Japan Agency for Medical Research and Development (AMED)
JP21am0101077
日本
Japan Agency for Medical Research and Development (AMED)
JP21am0101071
日本
引用
ジャーナル: Nat Commun / 年: 2022 タイトル: Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase. 著者: Takuya Miyakawa / Jian Yang / Masato Kawasaki / Naruhiko Adachi / Ayumu Fujii / Yumiko Miyauchi / Tomonari Muramatsu / Toshio Moriya / Toshiya Senda / Masaru Tanokura / 要旨: Cyanophycin is a natural biopolymer consisting of equimolar amounts of aspartate and arginine as the backbone and branched sidechain, respectively. It is produced by a single enzyme, cyanophycin ...Cyanophycin is a natural biopolymer consisting of equimolar amounts of aspartate and arginine as the backbone and branched sidechain, respectively. It is produced by a single enzyme, cyanophycin synthetase (CphA1), and accumulates as a nitrogen reservoir during N fixation by most cyanobacteria. A recent structural study showed that three constituent domains of CphA1 function as two distinct catalytic sites and an oligomerization interface in cyanophycin synthesis. However, it remains unclear how the ATP-dependent addition of aspartate to cyanophycin is initiated at the catalytic site of the glutathione synthetase-like domain. Here, we report the cryogenic electron microscopy structures of CphA1, including a complex with aspartate, cyanophycin primer peptide, and ATP analog. These structures reveal the aspartate binding mode and phosphate-binding loop movement to the active site required for the reaction. Furthermore, structural and mutational data show a potential role of protein dynamics in the catalytic efficiency of the arginine condensation reaction.
フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: COUNTING / 撮影したグリッド数: 1 / 実像数: 2109 / 平均露光時間: 55.75 sec. / 平均電子線量: 50.0 e/Å2
実験機器
モデル: Talos Arctica / 画像提供: FEI Company
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画像解析
粒子像選択
選択した数: 556730
CTF補正
ソフトウェア:
名称
詳細
Gctf
Initial estimation
RELION (ver. 3.1)
CTF refinement
初期モデル
モデルのタイプ: OTHER 詳細: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 60 A for use as an initial model for 3D classification.
初期 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.1)