1L1R

Crystal Structure of APRTase from Giardia lamblia Complexed with 9-deazaadenine, Mg2+ and PRPP

Summary for 1L1R

• Entry DOI: 10.2210/pdb1l1r/pdb
• Related: 1L1Q
• Descriptor: Adenine phosphoribosyltransferase, MAGNESIUM ION, 9-DEAZAADENINE, ... (5 entities in total)
• Functional Keywords: aprtase, adenine, giardia lamblia, purine metabolism, catalytic loop, transferase
• Biological source: Giardia intestinalis
• Total number of polymer chains: 1
• Total formula weight: 20839.13

Authors

Shi, W.,Sarver, A.E.,Wang, C.C.,Tanaka, K.S.,Almo, S.C.,Schramm, V.L. (deposition date: 2002-02-19, release date: 2002-11-27, Last modification date: 2023-08-16)

Primary citation

Shi, W.,Sarver, A.E.,Wang, C.C.,Tanaka, K.S.,Almo, S.C.,Schramm, V.L.
Closed Site Complexes of Adenine Phosphoribosyltransferase from Giardia lamblia Reveal a Mechanism of Ribosyl Migration.
J.Biol.Chem., 277:39981-39988, 2002

PubMed Abstract: The adenine phosphoribosyltransferase (APRTase) from Giardia lamblia was co-crystallized with 9-deazaadenine and sulfate or with 9-deazaadenine and Mg-phosphoribosylpyrophosphate. The complexes were solved and refined to 1.85 and 1.95 A resolution. Giardia APRTase is a symmetric homodimer with the monomers built around Rossman fold cores, an element common to all known purine phosphoribosyltransferases. The catalytic sites are capped with a small hood domain that is unique to the APRTases. These structures reveal several features relevant to the catalytic function of APRTase: 1) a non-proline cis peptide bond (Glu(61)-Ser(62)) is required to form the pyrophosphate binding site in the APRTase.9dA.MgPRPP complex but is a trans peptide bond in the absence of pyrophosphate group, as observed in the APRTase.9dA.SO4 complex; 2) a catalytic site loop is closed and fully ordered in both complexes, with Glu(100) from the catalytic loop acting as the acid/base for protonation/deprotonation of N-7 of the adenine ring; 3) the pyrophosphoryl charge is neutralized by a single Mg2+ ion and Arg(63), in contrast to the hypoxanthine-guanine phosphoribosyltransferases, which use two Mg2+ ions; and 4) the nearest structural neighbors to APRTases are the orotate phosphoribosyltransferases, suggesting different paths of evolution for adenine relative to other purine PRTases. An overlap comparison of AMP and 9-deazaadenine plus Mg-PRPP at the catalytic sites of APRTases indicated that reaction coordinate motion involves a 2.1-A excursion of the ribosyl anomeric carbon, whereas the adenine ring and the 5-phosphoryl group remained fixed. G. lamblia APRTase therefore provides another example of nucleophilic displacement by electrophile migration.

PubMed: 12171925
DOI: 10.1074/jbc.M205596200

Experimental method

X-RAY DIFFRACTION (1.95 Å)