2NP9

Crystal structure of a dioxygenase in the Crotonase superfamily

2NP9 の概要

• エントリーDOI: 10.2210/pdb2np9/pdb
• 分子名称: DpgC, [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE, OXYGEN MOLECULE, ... (4 entities in total)
• 機能のキーワード: protein inhibitor complex, oxidoreductase
• 由来する生物種: Streptomyces toyocaensis
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 147905.63

構造登録者

Bruner, S.D.,Widboom, P.F.,Fielding, E.N. (登録日: 2006-10-26, 公開日: 2007-05-22, 最終更新日: 2024-04-03)

主引用文献

Widboom, P.F.,Fielding, E.N.,Liu, Y.,Bruner, S.D.
Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis.
Nature, 447:342-345, 2007

PubMed Abstract: Enzyme-catalysed oxidations are some of the most common transformations in primary and secondary metabolism. The vancomycin biosynthetic enzyme DpgC belongs to a small class of oxygenation enzymes that are not dependent on an accessory cofactor or metal ion. The detailed mechanism of cofactor-independent oxygenases has not been established. Here we report the first structure of an enzyme of this oxygenase class in complex with a bound substrate mimic. The use of a designed, synthetic substrate analogue allows unique insights into the chemistry of oxygen activation. The structure confirms the absence of cofactors, and electron density consistent with molecular oxygen is present adjacent to the site of oxidation on the substrate. Molecular oxygen is bound in a small hydrophobic pocket and the substrate provides the reducing power to activate oxygen for downstream chemical steps. Our results resolve the unique and complex chemistry of DpgC, a key enzyme in the biosynthetic pathway of an important class of antibiotics. Furthermore, mechanistic parallels exist between DpgC and cofactor-dependent flavoenzymes, providing information regarding the general mechanism of enzymatic oxygen activation.

PubMed: 17507985
DOI: 10.1038/nature05702

実験手法

X-RAY DIFFRACTION (2.45 Å)