PDBsum entry: 1f7s

Plant protein

PDB id: 1f7s

Contents

Protein chain

124 a.a. *

Ligands

LDA

Waters ×89

* Residue conservation analysis

PDB id:

1f7s

Name:

Plant protein

Title:

Crystal structure of adf1 from arabidopsis thaliana

Structure:

Actin depolymerizing factor (adf). Chain: a. Fragment: actin binding domain. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.210 R-free: 0.248

Authors:

G.D.Bowman,I.M.Nodelman,U.Lindberg,N.H.Chua,C.E.Schutt

Key ref:

G.D.Bowman et al. (2000). A comparative structural analysis of the ADF/cofilin family. Proteins, 41, 374-384. PubMed id: 11025548 DOI: 10.1002/1097-0134(20001115)41:3<374::AID-PROT90>3.0.CO;2-F

Date:

27-Jun-00 Release date: 15-Nov-00

Protein chain

Q39250  (ADF1_ARATH) -  Actin-depolymerizing factor 1

Seq: 139 a.a.

Struc: 124 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: actin filament organization (1 term)
• Biochemical function: actin binding (1 term)

DOI no: 10.1002/1097-0134(20001115)41:3<374::AID-PROT90>3.0.CO;2-F

Proteins 41:374-384 (2000)

PubMed id: 11025548

A comparative structural analysis of the ADF/cofilin family.

G.D.Bowman, I.M.Nodelman, Y.Hong, N.H.Chua, U.Lindberg, C.E.Schutt.

ABSTRACT

Actin-depolymerizing factor (ADF) and cofilin define a family of actin-binding proteins essential for the rapid turnover of filamentous actin in vivo. Here we present the 2.0 A crystal structure of Arabidopsis thaliana ADF1 (AtADF1), the first plant crystal structure from the ADF/cofilin (AC) family. Superposition of the four AC isoform structures permits an accurate sequence alignment that differs from previously reported data for the location of vertebrate-specific inserts and reveals a contiguous, vertebrate-specific surface opposite the putative actin-binding surface. Extending the structure-based sequence alignment to include 30 additional isoforms indicates three major groups: vertebrates, plants, and "other eukaryotes." Within these groups, several structurally conserved residues that are not conserved throughout the entire AC family have been identified. Residues that are highly conserved among all isoforms tend to cluster around the tryptophan at position 90 and a structurally conserved kink in alpha-helix 3. Analysis of surface character shows the presence of a hydrophobic patch and a highly conserved acidic cluster, both of which include several residues previously implicated in actin binding.

Selected figure(s)

Figure 3.
Figure 3. A molecular surface rendering of human destrin, highlighting the vertebrate specific inserts and C-terminal extension (mesh surfaces). The loop between -strands 4 and 5 (green) appears to be stabilized by these interactions, displaying a low to average r.m.s. deviation among the 20 top solutions, in contrast to the relatively high B-factors of the three crystal structures. Mutations that have been found to weaken or abolish actin binding are represented as a solid surface.

Figure 4.
Figure 4. A: Trp90 lies in the center of and interacts with a cluster of conserved residues. The tryptophan ring packs against two prolines at positions 61 and 92, a proline/aromatic typically observed at position 126, and the hydrophobic side chains of Leu60 and residue 129. A single hydrogen bond between the indole ring and the backbone carbonyl of residue 61 is conserved in all structures. These interactions constrain the positioning of the loops preceding helices 3, 4, and -strand 4 from which the conserved residues 64-66, Lys100, and the acidic residues at positions 93, 123, and 126 project. Note that the yeast cofilin leucine replaces the conventional AC arginine at position 66, losing the conserved electrostatic interaction with Asp/Glu64 but maintaining the hydrophobic character. This figure was prepared by using the program O[59] and the coordinates of yeast cofilin.[30] B: Stabilizing interactions in and around the kink in -helix 3. Bending of the -helix about residue 106 disrupts the -helical hydrogen bonding pattern between the carbonyl:amide pairs 104:108 and 105:109. The hydroxyl group of Tyr103 makes a hydrogen bond to the backbone amide of residue 34 (not shown), whereas the hydroxyl of Tyr67 hydrogen bonds to the backbone carbonyl of residue 103. Mutagenesis of either of these tyrosines to phenylalanine disrupts or weakens actin binding, emphasizing the structural importance of this region.[21][45] In the crystal structures of AtADF1 and the phosphorylated form of actophorin, two water molecules were observed at the kink, each making hydrogen bonds to otherwise unsatisfied carbonyl and amide backbone atoms. This figure was prepared by using the program O[59] and the coordinates of AtADF1.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2000, 41, 374-384) copyright 2000.

Figures were selected by an automated process.