PDBsum entry 1xwi

Protein transport

PDB id: 1xwi

Contents

Protein chain

322 a.a. *

Ligands

SO4 ×2

Waters ×9

* Residue conservation analysis

PDB id:

1xwi

Name:

Protein transport

Title:

Crystal structure of vps4b

Structure:

Skd1 protein. Chain: a. Fragment: residues 123-444. Synonym: vacuolar sorting protein 4b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: vps4b, skd1, vps42. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.199 R-free: 0.260

Authors:

A.Scott,W.I.Sundquist,C.P.Hill

Key ref:

A.Scott et al. (2005). Structural and mechanistic studies of VPS4 proteins. EMBO J, 24, 3658-3669. PubMed id: 16193069 DOI: 10.1038/sj.emboj.7600818

Date:

01-Nov-04 Release date: 11-Oct-05

Protein chain

O75351  (VPS4B_HUMAN) -  Vacuolar protein sorting-associated protein 4B from Homo sapiens

Seq: 444 a.a.

Struc: 322 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.4.6 - vesicle-fusing ATPase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/sj.emboj.7600818

EMBO J 24:3658-3669 (2005)

PubMed id: 16193069

Structural and mechanistic studies of VPS4 proteins.

A.Scott, H.Y.Chung, M.Gonciarz-Swiatek, G.C.Hill, F.G.Whitby, J.Gaspar, J.M.Holton, R.Viswanathan, S.Ghaffarian, C.P.Hill, W.I.Sundquist.

ABSTRACT

VPS4 ATPases function in multivesicular body formation and in HIV-1 budding. Here, we report the crystal structure of monomeric apo human VPS4B/SKD1 (hVPS4B), which is composed of five distinct elements: a poorly ordered N-terminal MIT domain that binds ESCRT-III substrates, large (mixed alpha/beta) and small (alpha) AAA ATPase domains that closely resemble analogous domains in the p97 D1 ATPase cassette, a three-stranded antiparallel beta domain inserted within the small ATPase domain, and a novel C-terminal helix. Apo hVPS4B and yeast Vps4p (yVps4p) proteins dimerized in solution, and assembled into larger complexes (10-12 subunits) upon ATP binding. Human and yeast adaptor proteins (LIP5 and yVta1p, respectively) bound the beta domains of the fully assembled hVPS4B and yVps4p proteins. We therefore propose that Vps4 proteins cycle between soluble, inactive low molecular weight complexes and active, membrane-associated double-ring structures that bind ATP and coassemble with LIP5/Vta1. Finally, HIV-1 budding was inhibited by mutations in a loop that projects into the center of the modeled hVPS4B rings, suggesting that hVPS4B may release the assembled ESCRT machinery by pulling ESCRT-III substrates up into the central pore.

Selected figure(s)

Figure 1.
Figure 1 Structure of hVPS4B. (A) Domain map and numbering scheme for hVPS4B. The domain color coding scheme shown here is also used in Figures 2A, B, and 6. (B) Ribbon diagram (stereoview) of the hVPS4B[123-444] structure. Note that the 2/ 3 and 3/ 4 loops were not defined by experimental density (dashed lines).

Figure 6.
Figure 6 Model for the functional cycle of VPS4 proteins. Left: At steady state, hVPS4B is primarily a monomeric cytoplasmic protein (Fujita et al, 2004), and exhibits a monomer-dimer equilibrium in the absence of bound nucleotide (Babst et al, 1998; Supplementary Figure S3). LIP5/Vta1p is an oligomer of uncertain stoichiometry. Middle: Vps4 proteins are recruited to sites of vesicle formation at the endosomal membrane by interactions between the N-terminal MIT domain and the C-proximal domains of assembled ESCRT-III lattice/cage (Babst et al, 2002; Lin et al, 2005; Scott et al, 2005). The assembled Vps4 proteins can also bind ATP and LIP5/Vta1p oligomers via domain interactions to form an enzymatically active complex. Note that a head-to-tail orientation of the two Vps4 rings (not shown) is equally consistent with our data. Right: We propose that bound ESCRT-III subunits are freed from the assembled lattice/cage and released into the cytoplasm as they are pulled up into the narrow central chamber of the hVPS4B ring.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2005, 24, 3658-3669) copyright 2005.

Figures were selected by an automated process.