5NE6

Crystal structure of dimeric TmPep1050 aminopeptidase

Summary for 5NE6

• Entry DOI: 10.2210/pdb5ne6/pdb
• Descriptor: AMINOPEPTIDASE, CITRIC ACID (3 entities in total)
• Functional Keywords: aminopeptidase, peptidase m42, tetrahedral structure, metal ion binding, lyase
• Biological source: Thermotoga maritima MSB8
• Total number of polymer chains: 2
• Total formula weight: 72604.84

Authors

Dutoit, R.,Brandt, N.,Bauvois, C. (deposition date: 2017-03-10, release date: 2018-05-16, Last modification date: 2024-01-17)

Primary citation

Dutoit, R.,Van Gompel, T.,Brandt, N.,Van Elder, D.,Van Dyck, J.,Sobott, F.,Droogmans, L.
How metal cofactors drive dimer-dodecamer transition of the M42 aminopeptidase TmPep1050 ofThermotoga maritima.
J.Biol.Chem., 294:17777-17789, 2019

PubMed Abstract: The M42 aminopeptidases are dinuclear aminopeptidases displaying a peculiar tetrahedron-shaped structure with 12 subunits. Their quaternary structure results from the self-assembly 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 , along with the dodecamer structure. The comparison of both structures has allowed us 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.

PubMed: 31611236
DOI: 10.1074/jbc.RA119.009281

Experimental method

X-RAY DIFFRACTION (2 Å)