1KYX

Lumazine Synthase from S.pombe bound to carboxyethyllumazine

1KYX の概要

• エントリーDOI: 10.2210/pdb1kyx/pdb
• 関連するPDBエントリー: 1KYV 1KYY 1KZ1 1KZ4 1KZ6 1KZ9
• 分子名称: 6,7-Dimethyl-8-ribityllumazine Synthase, PHOSPHATE ION, 3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID, ... (4 entities in total)
• 機能のキーワード: riboflavin biosynthesis, lumazine synthase, schizosaccharomyces pombe, ligand binding, transferase
• 由来する生物種: Schizosaccharomyces pombe (fission yeast)
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 88440.38

構造登録者

Gerhardt, S.,Haase, I.,Steinbacher, S.,Kaiser, J.T.,Cushman, M.,Bacher, A.,Huber, R.,Fischer, M. (登録日: 2002-02-06, 公開日: 2002-07-24, 最終更新日: 2024-03-13)

主引用文献

Gerhardt, S.,Haase, I.,Steinbacher, S.,Kaiser, J.T.,Cushman, M.,Bacher, A.,Huber, R.,Fischer, M.
The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.
J.Mol.Biol., 318:1317-1329, 2002

PubMed Abstract: Riboflavin is an essential cofactor in all organisms. Its direct biosynthetic precursor, 6,7-dimethyl-8-ribityllumazine, is synthesised by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. Recently, we have found that the enzyme from Schizosaccharomyces pombe binds riboflavin, the final product of the pathway with a relatively high affinity with a KD of 1.2 microM. Here, we report on the crystal structure of lumazine synthase from S. pombe with bound riboflavin and compare the binding mode with those of the substrate analogue inhibitor 5-nitro-6-(D-ribitylamino)-2,4(1H,3H)-pyrimidinedione and of the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine. In all complexes the pyrimidinedione moieties of each respective ligand bind in a very similar orientation. Binding of riboflavin additionally involves a stacking interaction of the dimethylbenzene moiety with the side-chain of His94, a highly conserved residue in all lumazine synthases. The enzyme from Bacillus subtilis showed a KD of at least 1 mM whereas the very homologous enzyme from Saccharomyces cerevisiae had a comparable KD of 3.9 microM. Structural comparison of the S. cerevisiae, the S. pombe, and the mutant enzymes suggests that fine tuning of affinity is achieved by influencing this stacking interaction.

PubMed: 12083520
DOI: 10.1016/S0022-2836(02)00116-X

実験手法

X-RAY DIFFRACTION (2.6 Å)