PDBsum entry 2j1d

Protein binding

PDB id: 2j1d

Contents

Protein chain

396 a.a. *

Ligands

PO4

GOL

Waters ×75

* Residue conservation analysis

PDB id:

2j1d

Name:

Protein binding

Title:

Crystallization of hdaam1 c-terminal fragment

Structure:

Disheveled-associated activator of morphogenesis 1. Chain: g. Fragment: fh2 domain, residues 596-1078. Synonym: daam1. Engineered: yes

Source:

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

Resolution:

2.25Å R-factor: 0.220 R-free: 0.250

Authors:

J.Lu,W.Meng,F.Poy,M.J.Eck

Key ref:

J.Lu et al. (2007). Structure of the FH2 domain of Daam1: implications for formin regulation of actin assembly. J Mol Biol, 369, 1258-1269. PubMed id: 17482208 DOI: 10.1016/j.jmb.2007.04.002

Date:

10-Aug-06 Release date: 15-May-07

Protein chain

Q9Y4D1  (DAAM1_HUMAN) -  Disheveled-associated activator of morphogenesis 1 from Homo sapiens

Seq: 1078 a.a.

Struc: 396 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2007.04.002

J Mol Biol 369:1258-1269 (2007)

PubMed id: 17482208

Structure of the FH2 domain of Daam1: implications for formin regulation of actin assembly.

J.Lu, W.Meng, F.Poy, S.Maiti, B.L.Goode, M.J.Eck.

ABSTRACT

Daam1 (dishevelled-associated activator of morphogenesis-1) is a diaphanous-related formin first studied as a novel dishevelled binding protein and shown to be crucial for the planar cell polarity (PCP) pathway in Xenopus. Daam1, like other formins, directs nucleation and elongation of new actin filaments using its conserved formin-homology-2 (FH2) domain. Here we report the crystal structure of a large C-terminal fragment of human Daam1 containing the FH2 domain. The structure, determined at 2.25 A resolution using the single-wavelength anomalous diffraction (SAD) phasing method, reveals a "tethered dimer" architecture that is similar to that previously described for the FH2 domain of the yeast formin Bni1, which shares approximately 21% sequence identity with Daam1. Despite the overall similarity with the dimeric FH2 domain of Bni1 and with a truncated monomeric structure of mDia1, the Daam1 FH2 structure reveals a number of differences in secondary structure elements and in the "lasso/post" dimerization interface that may be functionally important. Most strikingly, the two halves of the crystallographic dimer pack together in a manner that occludes their actin binding surfaces. This "locked" conformation is stabilized by two novel, interacting beta-strands formed by the ends of the linkers that connect the two sides of the dimer. The Daam1 FH2 domain has weak actin assembly activity as compared with other mammalian formins, but mutations that disrupt the beta-strand lock increase activity about tenfold to a level comparable to other formins, suggesting that this occluded conformation may represent an auto-inhibited conformation of the Daam1 FH2 domain.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of the Daam1 FH2 domain. (a) The domain structure of human Daam1. (b) Ribbon diagram showing the overall structure of Daam1 FH2 domain. Sub-domains including the lasso, the knob, the coiled-coil and the post region are labeled. The invisible linker region is drawn manually with a broken line for the purpose of illustration. The molecule is colored using the visible spectrum (from blue at the N terminus to red at the C terminus). (c) Ribbon diagram of the structure of Daam1 FH2 dimer. The broken line separates the two hemidimers. One molecule is colored the same way as in (b), while the other is colored tan. (d) Sequence alignment and secondary structure of the FH2 and DAD domains. Aligned sequences are from human Daam1, murine Daam1, human Daam2, murine Daam2, murine Dia1 and yeast (Saccharomyces cerevisiae) Bni1p. Secondary structure elements are shown above the sequences, with rectangles representing helices and thin lines indicating non-helical regions. Conserved residues are colored red. Figures were prepared using the program PyMoL [Delano, W.L., The PyMol Molecular Graphics System (2002) http://www.pymol.org].

Figure 4.
Figure 4. Insights into interactions with actin via comparisons with the structure of the Bni1/actin complex. (a) and (b) The Daam1 FH2 structure is superimposed on the Bni1/actin complex (PDB ID, 1Y64) in the regions of the knob actin-binding site (a) and the lasso/post binding site (b). The actin is colored blue, Daam1 magenta and Bni1 green. Selected residues that are known to be important for actin assembly by Bni1 are shown in stick form and labeled. (c) Overall views of the Daam1 FH2 domain (magenta) superimposed on the Bni1/actin complex (1Y64). Two actin subunits (yellow and orange) and two Bni1 FH2 domains (green) from the Bni1/actin structure are shown; this configuration may represent a “strained” intermediate in FH2-mediated assembly or actin filaments.^29 The side-chains of key actin binding residues are shown in CPK form and are colored red (Ile698 and Lys847 in Daam1; Ile1431 and Lys1601 in Bni1). The superposition was carried out using the knob sub-domain only. Note that while the knob and post sites independently superimpose well on the actin complex ((a) and (b)), both cannot be simultaneously brought into register with actin due to a different relative orientation of the knob sub-domain. Bringing the knob into register (side view) leaves the actin binding residues in the lasso/post region displaced from actin by vert, similar 17 Å (best seen in the top view).

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 369, 1258-1269) copyright 2007.

Figures were selected by the author.