3FWQ

Inactive conformation of human protein kinase CK2 catalytic subunit

Summary for 3FWQ

• Entry DOI: 10.2210/pdb3fwq/pdb
• Related: 1JWH 1LP4 2PVR 2RKP
• Descriptor: Casein kinase II subunit alpha, GLYCEROL, SULFATE ION, ... (5 entities in total)
• Functional Keywords: casein kinase 2, protein kinase ck2, eukaryotic protein kinases, inactive conformation, atp-binding, kinase, nucleotide-binding, phosphoprotein, serine/threonine-protein kinase, transferase, wnt signaling pathway
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 80683.09

Authors

Niefind, K.,Raaf, J.,Issinger, O.G. (deposition date: 2009-01-19, release date: 2009-02-17, Last modification date: 2023-11-01)

Primary citation

Raaf, J.,Issinger, O.G.,Niefind, K.
First inactive conformation of CK2 alpha, the catalytic subunit of protein kinase CK2
J.Mol.Biol., 386:1212-1221, 2009

PubMed Abstract: The Ser/Thr kinase casein kinase 2 (CK2) is a heterotetrameric enzyme composed of two catalytic chains (CK2alpha, catalytic subunit of CK2) attached to a dimer of two noncatalytic subunits (CK2beta, noncatalytic subunit of CK2). CK2alpha belongs to the superfamily of eukaryotic protein kinases (EPKs). To function as regulatory key components, EPKs normally exist in inactive ground states and are activated only upon specific signals. Typically, this activation is accompanied by large conformational changes in helix alpha C and in the activation segment, leading to a characteristic arrangement of catalytic key elements. For CK2alpha, however, no strict physiological control of activity is known. Accordingly, CK2alpha was found so far exclusively in the characteristic conformation of active EPKs, which is, in this case, additionally stabilized by a unique intramolecular contact between the N-terminal segment on one side, and helix alpha C and the activation segment on the other side. We report here the structure of a C-terminally truncated variant of human CK2alpha in which the enzyme adopts a decidedly inactive conformation for the first time. In this CK2alpha structure, those regulatory key regions still are in their active positions. Yet the glycine-rich ATP-binding loop, which is normally part of the canonical anti-parallel beta-sheet, has collapsed into the ATP-binding site so that ATP is excluded from binding; specifically, the side chain of Arg47 occupies the ribose region of the ATP site and Tyr50, the space required by the triphospho moiety. We discuss some factors that may support or disfavor this inactive conformation, among them coordination of small molecules at a remote cavity at the CK2alpha/CK2beta interaction region and binding of a CK2beta dimer. The latter stabilizes the glycine-rich loop in the extended active conformation known from the majority of CK2alpha structures. Thus, the novel inactive conformation for the first time provides a structural basis for the stimulatory impact of CK2beta on CK2alpha.

PubMed: 19361447
DOI: 10.1016/j.jmb.2009.01.033

Experimental method

X-RAY DIFFRACTION (2.3 Å)