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PDBsum entry 3cf1
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Transport protein
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PDB id
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3cf1
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References listed in PDB file
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Key reference
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Title
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Improved structures of full-Length p97, An aaa atpase: implications for mechanisms of nucleotide-Dependent conformational change.
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Authors
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J.M.Davies,
A.T.Brunger,
W.I.Weis.
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Ref.
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Structure, 2008,
16,
715-726.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2008,
16,
715-726)
copyright 2008.
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Secondary reference #1
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Title
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Complete structure of p97/valosin-Containing protein reveals communication between nucleotide domains.
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Authors
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B.Delabarre,
A.T.Brunger.
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Ref.
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Nat Struct Biol, 2003,
10,
856-863.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. p97/VCP protomer and pore schematic. (a,b) Two
orthogonal views of molecular surfaces of the p97/VCP hexamer,
with the subdomains of alternate protomers colored red or as in
Figure 1a. The Zn2+ and the putative His317 ligands are shown in
the central pore. Molecular dimensions are based on C  -C
distances,
with radii shown for the top view and diameters given for the
side view at the narrowest region in the middle and as well as
between opposing helices 12'.
(c) Schematic view of the pore with dimensions as indicated. The
protrusions shown within the D2 region of the pore indicate the
presence of a disordered section of the protein (residues 586
-597) that may point into the central pore. (d)
Protomer-protomer interactions. The 'A-facing' elements are
colored and labeled in red, the 'B-facing' elements are colored
according to subdomain. The view has been selected to highlight
the 'wrap-around' interaction involving helix 5/
5'.
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Figure 3.
Figure 3. Protomer views and schematic. (a,b) Orthogonal
views of the p97/VCP protomer with subdomains colored as in
Figure 1a. The disordered connection between 12'
and 13'
is indicated as a dashed green line. Selected helices are
labeled. (c) Schematic models of the p97/VCP protomer in the ADP
-AlF[x] and ADP states colored according to subdomain. The model
of the ADP state is derived from the comparison of the p97/VCP
crystal structure with the cryo-EM map of the ADP state^27; in
the ADP state the N-terminal domain is highly mobile and the
protrusion following helix 12'
of the D2 helical domain becomes ordered.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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Secondary reference #2
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Title
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Nucleotide dependent motion and mechanism of action of p97/vcp.
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Authors
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B.Delabarre,
A.T.Brunger.
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Ref.
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J Mol Biol, 2005,
347,
437-452.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Conformational variability; deviation from 6-fold
symmetry. Conformational differences between the three
independent protomers in the asymmetric unit are shown for the
(a) ATP/= and (b) ADP crystal structures. The same view was used
for both panels. Pseudo-ellipsoids were generated as described
in Materials and Methods. The color scale (blue to red)
indicates the magnitude of the deviation from 6-fold symmetry
(0.5-5.0 Å). Ellipsoids that are pointing in a similar
direction indicate groups of residues that are moving as rigid
bodies.
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Figure 3.
Figure 3. Nucleotide-dependent domain motions. Motions for
the (a) D2a/b, (b) D1a, and (c) N domains are displayed between
pairs of the ATP (red), ATP/= (blue), ADP (green), and APO
(yellow) state structures. Adjacent domains for the principle
domain shown in (a), (b) or (c) are shown, in gray, for
reference. The superposition of the APO and ATP structures
showed minimal differences and is therefore not depicted here.
The orientations of the views are the same for each transition.
The views were chosen such that the axis of rotation for a
particular domain motion is perpendicular to the plane of the
page, with the exception of the ATP/= to ADP (blue to green)
transition, for which the view has been oriented such that the
rotation axis is  vert,
similar 45° off the perpendicular toward the right-hand side
of the page. Arrows indicate the direction of the motions.
Helices are numbered according to the p97/VCP numbering scheme
(WB, Walker B helix; L, linker helix).30 (d) A simplified
diagram summarizing the domain motions from the ATP to the ATP/=
state. The N-D1 linker is shown in solid color, the D2a domain
and D1D2 linker are shown with broken lines. The D2a domain and
the D1D2 linker become ordered in the transition from the ATP to
the ATP/= state. All motions are described relative to the
invariant D1a/b domain.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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