Structural Asymmetry and Disulfide Bridges among Subunits Modulate the Activity of Human Malonyl-CoA Decarboxylase

David Aparicio,Rosa Pérez-Luque,Xavier Carpena,Mireia Díaz,Joan C Ferrer,Peter C Loewen,Ignacio Fita

doi:10.1074/jbc.m112.443846

Abstract

Decarboxylation of malonyl-CoA to acetyl-CoA by malonyl-CoA decarboxylase (MCD; EC 4.1.1.9) is an essential facet in the regulation of fatty acid metabolism. The structure of human peroxisomal MCD reveals a molecular tetramer that is best described as a dimer of structural heterodimers, in which the two subunits present markedly different conformations. This molecular organization is consistent with half-of-the-sites reactivity. Each subunit has an all-helix N-terminal domain and a catalytic C-terminal domain with an acetyltransferase fold (GNAT superfamily). Intersubunit disulfide bridges, Cys-206-Cys-206 and Cys-243-Cys-243, can link the four subunits of the tetramer, imparting positive cooperativity to the catalytic process. The combination of a half-of-the-sites mechanism within each structural heterodimer and positive cooperativity in the tetramer produces a complex regulatory picture that is further complicated by the multiple intracellular locations of the enzyme. Transport into the peroxisome has been investigated by docking human MCD onto the peroxisomal import protein peroxin 5, which revealed interactions that extend beyond the C-terminal targeting motif.

Highlights

Malonyl-CoA, a key molecule playing central roles in fatty acids metabolism, is associated with human diseases such as malonic aciduria
Each malonyl-CoA decarboxylase (MCD) subunit is organized as an all-helical N-terminal domain and a catalytic C-terminal domain exhibiting the GNAT (GCN5-related N-acetyltransferase) fold (Protein Data Bank code 4F0X) (Fig. 2, A and B)
Transport of MCD into the peroxisome involves the interaction with the peroxisomal transport protein PEX5, and this interaction was investigated by superimposing the C-terminal PTS1 motif (Ser491–Lys-492–Leu-493) found in one of the MCD subunits onto the structure of the Ser-Lys-Leu peptide in complex with PEX5 (Protein Data Bank code 1FCH) (Fig. 8, A–C)

Summary

Background

Malonyl-CoA, a key molecule playing central roles in fatty acids metabolism, is associated with human diseases such as malonic aciduria. The structure of human peroxisomal MCD reveals a molecular tetramer that is best described as a dimer of structural heterodimers, in which the two subunits present markedly different conformations This molecular organization is consistent with half-of-the-sites reactivity. Malonyl-CoA is a key metabolite (Fig. 1A) in the synthesis, degradation, and regulation of fatty acids It is the direct precursor of most of the carbon atoms of fatty acids (i.e. 14 of 16 carbons in palmitic acid), and its availability is the rate-determining factor of fatty acid biosynthesis. The structure reveals what at first glance appears to be a homotetrameric protein, but which is a dimer of structural heterodimers This organization and biochemical data are consistent with an enzyme subject to half-of-the-sites reactivity. Even greater regulatory complexity is suggested by the presence of disulfide bonds connecting the four subunits, which are responsible for the positive cooperativity exhibited by MCD under oxidative conditions

EXPERIMENTAL PROCEDURES

RESULTS

DISCUSSION