6XQK

Crystal structure of the D/D domain of PKA from S. cerevisiae

Summary for 6XQK

• Entry DOI: 10.2210/pdb6xqk/pdb
• Descriptor: cAMP-dependent protein kinase regulatory subunit, GLYCEROL, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: protein kinase a, signaling protein
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Total number of polymer chains: 8
• Total formula weight: 47576.64

Authors

Larrieux, N.,Gonzalez Bardeci, N.,Trajtenberg, F.,Buschiazzo, A. (deposition date: 2020-07-09, release date: 2021-04-14, Last modification date: 2024-03-06)

Primary citation

Bardeci, N.G.,Tofolon, E.,Trajtenberg, F.,Caramelo, J.,Larrieux, N.,Rossi, S.,Buschiazzo, A.,Moreno, S.
The crystal structure of yeast regulatory subunit reveals key evolutionary insights into Protein Kinase A oligomerization.
J.Struct.Biol., 213:107732-107732, 2021

PubMed Abstract: Protein Kinase A (PKA) is a widespread enzyme that plays a key role in many signaling pathways from lower eukaryotes to metazoans. In mammals, the regulatory (R) subunits sequester and target the catalytic (C) subunits to proper subcellular locations. This targeting is accomplished by the dimerization and docking (D/D) domain of the R subunits. The activation of the holoenzyme depends on the binding of the second messenger cAMP. The only available structures of the D/D domain proceed from mammalian sources. Unlike dimeric mammalian counterparts, the R subunit from Saccharomyces cerevisiae (Bcy1) forms tetramers in solution. Here we describe the first high-resolution structure of a non-mammalian D/D domain. The tetramer in the crystals of the Bcy1 D/D domain is a dimer of dimers that retain the classical D/D domain fold. By using phylogenetic and structural analyses combined with site-directed mutagenesis, we found that fungal R subunits present an insertion of a single amino acid at the D/D domain that shifts the position of a downstream, conserved arginine. This residue participates in intra-dimer interactions in mammalian D/D domains, while due to this insertion it is involved in inter-dimer contacts in Bcy1, which are crucial for the stability of the tetramer. This surprising finding challenges well-established concepts regarding the oligomeric state within the PKAR protein family and provides important insights into the yet unexplored structural diversity of the D/D domains and the molecular determinants of R subunit oligomerization.

PubMed: 33819633
DOI: 10.1016/j.jsb.2021.107732

Experimental method

X-RAY DIFFRACTION (2.56 Å)