PDBsum entry 2znd

Apoptosis

PDB id: 2znd

Contents

Protein chain

167 a.a. *

Ligands

MRD ×5

PO4 ×2

Metals

_NA ×3

Waters ×131

* Residue conservation analysis

PDB id:

2znd

Name:

Apoptosis

Title:

Crystal structure of ca2+-free form of des3-20alg-2

Structure:

Programmed cell death protein 6. Chain: a. Fragment: residues 20-191. Synonym: apoptosis-linked gene 2 protein, probable calcium-binding protein alg-2. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pdcd6, alg2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.195 R-free: 0.222

Authors:

H.Suzuki,M.Kawasaki,T.Inuzuka,T.Kakiuchi,H.Shibata,S.Wakatsuki,M.Maki

Key ref:

H.Suzuki et al. (2008). Structural basis for Ca2+ -dependent formation of ALG-2/Alix peptide complex: Ca2+/EF3-driven arginine switch mechanism. Structure, 16, 1562-1573. PubMed id: 18940611 DOI: 10.1016/j.str.2008.07.012

Date:

22-Apr-08 Release date: 09-Sep-08

Protein chain

O75340  (PDCD6_HUMAN) -  Programmed cell death protein 6 from Homo sapiens

Seq: 191 a.a.

Struc: 167 a.a.

DOI no: 10.1016/j.str.2008.07.012

Structure 16:1562-1573 (2008)

PubMed id: 18940611

Structural basis for Ca2+ -dependent formation of ALG-2/Alix peptide complex: Ca2+/EF3-driven arginine switch mechanism.

H.Suzuki, M.Kawasaki, T.Inuzuka, M.Okumura, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki.

ABSTRACT

ALG-2 belongs to the penta-EF-hand (PEF) protein family and interacts with various intracellular proteins, such as Alix and TSG101, that are involved in endosomal sorting and HIV budding. Through X-ray crystallography, we solved the structures of Ca(2+)-free and -bound forms of N-terminally truncated human ALG-2 (des3-20ALG-2), Zn(2+)-bound form of full-length ALG-2, and the structure of the complex between des3-23ALG-2 and the peptide corresponding to Alix799-814 in Zn(2+)-bound form. Binding of Ca(2+) to EF3 enables the side chain of Arg125, present in the loop connecting EF3 and EF4, to move enough to make a primary hydrophobic pocket accessible to the critical PPYP motif, which partially overlaps with the GPP motif for the binding of Cep55 (centrosome protein 55 kDa). Based on these results, together with the results of in vitro binding assay with mutant ALG-2 and Alix proteins, we propose a Ca(2+)/EF3-driven arginine switch mechanism for ALG-2 binding to Alix.

Selected figure(s)

Figure 1.
Figure 1. Schematic Representations of ALG-2 and Alix
Human ALG-2 has a Gly/Pro-rich N-terminal region followed by the PEF domain containing five EF-hands (EF1–EF5) with eight α helices (α1–α8). The first and second helices in each EF hand are alternatively named, for instance, helix E1 and helix F1, respectively. An alternatively spliced isoform (lacking Gly121-Phe122) is designated ALG-2^ΔGF122 in this article. Recombinant proteins of full-length ALG-2 and two types of N-terminal deletion mutants (des3-20ALG-2 and des3-23ALG-2) were crystallized. Alix has three distinct domains, named Bro1, V, and Pro-rich. A 16-mer synthetic oligopeptide of the ABS in Alix (Alix ABS peptide) was used for cocrystallization.

Figure 2.
Figure 2. Comparison of Ca^2+-Free and Ca^2+-Bound Forms and Zn^2+-Bound Form of ALG-2
(A–C) Structures of EF1 (A), EF3 (B), and EF5 (C) of Ca^2+-free form (cyan) and Ca^2+-bound form (magenta) of des3-20ALG-2 and Zn^2+-bound form (green) of full-length ALG-2 are superimposed and shown in ribbon representation in side views and top views by aligning helices of (A) α1 (E1), (B) α4 (E3), and (C) α7 (E5), respectively, with the secondary structure matching program in COOT. Calcium atoms and zinc atoms are shown as yellow spheres and gray spheres, respectively.
(D) Overall structures of dimeric ALG-2 molecules in the three forms are aligned at α7 of molecule A and shown in wire presentation. The N-terminal Gly/Pro-rich region is invisible.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 1562-1573) copyright 2008.

Figures were selected by an automated process.