PDBsum entry 2npq

Transferase

PDB id

2npq

Contents

			Protein chain

					326 a.a.

			Ligands

					BOG ×2

			Waters ×331

References listed in PDB file

Key reference

Title

A novel lipid binding site formed by the map kinase insert in p38 alpha.

Authors

R.Diskin, D.Engelberg, O.Livnah.

Ref.

J Mol Biol, 2008, 375, 70-79. [DOI no: 10.1016/j.jmb.2007.09.002]

PubMed id

17999933

Abstract

The p38 mitogen-activated protein (MAP) kinases function as signaling molecules essential for many cellular processes, particularly mediating stress response. The activity of p38 MAP kinases is meticulously regulated to reach the desired cellular phenotype. Several alternative activation and attenuation mechanisms have been characterized recently which include new phosphorylation sites. Here we present the crystal structure of p38 alpha MAP kinase in complex with n-octyl-beta-glucopyranoside detergent. The complex unveils a novel lipid-binding site formed by a local conformational change of the MAP kinase insert. This binding is the first attribution for a possible role of the MAP kinase insert in p38. The binding site can accommodate a large selection of lipidic molecules. In addition, we also show via biophysical methods that arachidonic acid and its derivatives bind p38 alpha in vitro. Based on our analysis we propose that the binding of lipids could fine-tune p38 alpha catalytic activity towards a preferred phenotype.



	Figure 1. Figure 1. Overall structure. (a) Structural alignment of the p38α – β-OG complex (green) and native p38α (gray) using the coordinate of PDB ID 1P38.^19 The phosphorylation lip of the native p38 as well as the N′ and C′ lobes are indicated. The phosphorylation lip of the β-OG complex is not shown due to local disorder. The overall kinase topology is maintained although a minor change in the inter-lobe orientation is apparent. All molecular graphics shown here were rendered using PyMol [http://pymol.sourceforge.net/]. (b) Ribbon representation of the p38α – β-OG complex with the two β-OG molecules shown as spheres. The MAP kinase insert is shown in gray. The β-OG 1 (carbon atoms shown in orange) is characterized by the relatively lower B-factor whereas β-OG 2 (carbon atoms shown in magenta) by higher values (see Table 1). (c) Difference electron density map (F[obs]–F[calc]) calculated at a 2.0σ cutoff at the resolution range of 32.7 Å−1.8 Å after the initial cycle of refinement without β-OG in the model, superimposed with the final coordinates of the p38α – β-OG complex. The map clearly indicates the presence of β-OG in site 1.		Figure 3. Figure 3. Structural characteristics of β-OG binding to p38α. (a) Superimposition of the p38α – β-OG complex (green) and native p38α (gray) in the vicinity of the MAP kinase insert. The β-OG molecules are represented as spheres in orange and magenta for β-OG 1 and 2, respectively. Trp197 and Met198 from the αEF/αF loop of native p38α and the p38α – β-OG complex are shown as sticks. The MAP kinase insert goes through a conformational change and opens up to accommodate the β-OG molecule. In addition the αEF/αF loop including Trp197 and Met198 goes through a substantial conformational change. In this context, Trp197 forms a hydrophobic interaction with the aliphatic segment of the detergent molecule. (b) Surface representation of p38α displaying the shape of the lipid binding site that accommodates β-OG 1 (orange) and β-OG 2 (magenta). β-OG 1 is extensively buried in the binding site whereas only the lipid tail of β-OG 2 interacts with the protein. The MAP kinase insert is highlighted in a darker surface colour.

PROCHECK

	Headers