3IDB

Crystal structure of (108-268)RIIb:C holoenzyme of cAMP-dependent protein kinase

3IDB の概要

• エントリーDOI: 10.2210/pdb3idb/pdb
• 関連するPDBエントリー: 1CX4 1RGS 2QCS 2QVS 3IDC
• 分子名称: cAMP-dependent protein kinase catalytic subunit alpha, cAMP-dependent protein kinase type II-beta regulatory subunit, MANGANESE (II) ION, ... (5 entities in total)
• 機能のキーワード: pka, camp, spr, affinity, kinase, linker, rii holoenzyme, alternative splicing, atp-binding, cytoplasm, lipoprotein, myristate, nucleotide-binding, nucleus, phosphoprotein, serine/threonine-protein kinase, transferase, acetylation, camp-binding
• 由来する生物種: Mus musculus (mouse); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 59647.96

構造登録者

Brown, S.H.J.,Wu, J.,Kim, C.,Alberto, K.,Taylor, S.S. (登録日: 2009-07-20, 公開日: 2009-09-29, 最終更新日: 2023-09-06)

主引用文献

Brown, S.H.,Wu, J.,Kim, C.,Alberto, K.,Taylor, S.S.
Novel isoform-specific interfaces revealed by PKA RIIbeta holoenzyme structures.
J.Mol.Biol., 393:1070-1082, 2009

PubMed Abstract: The cAMP-dependent protein kinase catalytic (C) subunit is inhibited by two classes of functionally nonredundant regulatory (R) subunits, RI and RII. Unlike RI subunits, RII subunits are both substrates and inhibitors. Because RIIbeta knockout mice have important disease phenotypes, the RIIbeta holoenzyme is a target for developing isoform-specific agonists and/or antagonists. We also know little about the linker region that connects the inhibitor site to the N-terminal dimerization domain, although this linker determines the unique globular architecture of the RIIbeta holoenzyme. To understand how RIIbeta functions as both an inhibitor and a substrate and to elucidate the structural role of the linker, we engineered different RIIbeta constructs. In the absence of nucleotide, RIIbeta(108-268), which contains a single cyclic nucleotide binding domain, bound C subunit poorly, whereas with AMP-PNP, a non-hydrolyzable ATP analog, the affinity was 11 nM. The RIIbeta(108-268) holoenzyme structure (1.62 A) with AMP-PNP/Mn(2+) showed that we trapped the RIIbeta subunit in an enzyme:substrate complex with the C subunit in a closed conformation. The enhanced affinity afforded by AMP-PNP/Mn(2+) may be a useful strategy for increasing affinity and trapping other protein substrates with their cognate protein kinase. Because mutagenesis predicted that the region N-terminal to the inhibitor site might dock differently to RI and RII, we also engineered RIIbeta(102-265), which contained six additional linker residues. The additional linker residues in RIIbeta(102-265) increased the affinity to 1.6 nM, suggesting that docking to this surface may also enhance catalytic efficiency. In the corresponding holoenzyme structure, this linker docks as an extended strand onto the surface of the large lobe. This hydrophobic pocket, formed by the alphaF-alphaG loop and conserved in many protein kinases, also provides a docking site for the amphipathic helix of PKI. This novel orientation of the linker peptide provides the first clues as to how this region contributes to the unique organization of the RIIbeta holoenzyme.

PubMed: 19748511
DOI: 10.1016/j.jmb.2009.09.014

実験手法

X-RAY DIFFRACTION (1.62 Å)