2D2X

Crystal structure of 2-deoxy-scyllo-inosose synthase

2D2X の概要

• エントリーDOI: 10.2210/pdb2d2x/pdb
• 分子名称: 2-deoxy-scyllo-inosose synthase, COBALT (II) ION, SULFITE ION, ... (5 entities in total)
• 機能のキーワード: aminoglycoside, 2-deoxystreptamine, dehydroquinate synthase, lyase
• 由来する生物種: Bacillus circulans
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 82257.78

構造登録者

Nango, E.,Kumasaka, T.,Tanaka, N.,Kakinuma, K.,Eguchi, T. (登録日: 2005-09-20, 公開日: 2006-10-03, 最終更新日: 2024-11-13)

主引用文献

Nango, E.,Kumasaka, T.,Hirayama, T.,Tanaka, N.,Eguchi, T.
Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+
Proteins, 70:517-527, 2008

PubMed Abstract: A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction. This reaction mechanism is similar to the catalysis by dehydroquinate synthase (DHQS) of the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate in the shikimate pathway, but significant dissimilarity between these enzymes is also known, particularly in the stereochemistry of the phosphate elimination reaction and the cyclization. Here, the crystal structures of DOIS from Bacillus circulans and its complex with the substrate analog inhibitor carbaglucose-6-phosphate, NAD+, and Co2+ have been determined to provide structural insights into the reaction mechanism. The complex structure shows that an active site exists between the N-terminal and C-terminal domains and that the inhibitor coordinates a cobalt ion in this site. Two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer were observed to be different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change. The present study suggested that phosphate elimination proceeds through syn-elimination assisted by Glu 243 and the aldol condensation proceeds via a boat conformation. Also discussed are significant similarities and dissimilarities between DOIS and DHQS, particularly in terms of the structure at the active site and the reaction mechanism.

PubMed: 17879343
DOI: 10.1002/prot.21526

実験手法

X-RAY DIFFRACTION (2.3 Å)