3A3U

Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8

「2DBP」から置き換えられました

3A3U の概要

• エントリーDOI: 10.2210/pdb3a3u/pdb
• 関連するPDBエントリー: 2CZL
• 分子名称: Menaquinone biosynthetic enzyme, POTASSIUM ION, L(+)-TARTARIC ACID, ... (5 entities in total)
• 機能のキーワード: alpha/beta structure, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, biosynthetic protein
• 由来する生物種: Thermus thermophilus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 30567.98

構造登録者

Arai, R.,Nishino, A.,Nagano, K.,Uchikubo-Kamo, T.,Katsura, K.,Nishimoto, M.,Toyama, M.,Terada, T.,Kuramitsu, S.,Murayama, K.,Shirouzu, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2009-06-20, 公開日: 2009-07-14, 最終更新日: 2023-11-01)

主引用文献

Arai, R.,Murayama, K.,Uchikubo-Kamo, T.,Nishimoto, M.,Toyama, M.,Kuramitsu, S.,Terada, T.,Shirouzu, M.,Yokoyama, S.
Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.
J.Struct.Biol., 168:575-581, 2009

PubMed Abstract: In many microorganisms, menaquinone is an essential lipid-soluble electron carrier. Recently, an alternative menaquinone biosynthetic pathway was found in some microorganisms [Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H., Dairi, T., 2008. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321, 1670-1673]. Here, we report the 1.55 A crystal structure of MqnD (TTHA1568) from Thermus thermophilus HB8, an enzyme within the alternative menaquinone biosynthetic pathway. The structure comprises two domains with alpha/beta structures, a large domain and a small domain. L(+)-Tartaric acid was bound to the pocket between the two domains, suggesting that this pocket is a putative active site. The conserved glycine residues at positions 78, 80 and 82 seem to act as hinges, allowing the substrate to access the pocket. Highly conserved residues, such as Asp14, Asp38, Asn43, Ser57, Thr107, Ile144, His145, Glu146, Leu176 and Tyr234, are located at this pocket, suggesting that these residues are involved in substrate binding and/or catalysis, and especially, His145 could function as a catalytic base. Since humans and their commensal intestinal bacteria, including lactobacilli, lack the alternative menaquinone biosynthetic pathway, this enzyme in pathogenic species, such as Helicobacter pylori and Campylobacter jejuni, is an attractive target for the development of chemotherapeutics. This high-resolution structure may contribute toward the development of its inhibitors.

PubMed: 19602440
DOI: 10.1016/j.jsb.2009.07.007

実験手法

X-RAY DIFFRACTION (1.65 Å)