1JCX

Aquifex aeolicus KDO8P synthase in complex with API and Cadmium

1JCX の概要

• エントリーDOI: 10.2210/pdb1jcx/pdb
• 関連するPDBエントリー: 1FWW 1JCY
• 分子名称: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE, CADMIUM ION, {[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID, ... (4 entities in total)
• 機能のキーワード: kdo8ps, kdo8p, kdo, api, beta/alpha barrel, lyase
• 由来する生物種: Aquifex aeolicus
• 細胞内の位置: Cytoplasm : O66496
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 60604.08

構造登録者

Wang, J.,Duewel, H.S.,Woodard, R.W.,Gatti, D.L. (登録日: 2001-06-11, 公開日: 2002-01-16, 最終更新日: 2024-02-07)

主引用文献

Wang, J.,Duewel, H.S.,Woodard, R.W.,Gatti, D.L.
Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis.
Biochemistry, 40:15676-15683, 2001

PubMed Abstract: We have determined the crystal structures of the metalloenzyme 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase from Aquifex aeolicus in complex with phosphoenolpyruvate (PEP) and ribose 5-phosphate (R5P), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. R5P, which is not a substrate for KDO8P synthase, binds in a manner similar to that of arabinose 5-phosphate (A5P), which is the natural substrate. The lack of reactivity of R5P appears to be primarily a consequence of the loss of a water molecule coordinated to Cd(2+) and located on the si side of PEP. This water molecule is no longer present because it cannot form a hydrogen bond with C2-OH(R5P), which is oriented in a different direction from C2-OH(A5P). The bisubstrate inhibitor binds with its phosphate and phosphonate moieties occupying the positions of the phosphate groups of A5P and PEP, respectively. One of the inhibitor hydroxyls replaces water as a ligand of Cd(2+). The current work supports a mechanism for the synthesis of KDO8P, in which a hydroxide ion on the si side of PEP attacks C2(PEP), forming a tetrahedral-like intermediate with a buildup of negative charge at C3(PEP). The ensuing condensation of C3(PEP) with C1(A5P) would be favored by a proton transfer from the phosphate moiety of PEP to the aldehyde carbonyl of A5P to generate the hydroxyl. Overall, the process can be described as a syn addition of water and A5P to the si side of PEP.

PubMed: 11747443
DOI: 10.1021/bi015568e

実験手法

X-RAY DIFFRACTION (1.8 Å)