3A3U

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

Replaces:  2DBP

Summary for 3A3U

• Entry DOI: 10.2210/pdb3a3u/pdb
• Related: 2CZL
• Descriptor: Menaquinone biosynthetic enzyme, POTASSIUM ION, L(+)-TARTARIC ACID, ... (5 entities in total)
• Functional Keywords: alpha/beta structure, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, biosynthetic protein
• Biological source: Thermus thermophilus
• Total number of polymer chains: 1
• Total formula weight: 30567.98

Authors

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) (deposition date: 2009-06-20, release date: 2009-07-14, Last modification date: 2023-11-01)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.65 Å)