1OQF

Crystal structure of the 2-methylisocitrate lyase

1OQF の概要

• エントリーDOI: 10.2210/pdb1oqf/pdb
• 分子名称: 2-methylisocitrate lyase (2 entities in total)
• 機能のキーワード: structural genomics, alpha-beta barrel, swapped helix across a dimer, structure 2 function project, s2f, lyase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 64076.84

構造登録者

Liu, S.,Lu, Z.,Dunaway-Mariano, D.,Herzberg, O.,Structure 2 Function Project (S2F) (登録日: 2003-03-08, 公開日: 2004-04-27, 最終更新日: 2024-02-14)

主引用文献

Liu, S.,Lu, Z.,Han, Y.,Melamud, E.,Dunaway-Mariano, D.,Herzberg, O.
Crystal structures of 2-methylisocitrate lyase in complex with product and with isocitrate inhibitor provide insight into lyase substrate specificity, catalysis and evolution.
Biochemistry, 44:2949-2962, 2005

PubMed Abstract: Two crystal structures of the C123S mutant of 2-methylisocitrate lyase have been determined, one with the bound reaction products, Mg(2+)-pyruvate and succinate, and the second with a bound Mg(2+)-(2R,3S)-isocitrate inhibitor. Comparison with the structure of the wild-type enzyme in the unbound state reveals that the enzyme undergoes a conformational transition that sequesters the ligand from solvent, as previously observed for two other enzyme superfamily members, isocitrate lyase and phosphoenolpyruvate mutase. The binding modes reveal the determinants of substrate specificity and stereoselectivity, and the stringent specificity is verified in solution using various potential substrates. A model of bound 2-methylisocitrate has been developed based on the experimentally determined structures. We propose a catalytic mechanism involving an alpha-carboxy-carbanion intermediate/transition state, which is consistent with previous stereochemical experiments showing inversion of configuration at the C(3) of 2-methylisocitrate. Structure-based sequence analysis and phylogenic tree construction reveal determinants of substrate specificity, highlight nodes of divergence of families, and predict enzyme families with new functions.

PubMed: 15723538
DOI: 10.1021/bi0479712

実験手法

X-RAY DIFFRACTION (1.93 Å)