1POT

SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (MONOMER FORM)

1POT の概要

• エントリーDOI: 10.2210/pdb1pot/pdb
• 関連するPDBエントリー: 1POY
• 分子名称: SPERMIDINE/PUTRESCINE-BINDING PROTEIN, SPERMIDINE (3 entities in total)
• 機能のキーワード: polyamine transport protein, binding protein
• 由来する生物種: Escherichia coli
• 細胞内の位置: Periplasm: P23861
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 36673.30

構造登録者

Sugiyama, S.,Maenaka, K.,Matsushima, M.,Morikawa, K. (登録日: 1996-02-02, 公開日: 1996-12-07, 最終更新日: 2024-02-14)

主引用文献

Sugiyama, S.,Matsuo, Y.,Maenaka, K.,Vassylyev, D.G.,Matsushima, M.,Kashiwagi, K.,Igarashi, K.,Morikawa, K.
The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding.
Protein Sci., 5:1984-1990, 1996

PubMed Abstract: The PotD protein from Escherichia coli is one of the components of the polyamine transport system present in the periplasm. This component specifically binds either spermidine or putrescine. The crystal structure of the E. coli PotD protein complexed with spermidine was solved at 1.8 A resolution and revealed the detailed substrate-binding mechanism. The structure provided the detailed conformation of the bound spermidine. Furthermore, a water molecule was clearly identified in the binding site lying between the amino-terminal domain and carboxyl-terminal domain. Through this water molecule, the bound spermidine molecule forms two hydrogen bonds with Thr 35 and Ser 211. Another periplasmic component of polyamine transport, the PotF protein, exhibits 35% sequence identity with the PotD protein, and it binds only putrescine, not spermidine. To understand these different substrate specificities, model building of the PotF protein was performed on the basis of the PotD crystal structure. The hypothetical structure suggests that the side chain of Lys 349 in PotF inhibits spermidine binding because of the repulsive forces between its positive charge and spermidine. On the other hand, putrescine could be accommodated into the binding site without any steric hindrance because its molecular size is much smaller than that of spermidine, and the positively charged amino group is relatively distant from Lys 349.

PubMed: 8897598

実験手法

X-RAY DIFFRACTION (1.8 Å)