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TitleDivergent acetyl-CoA binding modes mediate allosteric inhibition of bacterial hybrid-type malic enzymes.
Journal, issue, pagesJ Biol Chem, Vol. 301, Issue 12, Page 110887, Year 2025
Publish dateNov 4, 2025
AuthorsMunetoshi Sassa / Haruka Yamato / Hiroki Tanino / Yohta Fukuda / Tsuyoshi Inoue /
PubMed AbstractMalic 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 ...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.
External linksJ Biol Chem / PubMed:41197718 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.03 - 3.85 Å
Structure data

62540

9krt

EMDB-62540, PDB-9krt:
E. coli MaeB holo form
Method: EM (single particle) / Resolution: 2.73 Å

62541

9kru

EMDB-62541, PDB-9kru:
B. bacteriovorus MaeB holo form
Method: EM (single particle) / Resolution: 2.59 Å

62542

9krv

EMDB-62542, PDB-9krv:
B. bacteriovorus MaeB acetyl-CoA bound form
Method: EM (single particle) / Resolution: 3.18 Å

62816

9l4n

EMDB-62816, PDB-9l4n:
E. coli MaeB acetyl-CoA bound form
Method: EM (single particle) / Resolution: 2.03 Å

63586

9m2i

EMDB-63586, PDB-9m2i:
E. coli MaeB holo form ME domain dimer
Method: EM (single particle) / Resolution: 3.19 Å

63599

9m35

EMDB-63599, PDB-9m35:
E. coli MaeB acetyl-CoA bound form ME domain dimer
Method: EM (single particle) / Resolution: 2.39 Å

PDB-9krw:
E. coli MaeB apo form
Method: X-RAY DIFFRACTION / Resolution: 3.85 Å

Chemicals

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-MG:
Unknown entry

ChemComp-ACO:
ACETYL COENZYME *A

ChemComp-HOH:
WATER

Source
  • escherichia coli k-12 (bacteria)
  • bdellovibrio bacteriovorus (bacteria)
KeywordsSTRUCTURAL PROTEIN / oxidoreductase / cryo-EM / allostery

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