1. Briefly describe the dimerization interface of Isocitrate dehydrogenase - how
ID: 145709 • Letter: 1
Question
1. Briefly describe the dimerization interface of Isocitrate dehydrogenase - how are the 2 subunits held together? (Describe how secondtary structure elements come together)?
2. From Isocitrate dehydrogenase, which amino acids (name and number) are part of the sites binding the substrates?
a. Atom comes from which part of the residue? Interacts with which atom of isocitrate? Type(s) of interaction (e.g. H-bond, charge-charge)
3. Which residues (name and number) are most important for binding NADP+?
a. Atom comes from which part of the residue? Interacts with which atom of isocitrate? Type(s) of interaction (e.g. H-bond, charge-charge)
For Q2 anf Q3, please indicate as name and number of residues.
Explanation / Answer
Answer1: Isocitrate dehydrogenase enzyme is an enzyme which catalyzes decarboxylation reaction of Isocitrate, as substrate, and converted into alpha-ketoglutrate, as product. The structure of isocitrate dehydrogenase is composed of a binary complex containing two IDH molecules in an asymmetric unit and forms an asymmetric homodimer (octamer of two non-identical subunits IDH1 and IDH2). The final structure model of IDH contains two full IDH polypeptide chains each of them consists of residues 1–414,154 water molecules, and two NADP molecules.
The region consisting of residues 271–286 in subunit A and counterpart in subunit B has well-defined electron density and partially disordered with discontinuous electron density like feature. Dimerization between two subunits of IDH is mediated by extensive hydrophobic and hydrophilic interactions primarily between different domains like four alpha-helices of the small domains (alpha-9 and alpha-10 of each subunit) and the two clasp domains. The structure of the quaternary complex contains four IDH molecules per asymmetric unit that form two homodimers related by a pseudo-2-fold. IDH consists of three domains: one as a large domain, second as a small domain, and a clasp domain. The large domain of IDH comprises residues 1–103 and 286–414 with a typical Rossmann fold. The small domain contains 104–136 and 186–285 residues will forms an alpha/beta sandwich structure. However, the clasp domain ranges from 137 to 185 residues and folds as two-stranded anti-parallel beta-sheets stacked on each other.
The large and small domains are joined together by alpha-sheet and the are two clefts flanked on each side of the beta-sheet. The clasp domain functions as an interlocking manner in all dimeric NADP-IDH structures which hold the two subunits together to form the catalytic active site.
Answer 2: Amino acids of active site in IDH binds with substrate 'isocitrate' by hydrogenbonding and hydrophobic intractions. The alpha-carboxylate of isocitrate forms a hydrophilic interaction with the side chains of Arg-100, Arg-109, Arg-132, and Asp-275. Its hydroxyl group makes hydrogen bonding interactions with the side chain of Asp-275 and the side chains of Lys-212 and Asp-252 of the adjacent subunit. However, the beta-carboxylate group forms hydrophilic interactions with the side chains of Arg-100, Arg-132, Tyr-139, and Asp-275, and the side chain of Lys-212 of the adjacent subunit. The gamma-carboxylate group also forms hydrogen bonds with the side chains of Thr-77 and Ser-94.
(a).
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