PDBsum entry 3x2w

Transferase/peptide

PDB id: 3x2w

Contents

Protein chains

339 a.a.

20 a.a.

Ligands

ATP

CO3

Metals

_MG ×2

Waters ×459

References listed in PDB file

Key reference

• Title: Protein kinase a catalytic subunit primed for action: time-Lapse crystallography of michaelis complex formation.
• Authors: A.Das, O.Gerlits, J.M.Parks, P.Langan, A.Kovalevsky, W.T.Heller.
• Ref.: Structure, 2015, 23, 2331-2340. [DOI no: 10.1016/j.str.2015.10.005]
• PubMed id: 26585512

Abstract

The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg(2+) binds first to the M1 site as a complex with ATP and is followed by Mg(2+) binding to the M2 site. Concurrently, the target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. Lastly, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.