8HD2

Crystal structure of SAM dependent methyltransferase encoded in type II fatty acid biosynthesis gene cluster from ladderane lipid producing anammox bacteria

8HD2 の概要

• エントリーDOI: 10.2210/pdb8hd2/pdb
• 分子名称: Methyltransf_25 domain-containing protein, S-ADENOSYL-L-HOMOCYSTEINE (3 entities in total)
• 機能のキーワード: anammox, fatty acid synthesis, ladderane lipid, sam dependent methyltransferase, biosynthetic protein
• 由来する生物種: Candidatus Brocadia fulgida
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 41592.39

構造登録者

Uegaki, T.,Nagano, S.,Hino, T. (登録日: 2022-11-03, 公開日: 2023-05-17, 最終更新日: 2024-05-29)

主引用文献

Uegaki, T.,Takei, T.,Yamaguchi, S.,Fujiyama, K.,Sato, Y.,Hino, T.,Nagano, S.
Anammox Bacterial S -Adenosyl-l-Methionine Dependent Methyltransferase Crystal Structure and Its Interaction with Acyl Carrier Proteins.
Int J Mol Sci, 24:-, 2023

PubMed Abstract: Ladderane lipids (found in the membranes of anaerobic ammonium-oxidizing [anammox] bacteria) have unique ladder-like hydrophobic groups, and their highly strained exotic structure has attracted the attention of scientists. Although enzymes encoded in type II fatty acid biosynthesis (FASII) gene clusters in anammox bacteria, such as -adenosyl-l-methionine (SAM)-dependent enzymes, have been proposed to construct a ladder-like structure using a substrate connected to acyl carrier protein from anammox bacteria (AmxACP), no experimental evidence to support this hypothesis was reported to date. Here, we report the crystal structure of a SAM-dependent methyltransferase from anammox bacteria (AmxMT1) that has a substrate and active site pocket between a class I SAM methyltransferase-like core domain and an additional α-helix inserted into the core domain. Structural comparisons with homologous SAM-dependent -methyltransferases in polyketide synthase, AmxACP pull-down assays, AmxACP/AmxMT1 complex structure predictions by AlphaFold, and a substrate docking simulation suggested that a small compound connected to AmxACP could be inserted into the pocket of AmxMT1, and then the enzyme transfers a methyl group from SAM to the substrate to produce branched lipids. Although the enzymes responsible for constructing the ladder-like structure remain unknown, our study, for the first time, supports the hypothesis that biosynthetic intermediates connected to AmxACP are processed by SAM-dependent enzymes, which are not typically involved in the FASII system, to produce the ladder-like structure of ladderane lipids in anammox bacteria.

PubMed: 36614187
DOI: 10.3390/ijms24010744

実験手法

X-RAY DIFFRACTION (1.6 Å)