6II7

Crystal structure of Plasmodium falciparum adenosine deaminase C27Q+L227I mutant co-complexed with Zn ion, hypoxanthine and inosine

Summary for 6II7

• Entry DOI: 10.2210/pdb6ii7/pdb
• Descriptor: Adenosine deaminase, INOSINE, HYPOXANTHINE, ... (5 entities in total)
• Functional Keywords: tim barrel, hydrolase
• Biological source: Plasmodium falciparum 3D7 (isolate 3D7)
• Total number of polymer chains: 1
• Total formula weight: 43084.00

Authors

Chitnumsub, P.,Jaruwat, A. (deposition date: 2018-10-03, release date: 2019-05-01, Last modification date: 2023-11-22)

Primary citation

Jaruwat, A.,Riangrungroj, P.,Ubonprasert, S.,Sae-Ueng, U.,Kuaprasert, B.,Yuthavong, Y.,Leartsakulpanich, U.,Chitnumsub, P.
Crystal structure of Plasmodium falciparum adenosine deaminase reveals a novel binding pocket for inosine.
Arch. Biochem. Biophys., 667:6-13, 2019

PubMed Abstract: Plasmodium falciparum (Pf), a malarial pathogen, can only synthesize purine nucleotides employing a salvage pathway because it lacks de novo biosynthesis. Adenosine deaminase (ADA), one of the three purine salvage enzymes, catalyzes the irreversible hydrolytic deamination of adenosine to inosine, which is further converted to GMP and AMP for DNA/RNA production. In addition to adenosine conversion, Plasmodium ADA also catalyzes the conversion of 5'-methylthioadenosine, derived from polyamine biosynthesis, into 5'-methylthioinosine whereas the human enzyme is not capable of this function. Here we report the crystal structure of a surface engineered PfADA at a resolution of 2.48 Å, together with results on kinetic studies of PfADA wild-type and active site variants. The structure reveals a novel inosine binding pocket linked to a distinctive PfADA substructure (residues 172-179) derived from a non-conserved gating helix loop (172-188) in Plasmodium spp. and other ADA enzymes. Variants of PfADA and human (h) ADA active site amino acids were generated in order to study their role in catalysis, including PfADA- Phe136, -Thr174, -Asp176, and -Leu179, and hADA-Met155, equivalent to PfADA-Asp176. PfADA-Leu179His showed no effect on kinetic parameters. However, kinetic results of PfADA-Asp176Met/Ala mutants and hADA-Met155Asp/Ala showed that the mutation reduced adenosine and 5'-methylthioadenosine substrate affinity in PfADA and k in hADA, thereby reducing catalytic efficiency of the enzyme. Phe136Leu mutant showed increased K (>10-fold) for both substrates whereas Thr174Ile/Ala only affected 5'-methylthioadenosine binding affinity. Together, the structure with the novel inosine binding pocket and the kinetic data provide insights for rational design of inhibitors against PfADA.

PubMed: 31002765
DOI: 10.1016/j.abb.2019.04.002

Experimental method

X-RAY DIFFRACTION (2.48 Å)