4UR7

Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with pyruvate

4UR7 の概要

• エントリーDOI: 10.2210/pdb4ur7/pdb
• 関連するPDBエントリー: 4UR5 4UR8
• 分子名称: KETO-DEOXY-D-GALACTARATE DEHYDRATASE, GLYCEROL, FORMIC ACID, ... (4 entities in total)
• 機能のキーワード: lyase, decarboxylate, biocatalysis, oxidative pathway, d-galacturonic acid
• 由来する生物種: AGROBACTERIUM TUMEFACIENS
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 135630.65

構造登録者

Taberman, H.,Parkkinen, T.,Hakulinen, N.,Rouvinen, J. (登録日: 2014-06-26, 公開日: 2014-12-17, 最終更新日: 2024-01-10)

主引用文献

Taberman, H.,Andberg, M.B.,Parkkinen, T.,Janis, J.,Penttila, M.,Hakulinen, N.,Koivula, A.,Rouvinen, J.
Structure and Function of a Decarboxylating Agrobacterium Tumefaciens Keto-Deoxy-D-Galactarate Dehydratase.
Biochemistry, 53:8052-, 2014

PubMed Abstract: Agrobacterium tumefaciens (At) strain C58 contains an oxidative enzyme pathway that can function on both d-glucuronic and d-galacturonic acid. The corresponding gene coding for At keto-deoxy-d-galactarate (KDG) dehydratase is located in the same gene cluster as those coding for uronate dehydrogenase (At Udh) and galactarolactone cycloisomerase (At Gci) which we have previously characterized. Here, we present the kinetic characterization and crystal structure of At KDG dehydratase, which catalyzes the next step, the decarboxylating hydrolyase reaction of KDG to produce α-ketoglutaric semialdehyde (α-KGSA) and carbon dioxide. The crystal structures of At KDG dehydratase and its complexes with pyruvate and 2-oxoadipic acid, two substrate analogues, were determined to 1.7 Å, 1.5 Å, and 2.1 Å resolution, respectively. Furthermore, mass spectrometry was used to confirm reaction end-products. The results lead us to propose a structure-based mechanism for At KDG dehydratase, suggesting that while the enzyme belongs to the Class I aldolase protein family, it does not follow a typical retro-aldol condensation mechanism.

PubMed: 25454257
DOI: 10.1021/BI501290K

実験手法

X-RAY DIFFRACTION (1.499 Å)