PDBsum entry 3cf1

Transport protein

PDB id: 3cf1

Contents

Protein chains

719 a.a. *

Ligands

ADP ×4

ADP-AF3 ×2

AF3

* Residue conservation analysis

PDB id:

3cf1

Name:

Transport protein

Title:

Structure of p97/vcp in complex with adp/adp.Alfx

Structure:

Transitional endoplasmic reticulum atpase. Chain: a, b, c. Synonym: ter atpase. 15s mg(2+)- atpase p97 subunit. Valosin- containing protein. Vcp. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: vcp. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

4.40Å R-factor: 0.229 R-free: 0.286

Authors:

J.M.Davies,B.Delabarre,A.T.Brunger,W.I.Weis

Key ref:

J.M.Davies et al. (2008). Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change. Structure, 16, 715-726. PubMed id: 18462676 DOI: 10.1016/j.str.2008.02.010

Date:

01-Mar-08 Release date: 22-Apr-08

Supersedes:

1yq0

Protein chains

Q01853  (TERA_MOUSE) -  Transitional endoplasmic reticulum ATPase from Mus musculus

Seq: 806 a.a.

Struc: 719 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.4.6 - vesicle-fusing ATPase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2008.02.010

Structure 16:715-726 (2008)

PubMed id: 18462676

Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.

J.M.Davies, A.T.Brunger, W.I.Weis.

ABSTRACT

The ATPases associated with various cellular activities (AAA) protein p97 has been implicated in a variety of cellular processes, including endoplasmic reticulum-associated degradation and homotypic membrane fusion. p97 belongs to a subgroup of AAA proteins that contains two nucleotide binding domains, D1 and D2. We determined the crystal structure of D2 at 3.0 A resolution. This model enabled rerefinement of full-length p97 in different nucleotide states against previously reported low-resolution diffraction data to significantly improved R values and Ramachandran statistics. Although the overall fold remained similar, there are significant improvements, especially around the D2 nucleotide binding site. The rerefinement illustrates the importance of knowledge of high-resolution structures of fragments covering most of the whole molecule. The structures suggest that nucleotide hydrolysis is transformed into larger conformational changes by pushing of one D2 domain by its neighbor in the hexamer, and transmission of nucleotide-state information through the D1-D2 linker to displace the N-terminal, effector binding domain.

Selected figure(s)

Figure 1.
Figure 1. Structure of p97 D2 at 3.0 Å Resolution
(A) The heptameric state of p97 D2 is shown as crystallized. Protomers are uniquely colored.
(B) Schematic of transformations mapping D2 protomer from hepatmer to hexamer. The transformation consists of a 6 Å axial shift accompanied by an 11.4° counter-clockwise rotation about an axis parallel to the molecular 6-fold axis, resulting in relative preservation of the interdomain interface.
(C) Representative electron density of 14-fold averaged D2 domain.
(D) The conformation of the nucleotide binding site of D2 fragment is shown with characteristic AAA motifs highlighted as follows: Walker A (slate); Walker B (red); sensor 1 (purple); sensor 2 (purple); arginine finger (white); N-linker (pink).
(E) The D2 binding sites of the full-length models are superposed for the ATP (magenta), ADP-AlF[x] (blue), and ADP (green) state with ADP shown bound in the pocket.

Figure 6.
Figure 6. Comparison of Nucleotide Binding Sites in D1 and D2
(A) The nucleotide binding pockets for the D1 (dark green) and D2 (light green) domains are superposed. Note that a helix of the C-terminal region of D2 impinges on the sensor I region of that domain to bring sensor I into proximity of the bound ATP.
(B and C) The sensor I regions of D1 (B) and D2 (C) are shown in the ADP state. Distances of the arginine finger to the ADP β-phosphate and to the sensor I asparagine are indicated.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 715-726) copyright 2008.

Figures were selected by an automated process.