8JI1

Crystal structure of Ham1 from Plasmodium falciparum

Summary for 8JI1

• Entry DOI: 10.2210/pdb8ji1/pdb
• Descriptor: Inosine triphosphate pyrophosphatase (2 entities in total)
• Functional Keywords: pyrophosphohydrolase, hydrolase
• Biological source: Plasmodium falciparum (malaria parasite P. falciparum)
• Total number of polymer chains: 2
• Total formula weight: 46224.61

Authors

Pramanik, A.,Datta, S. (deposition date: 2023-05-25, release date: 2024-05-29, Last modification date: 2024-10-16)

Primary citation

Saha, D.,Pramanik, A.,Freville, A.,Siddiqui, A.A.,Pal, U.,Banerjee, C.,Nag, S.,Debsharma, S.,Pramanik, S.,Mazumder, S.,Maiti, N.C.,Datta, S.,van Ooij, C.,Bandyopadhyay, U.
Structure-function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum.
Febs J., 291:4349-4371, 2024

PubMed Abstract: Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure-function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography-multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.

PubMed: 39003571
DOI: 10.1111/febs.17216

Experimental method

X-RAY DIFFRACTION (2.4 Å)