1KNJ

Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+

1KNJ の概要

• エントリーDOI: 10.2210/pdb1knj/pdb
• 関連するPDBエントリー: 1KNK
• 分子名称: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, MANGANESE (II) ION, CYTIDINE-5'-MONOPHOSPHATE, ... (5 entities in total)
• 機能のキーワード: isoprenoids, deoxyxylulose/methyl-erythritol-phosphate pathway, cyclodiphosphate, mep, ygbb, ispf, mecdp, 2-c-methyl-d-erythritol-2, 4-cyclodiphosphate synthase, metal binding protein
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 17764.34

構造登録者

Richard, S.B.,Ferrer, J.L.,Bowman, M.E.,Lillo, A.M.,Tetzlaff, C.N.,Cane, D.E.,Noel, J.P. (登録日: 2001-12-18, 公開日: 2002-06-18, 最終更新日: 2024-11-06)

主引用文献

Richard, S.B.,Ferrer, J.L.,Bowman, M.E.,Lillo, A.M.,Tetzlaff, C.N.,Cane, D.E.,Noel, J.P.
Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway.
J.Biol.Chem., 277:8667-8672, 2002

PubMed Abstract: The enzyme 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to MECDP, a highly unusual cyclodiphosphate-containing intermediate on the mevalonate-independent pathway to isopentenyl diphosphate and dimethylallyl diphosphate. We now report two x-ray crystal structures of MECDP synthase refined to 2.8-A resolution. The first structure contains a bound Mn(2+) cation, and the second structure contains CMP, MECDP, and Mn(2+). The protein adopts a homotrimeric quaternary structure built around a central hydrophobic cavity and three externally facing active sites. Each of these active sites is located between two adjacent monomers. A tetrahedrally arranged transition metal binding site, potentially occupied by Mn(2+), sits at the base of the active site cleft. A phosphate oxygen of MECDP and the side chains of Asp(8), His(10), and His(42) occupy the metal ion coordination sphere. These structures reveal for the first time the structural determinants underlying substrate, product, and Mn(2+) recognition and the likely catalytic mechanism accompanying the biosynthesis of the cyclodiphosphate-containing isoprenoid precursor, MECDP.

PubMed: 11786530
DOI: 10.1074/jbc.C100739200

実験手法

X-RAY DIFFRACTION (2.8 Å)