1K49

Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase (cation free form)

1K49 の概要

• エントリーDOI: 10.2210/pdb1k49/pdb
• 分子名称: 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase, SULFATE ION (3 entities in total)
• 機能のキーワード: dihydroxybutanone phosphate synthase, riboflavin biosynthesis, antimicrobial target, structure-based design, isomerase
• 由来する生物種: Magnaporthe grisea
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 25420.59

構造登録者

Liao, D.-I.,Zheng, Y.-J.,Viitanen, P.V.,Jordan, D.B. (登録日: 2001-10-06, 公開日: 2002-03-06, 最終更新日: 2023-08-16)

主引用文献

Liao, D.I.,Zheng, Y.J.,Viitanen, P.V.,Jordan, D.B.
Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase.
Biochemistry, 41:1795-1806, 2002

PubMed Abstract: X-ray crystal structures of L-3,4-dihydroxy-2-butanone-4-phosphate synthase from Magnaporthe grisea are reported for the E-SO(4)(2-), E-SO(4)(2-)-Mg(2+), E-SO(4)(2)(-)-Mn(2+), E-SO(4)(2)(-)-Mn(2+)-glycerol, and E-SO(4)(2)(-)-Zn(2+) complexes with resolutions that extend to 1.55, 0.98, 1.60, 1.16, and 1.00 A, respectively. Active-site residues of the homodimer are fully defined. The structures were used to model the substrate ribulose 5-phosphate in the active site with the phosphate group anchored at the sulfate site and the placement of the ribulose group guided by the glycerol site. The model includes two Mg(2+) cations that bind to the oxygen substituents of the C2, C3, C4, and phosphate groups of the substrate, the side chains of Glu37 and His153, and water molecules. The position of the metal cofactors and the substrate's phosphate group are further stabilized by an extensive hydrogen-bond and salt-bridge network. On the basis of their proximity to the substrate's reaction participants, the imidazole of an Asp99-His136 dyad from one subunit, the side chains of the Asp41, Cys66, and Glu174 residues from the other subunit, and Mg(2+)-activated water molecules are proposed to serve specific roles in the catalytic cycle as general acid-base functionalities. The model suggests that during the 1,2-shift step of the reaction, the substrate's C3 and C4 hydroxyl groups are cis to each other. A cis transition state is calculated to have an activation barrier that is 2 kcal/mol greater than that of the trans transition state in the absence of the enzyme.

PubMed: 11827524
DOI: 10.1021/bi015652u

実験手法

X-RAY DIFFRACTION (1.5 Å)