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Published on: February 24, 2018
Structure of a highly NADP+-specific isocitrate dehydrogenase
Navdeep S Sidhu1, Louis T J Delbaere, George M Sheldrick
1Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany. nsidhu@shelx.uni-ac.gwdg.de
Acta Crystallographica. Section D, Biological Crystallography
|September 21, 2011
Summary
The crystal structure of isocitrate dehydrogenase from Corynebacterium glutamicum reveals how it binds its coenzyme. Conformational changes at hinge points suggest substrate binding regulates enzyme activity.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- Isocitrate dehydrogenase (IDH) is a key enzyme in the citric acid cycle and glyoxylate bypass.
- It plays a critical role in regulating carbon flow between CO2-generating and carbon-conserving pathways.
- Bacterial IDH typically requires nicotinamide adenine dinucleotide phosphate (NADP+) as a coenzyme.
Purpose of the Study:
- To elucidate the structural basis of coenzyme specificity and substrate-induced conformational changes in Corynebacterium glutamicum isocitrate dehydrogenase.
- To investigate the regulatory mechanisms governing the enzyme's activity through structural analysis.
Main Methods:
- X-ray crystallography was employed to determine the 1.9 Å resolution structure of the enzyme in complex with NADP+ and Mg2+.
- Comparison of the holoenzyme structure with the apoenzyme and other known holoenzyme structures (e.g., Azotobacter vinelandii).
Main Results:
- The structure reveals specific interactions, including ion pairs and hydrogen bonds, between the enzyme and the NADP+ 2'-phosphate group, explaining coenzyme specificity.
- A significant interdomain hinge-opening movement (36°) was observed in the C. glutamicum holoenzyme compared to A. vinelandii, rendering the active site accessible.
- The substrate-binding site appears disrupted in the open conformation, and movements at hinge points suggest substrate or inhibitor binding can induce conformational changes.
Conclusions:
- The binding of NADP+ is primarily mediated by charged residues, with the binding site preconfigured for coenzyme recognition.
- Conformational flexibility, particularly hinge-bending movements, is crucial for regulating IDH activity, potentially allowing substrate access but disrupting the active site in an open state.
- Small molecules binding near hinge regions may trigger large conformational shifts, leading to catalytically active or inactive states, as possibly seen with glyoxylate and oxaloacetate inhibition.
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