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PDBsum entry 2zan
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Protein transport
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PDB id
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2zan
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Protein transport
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Title:
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Crystal structure of mouse skd1/vps4b atp-form
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Structure:
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Vacuolar protein sorting-associating protein 4b. Chain: a. Synonym: protein skd1, suppressor of k+, transport growth defect 1. Engineered: yes
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Source:
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Mus musculus. Mouse. Organism_taxid: 10090. Gene: skd1. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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3.00Å
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R-factor:
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0.224
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R-free:
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0.262
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Authors:
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M.Inoue,M.Kawasaki,H.Kamikubo,M.Kataoka,R.Kato,T.Yoshimori, S.Wakatsuki
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Key ref:
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M.Inoue
et al.
(2008).
Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B.
Traffic,
9,
2180-2189.
PubMed id:
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Date:
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08-Oct-07
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Release date:
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07-Oct-08
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PROCHECK
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Headers
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References
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P46467
(VPS4B_MOUSE) -
Vacuolar protein sorting-associated protein 4B from Mus musculus
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Seq:
Struc:
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444 a.a.
312 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.3.6.4.6
- vesicle-fusing ATPase.
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Reaction:
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ATP + H2O = ADP + phosphate + H+
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ATP
Bound ligand (Het Group name = )
corresponds exactly
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+
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H2O
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=
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ADP
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+
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phosphate
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Traffic
9:2180-2189
(2008)
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PubMed id:
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Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B.
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M.Inoue,
H.Kamikubo,
M.Kataoka,
R.Kato,
T.Yoshimori,
S.Wakatsuki,
M.Kawasaki.
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ABSTRACT
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SKD1/VPS4B belongs to the adenosine triphosphatases associated with diverse
cellular activities (AAA) family and regulates multivesicular body (MVB)
biogenesis. SKD1 changes its oligomeric state during the ATPase cycle and
subsequently releases endosomal sorting complex required for transport (ESCRT)
complexes from endosomes during the formation of MVBs. In this study, we
describe domain motions in monomeric SKD1 on ATP and ADP binding. Nucleotides
bind between the alpha/beta and the alpha-helical domains of SKD1, inducing a
approximately 20 degrees domain rotation and closure of the binding site, which
are similar to the changes observed in the AAA+ ATPase, HslU. Gel filtration and
small-angle X-ray scattering experiments showed that the ATP-bound form of SKD1
oligomerizes in solution, whereas ADP-bound and apo forms of SKD1 exist as
monomers, even though the conformations of the ADP- and ATP-bound forms are
nearly identical. Nucleotide-bound SKD1 structures are compatible with a
hexameric ring arrangement reminiscent of the AAA ATPase p97 D1 ring. In the
hexameric ring model of SKD1, Arg290 from a neighboring molecule binds to the
gamma-phosphate of ATP, which promotes oligomerization of the ATP-bound form.
ATP hydrolysis would eliminate this interaction and subsequent nucleotide
release causes the domains to rotate, which together lead to the disassembly of
the SKD1 oligomer.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.Zhao,
E.A.Matveeva,
Q.Ren,
and
S.W.Whiteheart
(2010).
Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.
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J Biol Chem,
285,
761-772.
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D.Yang,
and
J.H.Hurley
(2010).
Structural role of the Vps4-Vta1 interface in ESCRT-III recycling.
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Structure,
18,
976-984.
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PDB code:
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J.H.Hurley,
and
P.I.Hanson
(2010).
Membrane budding and scission by the ESCRT machinery: it's all in the neck.
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Nat Rev Mol Cell Biol,
11,
556-566.
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J.H.Hurley
(2010).
The ESCRT complexes.
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Crit Rev Biochem Mol Biol,
45,
463-487.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
