4R6X

Plasmodium falciparum phosphoethanolamine methyltransferase D128A mutant in complex with S-adenosylhomocysteine and phosphoethanolamine

Summary for 4R6X

• Entry DOI: 10.2210/pdb4r6x/pdb
• Related: 3UJ6 3UJ7 3UJ8 3UJ9 3UJA 3UJB 4R6W
• Descriptor: Phosphoethanolamine N-methyltransferase, PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER, S-ADENOSYL-L-HOMOCYSTEINE, ... (4 entities in total)
• Functional Keywords: methyltransferase, transferase
• Biological source: Plasmodium falciparum
• Total number of polymer chains: 2
• Total formula weight: 61272.97

Authors

Lee, S.G.,Jez, J.M. (deposition date: 2014-08-26, release date: 2014-10-08, Last modification date: 2023-09-20)

Primary citation

Saen-Oon, S.,Lee, S.G.,Jez, J.M.,Guallar, V.
An Alternative Mechanism for the Methylation of Phosphoethanolamine Catalyzed by Plasmodium falciparum Phosphoethanolamine Methyltransferase.
J.Biol.Chem., 289:33815-33825, 2014

PubMed Abstract: The phosphobase methylation pathway catalyzed by the phosphoethanolamine methyltransferase in Plasmodium falciparum (PfPMT), the malaria parasite, offers an attractive target for anti-parasitic drug development. PfPMT methylates phosphoethanolamine (pEA) to phosphocholine for use in membrane biogenesis. Quantum mechanics and molecular mechanics (QM/MM) calculations tested the proposed reaction mechanism for methylation of pEA involving the previously identified Tyr-19-His-132 dyad, which indicated an energetically unfavorable mechanism. Instead, the QM/MM calculations suggested an alternative mechanism involving Asp-128. The reaction coordinate involves the stepwise transfer of a proton to Asp-128 via a bridging water molecule followed by a typical Sn2-type methyl transfer from S-adenosylmethionine to pEA. Functional analysis of the D128A, D128E, D128Q, and D128N PfPMT mutants shows a loss of activity with pEA but not with the final substrate of the methylation pathway. X-ray crystal structures of the PfPMT-D128A mutant in complex with S-adenosylhomocysteine and either pEA or phosphocholine reveal how mutation of Asp-128 disrupts a hydrogen bond network in the active site. The combined QM/MM, biochemical, and structural studies identify a key role for Asp-128 in the initial step of the phosphobase methylation pathway in Plasmodium and provide molecular insight on the evolution of multiple activities in the active site of the PMT.

PubMed: 25288796
DOI: 10.1074/jbc.M114.611319

Experimental method

X-RAY DIFFRACTION (2.5534 Å)