6l57 | pdb_00006l57

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with CIT , Mg and ATP binding at allosteric site.

spinqualitylabelsall models 6l57, resolution 2.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6l57 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.302Å Ligands: ATP, CIT, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function IDH3A_HUMAN Publication Abstract from PubMed Human NAD-dependent isocitrate dehydrogenase (NAD-IDH) is responsible for the catalytic conversion of isocitrate into alpha-ketoglutarate in the Krebs cycle. This enzyme exists as the alpha2betagamma heterotetramer composed of the alphabeta and alphagamma heterodimers. Our previous biochemical data showed that the alphagamma heterodimer and the holoenzyme can be activated by low concentrations of ATP but inhibited by high concentrations of ATP; however, the molecular mechanism was unknown. Here, we report the crystal structures of the alphagamma heterodimer with ATP binding only to the allosteric site (alpha(Mg)gamma(Mg+CIT+ATP)) and to both the allosteric site and the active site (alpha(Mg+ATP)gamma(Mg+CIT+ATP)). Structural data show that ATP at low concentrations can mimic ADP to bind to the allosteric site, which stabilizes CIT binding and leads the enzyme to adopt an active conformation, revealing why the enzyme can be activated by low concentrations of ATP. On the other hand, at high concentrations ATP is competitive with NAD for binding to the catalytic site. In addition, our biochemical data show that high concentrations of ATP promote the formation of metal ion-ATP chelates. This reduces the concentration of free metal ion available for the catalytic reaction, and thus further inhibits the enzymatic activity. The combination of these two effects accounts for the inhibition of the enzyme at high concentrations of ATP. Taken together, our structural and biochemical data reveal the molecular mechanism for the dual regulatory roles of ATP on the alphagamma heterodimer of human NAD-IDH. Molecular mechanism of the dual regulatory roles of ATP on the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.,Sun P, Bai T, Ma T, Ding J Sci Rep. 2020 Apr 10;10(1):6225. doi: 10.1038/s41598-020-63425-6. PMID:32277159 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Isocitrate dehydrogenase 3D structures

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