PDBsum entry 1unp

Transferase

PDB id: 1unp

Contents

Protein chain

119 a.a. *

Waters ×132

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Binding of phosphatidylinositol 3,4,5-Trisphosphate to the pleckstrin homology domain of protein kinase b induces a conformational change.

Authors

C.C.Milburn, M.Deak, S.M.Kelly, N.C.Price, D.R.Alessi, D.M.Van aalten.

Ref.

Biochem J, 2003, 375, 531-538.

PubMed id

12964941

Abstract

Protein kinase B (PKB/Akt) is a key regulator of cell growth, proliferation and metabolism. It possesses an N-terminal pleckstrin homology (PH) domain that interacts with equal affinity with the second messengers PtdIns(3,4,5)P3 and PtdIns(3,4)P2, generated through insulin and growth factor-mediated activation of phosphoinositide 3-kinase (PI3K). The binding of PKB to PtdIns(3,4,5)P3/PtdIns(3,4)P2 recruits PKB from the cytosol to the plasma membrane and is also thought to induce a conformational change that converts PKB into a substrate that can be activated by the phosphoinositide-dependent kinase 1 (PDK1). In this study we describe two high-resolution crystal structures of the PH domain of PKBalpha in a noncomplexed form and compare this to a new atomic resolution (0.98 A, where 1 A=0.1 nm) structure of the PH domain of PKBalpha complexed to Ins(1,3,4,5)P4, the head group of PtdIns(3,4,5)P3. Remarkably, in contrast to all other PH domains crystallized so far, our data suggest that binding of Ins(1,3,4,5)P4 to the PH domain of PKB, induces a large conformational change. This is characterized by marked changes in certain residues making up the phosphoinositide-binding site, formation of a short a-helix in variable loop 2, and a movement of variable loop 3 away from the lipid-binding site. Solution studies with CD also provided evidence of conformational changes taking place upon binding of Ins(1,3,4,5)P4 to the PH domain of PKB. Our data provides the first structural insight into the mechanism by which the interaction of PKB with PtdIns(3,4,5)P3/PtdIns(3,4)P2 induces conformational changes that could enable PKB to be activated by PDK1.

Secondary reference #1

Title

High-Resolution structure of the pleckstrin homology domain of protein kinase b/akt bound to phosphatidylinositol (3,4,5)-Trisphosphate.

Authors

C.C.Thomas, M.Deak, D.R.Alessi, D.M.Van aalten.

Ref.

Curr Biol, 2002, 12, 1256-1262. [DOI no: 10.1016/S0960-9822(02)00972-7]

PubMed id

12176338

Figure 1.
Figure 1. Structure of PKB[α]PH Complexed to Ins(1,3,4,5)P[4](A) A ribbon drawing of the PKB[α]PH-Ins(1,3,4,5)P[4] complex, with the seven β strands (labeled β1–7) shown in blue and the α helices (labeled α1–2) shown in red. Ins(1,3,4,5)P[4] is shown as purple carbons. The side chains of residues interacting with this molecule are shown as gray carbons. The basic residues thought to interact with the membrane have their side chains shown as sticks with green carbons. The negatively charged residues on VL2 that are hypothesized to interact with the kinase domain are shown as gray-blue carbons.(B) Ribbon diagrams of the Ins(1,3,4,5)P[4] binding sites of PKB, GRP1, DAPP1, and BTK. The Ins(1,3,4,5)P[4] is shown as purple carbons. For the PKB-Ins(1,3,4,5)P[4] structure, the experimental electron density map from SOLVE after density modification is shown in orange (contoured at 2.25σ). Residues that are hydrogen bonding the ligand are shown as sticks with gray carbons. Hydrogen bonds are shown as black dotted lines.

Figure 2.
Figure 2. Charge DistributionElectrostatic surface potential of PKB[α]PH-Ins(1,3,4,5)P[4] (calculated with GRASP), with the molecule in the same orientation as in Figure 1. Blue areas (+6kT) represent highly positively charged residues, and the red areas (−6kT) represent highly negatively charged residues. Ins(1,3,4,5)P[4] is shown as a stick model.

The above figures are reproduced from the cited reference with permission from Cell Press