PDBsum entry 3eks

Contractile protein

PDB id: 3eks

Contents

Protein chain

374 a.a.

Ligands

ATP

CY9

Metals

_CA ×2

Waters ×271

PDB id:

3eks

Name:

Contractile protein

Title:

Crystal structure of monomeric actin bound to cytochalasin d

Structure:

Actin-5c. Chain: a. Engineered: yes. Mutation: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: act5c, cg4027. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Resolution:

1.80Å R-factor: 0.237 R-free: 0.284

Authors:

U.B.Nair,P.B.Joel,Q.Wan,S.Lowey,M.A.Rould,K.M.Trybus

Key ref:

U.B.Nair et al. (2008). Crystal structures of monomeric actin bound to cytochalasin D. J Mol Biol, 384, 848-864. PubMed id: 18938176 DOI: 10.1016/j.jmb.2008.09.082

Date:

19-Sep-08 Release date: 07-Oct-08

Protein chain

P10987  (ACT1_DROME) -  Actin-5C from Drosophila melanogaster

Seq: 376 a.a.

Struc: 374 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.6.4.- - ?????

DOI no: 10.1016/j.jmb.2008.09.082

J Mol Biol 384:848-864 (2008)

PubMed id: 18938176

Crystal structures of monomeric actin bound to cytochalasin D.

U.B.Nair, P.B.Joel, Q.Wan, S.Lowey, M.A.Rould, K.M.Trybus.

ABSTRACT

The fungal toxin cytochalasin D (CD) interferes with the normal dynamics of the actin cytoskeleton by binding to the barbed end of actin filaments. Despite its widespread use as a tool for studying actin-mediated processes, the exact location and nature of its binding to actin have not been previously determined. Here we describe two crystal structures of an expressed monomeric actin in complex with CD: one obtained by soaking preformed actin crystals with CD, and the other obtained by cocrystallization. The binding site for CD, in the hydrophobic cleft between actin subdomains 1 and 3, is the same in the two structures. Polar and hydrophobic contacts play equally important roles in CD binding, and six hydrogen bonds stabilize the actin-CD complex. Many unrelated actin-binding proteins and marine toxins target this cleft and the hydrophobic pocket at the front end of the cleft (viewing actin with subdomain 2 in the upper right corner). CD differs in that it binds to the back half of the cleft. The ability of CD to induce actin dimer formation and actin-catalyzed ATP hydrolysis may be related to its unique binding site and the necessity to fit its bulky macrocycle into this cleft. Contacts with residues lining this cleft appear to be crucial to capping and/or severing. The cocrystallized actin-CD structure also revealed changes in actin conformation. An approximately 6 degrees rotation of the smaller actin domain (subdomains 1 and 2) with respect to the larger domain (subdomains 3 and 4) results in small changes in crystal packing that allow the D-loop to adopt an extended loop structure instead of being disordered, as it is in most crystal structures of actin. We speculate that these changes represent a potential conformation that the actin monomer can adopt on the pathway to polymerization or in the filament.

Selected figure(s)

Figure 3.
Fig. 3. Hydrogen-bonding interactions between actin and CD. (a) There are six hydrogen bonds between the protein and the ligand. Five of these are mediated by the isoindolone core and substituents on its rings, suggesting a key role for this moiety in stabilizing the actin–CD interaction. One hydrogen bond involves the macrocyclic ring. All but one hydrogen bond (Tyr143) involve the actin main chain. This figure was made using the structure of the soaked CD-bound complex; nearly identical interactions are observed in the cocrystal structure. (b) Schematic showing the molecular structure of CD and hydrogen-bonding interactions with amino acid residue chemical groups. CD possesses an isoindolone core (pink and yellow) carrying numerous substitutions, including a benzyl group (green) at C3; this core is fused to a large 11-membered macrocycle (blue). Five of the six hydrogen bonds involve the amide group of the lactam ring (pink) and the –OH at C7, suggesting a crucial role for these functional groups and their overall arrangement in actin–CD binding. Hydrogen-bonding distances are provided in angstroms, with the first number corresponding to the distance observed in the ligand-soaked complex structure and with the second number corresponding to the distance in the cocrystallized complex.

Figure 9.
Fig. 9. A comparison of the barbed-end-targeting compounds CD, bistramide A, and jaspisamide A as they would bind to the hydrophobic cleft. (a) ‘Back’ view of the actin molecule (spaghetti representation in blue). CD (orange) targets the back half of the cleft between subdomains 1 and 3. (b) ‘Front’ view of the actin molecule. The macrocyclic ring of jaspisamide A (green) binds to a hydrophobic patch on the front face of actin bordering the cleft. (c) View of the hydrophobic cleft. The binding regions of jaspisamide A and CD on actin barely overlap. Bistramide A (cyan) spans the length of the cleft. Apart from the present structure, this figure is based on the crystal structures of jaspisamide A (PDB ID 1QZ6) and bistramide A (PDB ID 2FXU) complexed with an actin monomer.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 384, 848-864) copyright 2008.

Figures were selected by an automated process.