PDBsum entry 2npq

Transferase

PDB id: 2npq

Contents

Protein chain

326 a.a. *

Ligands

BOG ×2

Waters ×331

* Residue conservation analysis

PDB id:

2npq

Name:

Transferase

Title:

A novel lipid binding site in the p38 alpha map kinase

Structure:

Mitogen-activated protein kinase 14. Chain: a. Synonym: mitogen-activated protein kinase p38 alpha, map kinase p38 alpha, cytokine suppressive anti-inflammatory drug-binding protein, csaid-binding protein, csbp, max-interacting protein 2, map kinase mxi2, sapk2a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.205 R-free: 0.245

Authors:

R.Diskin,D.Engelberg,O.Livnah

Key ref:

R.Diskin et al. (2008). A novel lipid binding site formed by the MAP kinase insert in p38 alpha. J Mol Biol, 375, 70-79. PubMed id: 17999933 DOI: 10.1016/j.jmb.2007.09.002

Date:

29-Oct-06 Release date: 16-Oct-07

Protein chain

Q16539  (MK14_HUMAN) -  Mitogen-activated protein kinase 14 from Homo sapiens

Seq: 360 a.a.

Struc: 326 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.11.24 - mitogen-activated protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2007.09.002

J Mol Biol 375:70-79 (2008)

PubMed id: 17999933

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

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

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.

Selected figure(s)

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 375, 70-79) copyright 2008.

Figures were selected by an automated process.