PDBsum entry 2zam

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protein links
Protein transport PDB id
Protein chain
308 a.a. *
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: Crystal structure of mouse skd1/vps4b apo-form
Structure: Vacuolar protein sorting-associating protein 4b. Chain: a. Synonym: protein skd1, suppressor of k+, transport growth d engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: skd1. Expressed in: escherichia coli. Expression_system_taxid: 562.
3.50Å     R-factor:   0.250     R-free:   0.304
Authors: M.Inoue,M.Kawasaki,H.Kamikubo,M.Kataoka,R.Kato,T.Yoshimori, S.Wakatsuki
Key ref: M.Inoue et al. (2008). Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B. Traffic, 9, 2180-2189. PubMed id: 18796009 DOI: 10.1111/j.1600-0854.2008.00831.x
08-Oct-07     Release date:   07-Oct-08    
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Protein chain
Pfam   ArchSchema ?
P46467  (VPS4B_MOUSE) -  Vacuolar protein sorting-associated protein 4B
444 a.a.
308 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Vesicle-fusing ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
+ H(2)O
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   12 terms 
  Biological process     cell cycle   14 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1111/j.1600-0854.2008.00831.x Traffic 9:2180-2189 (2008)
PubMed id: 18796009  
Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B.
M.Inoue, H.Kamikubo, M.Kataoka, R.Kato, T.Yoshimori, S.Wakatsuki, M.Kawasaki.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19887446 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.
  J Biol Chem, 285, 761-772.  
20696398 D.Yang, and J.H.Hurley (2010).
Structural role of the Vps4-Vta1 interface in ESCRT-III recycling.
  Structure, 18, 976-984.
PDB code: 3mhv
20588296 J.H.Hurley, and P.I.Hanson (2010).
Membrane budding and scission by the ESCRT machinery: it's all in the neck.
  Nat Rev Mol Cell Biol, 11, 556-566.  
  20653365 J.H.Hurley (2010).
The ESCRT complexes.
  Crit Rev Biochem Mol Biol, 45, 463-487.  
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