveal the location of the carboxyphosphate binding site, Conserved residues withi n the C-terminus of the C domain define a pocket that is proposed to bind A IR in collaboration with an N-terminal strand loop helix motif in the A dom ain (P loop, G(8)-L-12) The P loop is proposed to bind the phosphate of AIR on the basis of similar binding sites observed in PurN and PurE and propos ed in PurD and PurT, four other enzymes in the purine pathway.