Open AccessThe complex structures of isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila suggest a new active site locking mechanism
Author(s) -
Leiros Hanna-Kirsti S.,
Fedøy Anita-Elin,
Leiros Ingar,
Steen Ida Helene
Publication year - 2012
Publication title -
febs open bio
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.718
H-Index - 31
ISSN - 2211-5463
DOI - 10.1016/j.fob.2012.06.003
Subject(s) - clostridium thermocellum , mechanism (biology) , isocitrate dehydrogenase , active site , chemistry , biology , computational biology , biochemistry , enzyme , physics , cellulase , quantum mechanics
Isocitrate dehydrogenase (IDH) catalyzes the oxidative NAD(P) + ‐dependent decarboxylation of isocitrate into α‐ketoglutarate and CO 2 and is present in organisms spanning the biological range of temperature. We have solved two crystal structures of the thermophilic Clostridium thermocellum IDH ( Ct IDH), a native open apo Ct IDH to 2.35 Å and a quaternary complex of Ct IDH with NADP + , isocitrate and Mg 2+ to 2.5 Å. To compare to these a quaternary complex structure of the psychrophilic Desulfotalea psychrophila IDH ( Dp IDH) was also resolved to 1.93 Å. Ct IDH and Dp IDH showed similar global thermal stabilities with melting temperatures of 67.9 and 66.9 °C, respectively. Ct IDH represents a typical thermophilic enzyme, with a large number of ionic interactions and hydrogen bonds per residue combined with stabilization of the N and C termini. Ct IDH had a higher activity temperature optimum, and showed greater affinity for the substrates with an active site that was less thermolabile compared to Dp IDH. The uncompensated negative surface charge and the enlarged methionine cluster in the hinge region both of which are important for cold activity in Dp IDH, were absent in Ct IDH. These structural comparisons revealed that prokaryotic IDHs in subfamily II have a unique locking mechanism involving Arg310, Asp251′ and Arg255 ( Ct IDH). These interactions lock the large domain to the small domain and direct NADP + into the correct orientation, which together are important for NADP + selectivity.