9M2I
E. coli MaeB holo form ME domain dimer
Summary for 9M2I
| Entry DOI | 10.2210/pdb9m2i/pdb |
| EMDB information | 63586 |
| Descriptor | NADP-dependent malic enzyme, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, MAGNESIUM ION (3 entities in total) |
| Functional Keywords | oxidoreductase, cryo-em, allostery, structural protein |
| Biological source | Escherichia coli K-12 |
| Total number of polymer chains | 2 |
| Total formula weight | 96455.05 |
| Authors | Sassa, M.,Yamato, H.,Tanino, H.,Fukuda, Y.,Inoue, T. (deposition date: 2025-02-27, release date: 2025-12-10) |
| Primary citation | Sassa, M.,Yamato, H.,Tanino, H.,Fukuda, Y.,Inoue, T. Divergent acetyl-CoA binding modes mediate allosteric inhibition of bacterial hybrid-type malic enzymes. J.Biol.Chem., 301:110887-110887, 2025 Cited by PubMed Abstract: Malic enzymes (MEs) function as the bypass enzyme in the Krebs cycle and have attracted attention in a wide range of scientific and industrial fields. In contrast to eukaryotic MEs, there is currently a lack of understanding of the structure-function relationships of prokaryotic MEs. Especially, little is known about an allosteric inhibition mechanism by an effector ligand in multi-domain MEs called hybrid-type MEs. Many bacterial hybrid-type MEs are inhibited by acetyl-CoA; however, the proposed acetyl-CoA binding site is not conserved. Here, we determined crystal and cryo-EM structures of hybrid-type MEs from Escherichia coli (EcMaeB) and Bdellovibrio bacteriovorus including complexes with acetyl-CoA. They reveal that these MaeBs have totally different acetyl-CoA binding sites and show different overall structural changes. However, the binding acetyl-CoA molecules induce identical movements of several α helices near the ligand both in EcMaeB and BbMaeB. Enzymatic assays proved that residues at the acetyl-CoA binding site are needed for inhibition. Phylogenetic analysis uncovered that EcMaeB and BbMaeB are classified into different clades of hybrid-type MEs and that the amino acid residues at the acetyl-CoA binding sites in different clades have evolved exclusively from each other. These results not only provide insights into bacterial MEs but also expand our knowledge about allosteric regulation in enzymes. PubMed: 41197718DOI: 10.1016/j.jbc.2025.110887 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.19 Å) |
Structure validation
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