PDBsum entry: 1w4m

Signal transduction

PDB id: 1w4m

Contents

Protein chain

95 a.a. *

* Residue conservation analysis

PDB id:

1w4m

Name:

Signal transduction

Title:

Structure of the human pleckstrin dep domain by multidimensional nmr

Structure:

Pleckstrin. Chain: a. Fragment: human dep domain, residues 121-223. Synonym: human pleckstrin dep domain, platelet p47 protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008.

NMR struc:

10 models

Authors:

C.Civera,B.Simon,G.Stier,M.Sattler,M.J.Macias

Key ref:

C.Civera et al. (2005). Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily. Proteins, 58, 354-366. PubMed id: 15573383 DOI: 10.1002/prot.20320

Date:

26-Jul-04 Release date: 15-Dec-04

Protein chain

P08567  (PLEK_HUMAN) -  Pleckstrin

Seq: 350 a.a.

Struc: 95 a.a.

DOI no: 10.1002/prot.20320

Proteins 58:354-366 (2005)

PubMed id: 15573383

Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily.

C.Civera, B.Simon, G.Stier, M.Sattler, M.J.Macias.

ABSTRACT

Pleckstrin1 is a major substrate for protein kinase C in platelets and leukocytes, and comprises a central DEP (disheveled, Egl-10, pleckstrin) domain, which is flanked by two PH (pleckstrin homology) domains. DEP domains display a unique alpha/beta fold and have been implicated in membrane binding utilizing different mechanisms. Using multiple sequence alignments and phylogenetic tree reconstructions, we find that 6 subfamilies of the DEP domain exist, of which pleckstrin represents a novel and distinct subfamily. To clarify structural determinants of the DEP fold and to gain further insight into the role of the DEP domain, we determined the three-dimensional structure of the pleckstrin DEP domain using heteronuclear NMR spectroscopy. Pleckstrin DEP shares main structural features with the DEP domains of disheveled and Epac, which belong to different DEP subfamilies. However, the pleckstrin DEP fold is distinct from these structures and contains an additional, short helix alpha4 inserted in the beta4-beta5 loop that exhibits increased backbone mobility as judged by NMR relaxation measurements. Based on sequence conservation, the helix alpha4 may also be present in the DEP domains of regulator of G-protein signaling (RGS) proteins, which are members of the same DEP subfamily. In pleckstrin, the DEP domain is surrounded by two PH domains. Structural analysis and charge complementarity suggest that the DEP domain may interact with the N-terminal PH domain in pleckstrin. Phosphorylation of the PH-DEP linker, which is required for pleckstrin function, could regulate such an intramolecular interaction. This suggests a role of the pleckstrin DEP domain in intramolecular domain interactions, which is distinct from the functions of other DEP domain subfamilies found so far.

Selected figure(s)

Figure 2.
Figure 2. Secondary structure elements of the pleck-DEP domain. NOEs that define the -sheet structure are indicated by arrows. The characteristic NOEs expected for an -helix (d[NN], d[ N(i,i+3)], d[ N(i,i+4)], and d[[ i, (i+3)]] were observed for residues 1 (6-13), 2 (40-48), 3 (53-67), and 4 (76-81). Blue-colored hydrogens and the residue name refer to protons that do not exchange inmediatly in D[2]O. Hydrogen bonds supported by the amide H/D exchange data are indicated by dashed lines.

Figure 4.
Figure 4. Biophysical characterization and backbone dynamics. (a) Sedimentation equilibrium analysis of the pleck-DEP domain. The data were fitted to a single ideal specie as described in the methods. Residuals are plotted below. (b) ^15N relaxation data of the pleck-DEP domain measured at 295 K. R1, R2 relaxation rates and the heteronuclear {^1H}-^15N NOE are plotted in black, red, and green, respectively.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 354-366) copyright 2005.

Figures were selected by an automated process.