How metal cofactors drive dimer–dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima

Abstract

The M42 aminopeptidases are dinuclear aminopeptidases displaying a peculiar tetrahedral-shaped structure with twelve subunits. Their quaternary structure results from the selfassembly of six dimers controlled by their divalent metal ion cofactors. The oligomeric state transition remains debated despite the structural characterization of several archaeal M42 aminopeptidases. The main bottleneck is the lack of dimer structures, hindering the understanding of structural changes occurring during the oligomerization process. We present the first dimer structure of an M42 aminopeptidase, TmPep1050 of Thermotoga maritima, along with the dodecamer structure. The comparison of both structures allows to describe how the metal ion cofactors modulate the active site fold and, subsequently, affect the interaction interface between dimers. A mutational study shows that the M1 site strictly controls dodecamer formation. The dodecamer structure of TmPep1050 also reveals that a part of the dimerization domain delimits the catalytic pocket and could participate in substrate binding.

Mass spectrometry reveals the assembly pathway of encapsulated ferritins and highlights a dynamic ferroxidase interface

“…15,16 Metal-mediated multimerization is also widespread in metalloproteins. [17][18][19][20] In this work we have demonstrated the first instance of a ferritin whose assembly is mediated by iron-binding and the formation of the ferroxidase centre between EncFtn monomers. This assembly pathway of the EncFtn decamer, from non-FOC dimers, is distinct to other members of the ferritin family.…”

Metal Dependent Dynamic Equilibrium: A Regulatory Mechanism for M17 Aminopeptidases fromPlasmodium falciparumandPlasmodium vivax

“…Our results indicate that the M17 aminopeptidase oligomerization pathway and formation of the active hexamer is mediated by the acquisition and binding of metal ions within the active site. A similar metal-mediated oligomerization mechanism has previously been described to control the formation of catalytically active M42 dodecamers and PBGS octamers (54)(55)(56)(57).…”

“…This form of regulation is involved in countless biological systems; hemoglobin must form α2β2 tetramers to transport oxygen; actin forms long oligomers to facilitate cellular movements (53); porphobilinogen synthase (PBGS) must form homo-octamers to facilitate production of building blocks required to form chlorophyll and vitamin B12 (54). More specifically, many metalloenzymes show a propensity to self-associate into large oligomers; M42 (TET aminopeptidase) (55)(56)(57) and M18 (aspartyl aminopeptidase) family aminopeptidases both form tetrahedral dodecamers, while M12 (carboxyl peptidase) family aminopeptidases form tetramers (58). The M17 aminopeptidases are one such family that undergo oligomerization to form homo-hexamers, a process that is essential for catalytic activation of the enzyme.…”

M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue

“…7,8 The M42 aminopeptidases are characterized by a genuine quaternary structure made of twelve subunits organized spatially as a tetrahedron. 1,[3][4][5][6][9][10][11][12][13] The association of the twelve subunits is often described as the assembly of six dimers, each dimer being located at a tetrahedron edge. 1 Four gates are found at the middle of the tetrahedron faces, leading to a wide inner chamber.…”

“…The gate size (between 12 and 20 Å) probably restricts the access to the inner chamber to unfolded peptides only. 1,10,13,14 The 12 catalytic sites are oriented inward the chamber, compartmentalizing the activity. The amino acids, generated after peptide hydrolysis, exit the catalytic sites through four channels located at the tetrahedron vertexes.…”