PDBsum entry 1e32

Atpase

PDB id: 1e32

Contents

Protein chain

438 a.a. *

Ligands

ADP

Waters ×51

* Residue conservation analysis

PDB id:

1e32

Name:

Atpase

Title:

Structure of the n-terminal domain and the d1 aaa domain of membrane fusion atpase p97

Structure:

P97. Chain: a. Fragment: n terminal domain and d1 aaa domain, residues 1-458. Engineered: yes

Source:

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

Biol. unit:

Homo-Hexamer (from PDB file)

Resolution:

2.90Å R-factor: 0.224 R-free: 0.283

Authors:

X.Zhang,A.Shaw,P.A.Bates,M.A.Gorman,H.Kondo,P.Dokurno,G.Leonard M, J.E.Sternberg,P.S.Freemont

Key ref:

X.Zhang et al. (2000). Structure of the AAA ATPase p97. Mol Cell, 6, 1473-1484. PubMed id: 11163219 DOI: 10.1016/S1097-2765(00)00143-X

Date:

05-Jun-00 Release date: 31-May-01

Protein chain

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

Seq: 806 a.a.

Struc: 438 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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/S1097-2765(00)00143-X

Mol Cell 6:1473-1484 (2000)

PubMed id: 11163219

Structure of the AAA ATPase p97.

X.Zhang, A.Shaw, P.A.Bates, R.H.Newman, B.Gowen, E.Orlova, M.A.Gorman, H.Kondo, P.Dokurno, J.Lally, G.Leonard, H.Meyer, M.van Heel, P.S.Freemont.

ABSTRACT

p97, an abundant hexameric ATPase of the AAA family, is involved in homotypic membrane fusion. It is thought to disassemble SNARE complexes formed during the process of membrane fusion. Here, we report two structures: a crystal structure of the N-terminal and D1 ATPase domains of murine p97 at 2.9 A resolution, and a cryoelectron microscopy structure of full-length rat p97 at 18 A resolution. Together, these structures show that the D1 and D2 hexamers pack in a tail-to-tail arrangement, and that the N domain is flexible. A comparison with NSF D2 (ATP complex) reveals possible conformational changes induced by ATP hydrolysis. Given the D1 and D2 packing arrangement, we propose a ratchet mechanism for p97 during its ATP hydrolysis cycle.

Selected figure(s)

Figure 1.
Figure 1. Crystal Structure of p97 N D1 Domain(A) Ribbon representation of N D1 protomer structure. The domains are colored individually, with the N-terminal double ψ barrel domain (yellow), β barrel domain (gold), the D1 α/β domain (cyan), and the C-terminal α-helical domain (blue). Also highlighted are the Walker A (P loop) motif (black), Walker B (DExx box) motif (mauve), sensor loop (red), and the proposed hinge region between the N and D1 domains (magenta). Bound ADP nucleotide is shown as balls and sticks. For clarity, only the secondary structure elements discussed in the text are labeled.(B) A close-up view of the N D1 interface (boxed region in [A]). A small rotation was applied to optimize the view of the interface.(C) The N D1 hexamer forms a wheel-like structure of vert, similar 160 Å in diameter and a central hole vert, similar 15 Å in diameter. One protomer is colored as in (A). The α/β domain fold (cyan) forms the spokes of the wheel, while the helical domain (blue) forms the outer rim. N-terminal domains (yellow) are oriented counterclockwise off the main body of the wheel. Bound ADP moieties (brown) drawn as Van der Waal spheres are located between protomers. The arrow indicates the ADP binding pocket.(D) The N D1 hexamer is rotated 90° (relative to Figure 1C) so that the amino-terminal side is on top. The thickness of N D1 is vert, similar 20–40 Å. The N domain lies in the same plane as D1 and spans a similar thickness. Note the ADP moieties (brown spheres) bound in deep pockets.(E) A close-up view of the hexamer interface (boxed in [C]). For clarity, only secondary structure elements discussed in the text are labeled. The dashed line indicates the protomer–protomer interface. The sensor residues (Asn-348, yellow; Arg-359, blue) are shown as sticks near the interface.

Figure 3.
Figure 3. Cyro-EM Reconstruction of Rat Liver Cytosol p97 at 18 Å(A) Side view of p97, perpendicular to the 6-fold molecular axis, shows a truncated barrel-like structure with side holes. The main body of the molecule shows pseudo 2-fold symmetry along an axis perpendicular to the 6-fold, although there are protruding densities at one end (top). The overall molecular dimensions are indicated. The 145 Å diameter of the EM map is less than the 160 Å observed in the N D1 crystal structure, which we attribute to the ill-defined N domain in the EM reconstruction.(B) Cut-open view of (A) reveals a cage-like structure formed from the two-ring layers corresponding to the N D1 (blue) and D2 hexamers (green).(C) Top view, down the 6-fold axis, corresponding to the N D1 hexamer (blue), reveals a large annulus, surface pockets, and disconnected densities, and is different in appearance to the D2 layer. The black arrow indicates the pocket that coincides with the nucleotide binding pocket indicated by the arrow in Figure 1C.(D) Bottom view, corresponding to the D2 hexamer (green), shows a closed annulus and several distinctive surface features.

The above figures are reprinted by permission from Cell Press: Mol Cell (2000, 6, 1473-1484) copyright 2000.

Figures were selected by an automated process.