PDBsum entry 2d1k

Structural protein

PDB id: 2d1k

Contents

Protein chains

371 a.a.

260 a.a. *

29 a.a. *

Ligands

NAG-NAG-BMA

ATP

Metals

_MG

_CA ×2

Waters ×103

* Residue conservation analysis

PDB id:

2d1k

Name:

Structural protein

Title:

Ternary complex of the wh2 domain of mim with actin-dnase i

Structure:

Actin, alpha skeletal muscle. Chain: a. Synonym: alpha-actin 1. Deoxyribonuclease-1. Chain: b. Synonym: deoxyribonuclease i, dnase i. Metastasis suppressor protein 1. Chain: c. Fragment: wh2 domain (residues 724-755).

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: skeletal muscle. Bos taurus. Cattle. Organism_taxid: 9913. Tissue: pancreas. Synthetic: yes.

Biol. unit:

Trimer (from PQS)

Resolution:

2.50Å R-factor: 0.220 R-free: 0.284

Authors:

D.Chereau,F.Kerff,R.Dominguez

Key ref:

S.H.Lee et al. (2007). Structural basis for the actin-binding function of missing-in-metastasis. Structure, 15, 145-155. PubMed id: 17292833 DOI: 10.1016/j.str.2006.12.005

Date:

26-Aug-05 Release date: 12-Sep-06

Protein chain

P68135  (ACTS_RABIT) -  Actin, alpha skeletal muscle from Oryctolagus cuniculus

Seq: 377 a.a.

Struc: 371 a.a.*

Protein chain

P00639  (DNAS1_BOVIN) -  Deoxyribonuclease-1 from Bos taurus

Seq: 282 a.a.

Struc: 260 a.a.

Protein chain

O43312  (MTSS1_HUMAN) -  Protein MTSS 1 from Homo sapiens

Seq: 755 a.a.

Struc: 29 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chain B: E.C.3.1.21.1 - deoxyribonuclease I.
• Reaction: Endonucleolytic cleavage to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end-products.

DOI no: 10.1016/j.str.2006.12.005

Structure 15:145-155 (2007)

PubMed id: 17292833

Structural basis for the actin-binding function of missing-in-metastasis.

S.H.Lee, F.Kerff, D.Chereau, F.Ferron, A.Klug, R.Dominguez.

ABSTRACT

The adaptor protein missing-in-metastasis (MIM) contains independent F- and G-actin binding domains, consisting, respectively, of an N-terminal 250 aa IRSp53/MIM homology domain (IMD) and a C-terminal WASP-homology domain 2 (WH2). We determined the crystal structures of MIM's IMD and that of its WH2 bound to actin. The IMD forms a dimer, with each subunit folded as an antiparallel three-helix bundle. This fold is related to that of the BAR domain. Like the BAR domain, the IMD has been implicated in membrane binding. Yet, comparison of the structures reveals that the membrane binding surfaces of the two domains have opposite curvatures, which may determine the type of curvature of the interacting membrane. The WH2 of MIM is longer than the prototypical WH2, interacting with all four subdomains of actin. We characterize a similar WH2 at the C terminus of IRSp53 and propose that in these two proteins WH2 performs a scaffolding function.

Selected figure(s)

Figure 3.
Figure 3. Structural and Functional Relationship between the IMD and BAR Domains
(A) Electrostatic surface representation of the IMD dimer calculated with the program APBS (Baker et al., 2001) and displayed with the program PyMOL (http://www.pymol.org). Red and blue indicate negatively and positively charged regions, respectively (red, −6 kTe^−1; blue +6 kTe^−1). Note the positively charged and slightly convex surface, which is thought to mediate the interactions with membranes of the IMD (Suetsugu et al., 2006).
(B) Similar electrostatic representation of the BAR domain of amphiphysin (Peter et al., 2004). The orientation is the same as in (A). Note that the shape of the positively charged membrane binding surface of the BAR domain is concave.
(C) Superimposition of the structures of the IMD of MIM (blue, yellow) with that of the BAR domain of arfaptin complexed with Rac (Tarricone et al., 2001) (gray). The orientation is the same as in (A) and (B). The two folds have different curvatures, but superimpose well in the middle section where the dimers overlap, suggesting that this region may also mediate the binding of Rac in MIM and IRSp53.

Figure 4.
Figure 4. The WASP-Homology Domain 2 of MIM and IRSp53
(A) Comparison of a classical WH2 (represented by WASP, Wiskott-Aldrich syndrome protein) with the WH2s of MIM, ABBA, and IRSp53. Red, blue, green, and yellow correspond to negatively charged, positively charged, hydrophobic, and small (Thr, Val, Ser, Ala) conserved amino acids, respectively. The diagram above the sequences represents a secondary structure assignment based on the structure determined here (cylinder, α helix; arrow, β strand). Accession numbers are as in Figure 1, and WASP_HUMAN, P42768. Red arrows point to noncanonical amino acids present in the WH2 of IRSp53.
(B) Structure of the WH2 of MIM (red ribbon) bound to actin (gray surface). Numbers 1–4 indicate actin's four subdomains. The side chains of some of the amino acids involved in interactions with actin are shown (green, hydrophobic; blue, positively charged).
(C) Binding of the WH2 of IRSp53 to actin measured by ITC. The upper graph corresponds to the heat evolved upon repeated 10 μl injections of a 100 μM solution of the WH2 peptide into a 10 μM solution of actin in G buffer. The lower graph shows the binding isotherm produced by integration of the heat for each injection. The line represents a nonlinear least squares fit to the data using a single-site binding model. The following thermodynamic parameters were determined from the fitting: dissociation constant K[d] = 0.28 ± 0.04 μM; molar enthalpy ΔH = −7.2 ± 0.1 kcal.mol^−1; and stoichiometry n = 0.9.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 145-155) copyright 2007.

Figures were selected by the author.