2ZAN

Crystal structure of mouse SKD1/VPS4B ATP-form

Summary for 2ZAN

• Entry DOI: 10.2210/pdb2zan/pdb
• Related: 1XWI 2ZAM 2ZAO
• Descriptor: Vacuolar protein sorting-associating protein 4B, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: skd1, vps4b, aaa atpase, atp-binding, membrane, nucleotide-binding, phosphorylation, protein transport, transport
• Biological source: Mus musculus (Mouse)
• Cellular location: Prevacuolar compartment membrane; Peripheral membrane protein: P46467
• Total number of polymer chains: 1
• Total formula weight: 50019.67

Authors

Inoue, M.,Kawasaki, M.,Kamikubo, H.,Kataoka, M.,Kato, R.,Yoshimori, T.,Wakatsuki, S. (deposition date: 2007-10-08, release date: 2008-10-07, Last modification date: 2023-11-01)

Primary citation

Inoue, M.,Kamikubo, H.,Kataoka, M.,Kato, R.,Yoshimori, T.,Wakatsuki, S.,Kawasaki, M.
Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B
Traffic, 9:2180-2189, 2008

PubMed Abstract: 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.

PubMed: 18796009
DOI: 10.1111/j.1600-0854.2008.00831.x

Experimental method

X-RAY DIFFRACTION (3 Å)