b) Examine the active site in 1IDH. Which amino acids are part of the sites bind

Question

b) Examine the active site in 1IDH. Which amino acids are part of the sites binding the substrates? Fill out the tables on the next pages for the most important residues you identify for IDH's function. For the column in which you report distances, indicate which atoms you used to measure the distance (of the amino acid and the substrate or effector). Residues most important for binding isocitrate ("ICT1418") (1) Residue (name & #) Atom comes from which part of the residue? | Interacts with which atom of NADP"? Type(s) | | distance between atoms (A) | | 2o structural context of interaction (e.g. H-bond, charge-charge)

Explanation / Answer

NADP+-dependent isocitrate dehydrogenase is a member of the -decarboxylating dehydrogenase family and catalyzes the oxidative decarboxylation reaction from 2R,3S-isocitrate to yield 2-oxoglutarate and CO2 in the Krebs cycle. Although most prokaryotic NADP+-dependent isocitrate dehydrogenases (IDHs) are homodimeric enzymes, the monomeric IDH with a molecular weight of 80–100 kDa has been found in a few species of bacteria. The 1.95 Å crystal structure of the monomeric IDH revealed that it consists of two distinct domains, and its folding topology is related to the dimeric IDH. The structure of the large domain repeats a motif observed in the dimeric IDH. Such a fusional structure by domain duplication enables a single polypeptide chain to form a structure at the catalytic site that is homologous to the dimeric IDH, the catalytic site of which is located at the interface of two identical subunits.

crystal structure

gene duplication

3D domain swapping

monomeric IDH

molecular evolution

-decarboxylating dehydrogenase family

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