4TXP

Crystal structure of LIP5 N-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Mechanism of Regulating the ATPase VPS4 by Its Cofactor LIP5 and the Endosomal Sorting Complex Required for Transport (ESCRT)-III Protein CHMP5.

Vild, C.J.Li, Y.Guo, E.Z.Liu, Y.Xu, Z.

(2015) J.Biol.Chem. 290: 7291-7303

  • DOI: 10.1074/jbc.M114.616730
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Disassembly of the endosomal sorting complex required for transport (ESCRT) machinery from biological membranes is a critical final step in cellular processes that require the ESCRT function. This reaction is catalyzed by VPS4, an AAA-ATPase whose ac ...

    Disassembly of the endosomal sorting complex required for transport (ESCRT) machinery from biological membranes is a critical final step in cellular processes that require the ESCRT function. This reaction is catalyzed by VPS4, an AAA-ATPase whose activity is tightly regulated by a host of proteins, including LIP5 and the ESCRT-III proteins. Here, we present structural and functional analyses of molecular interactions between human VPS4, LIP5, and the ESCRT-III proteins. The N-terminal domain of LIP5 (LIP5NTD) is required for LIP5-mediated stimulation of VPS4, and the ESCRT-III protein CHMP5 strongly inhibits the stimulation. Both of these observations are distinct from what was previously described for homologous yeast proteins. The crystal structure of LIP5NTD in complex with the MIT (microtubule-interacting and transport)-interacting motifs of CHMP5 and a second ESCRT-III protein, CHMP1B, was determined at 1 Å resolution. It reveals an ESCRT-III binding induced moderate conformational change in LIP5NTD, which results from insertion of a conserved CHMP5 tyrosine residue (Tyr(182)) at the core of LIP5NTD structure. Mutation of Tyr(182) partially relieves the inhibition displayed by CHMP5. Together, these results suggest a novel mechanism of VPS4 regulation in metazoans, where CHMP5 functions as a negative allosteric switch to control LIP5-mediated stimulation of VPS4.


    Organizational Affiliation

    From the Life Sciences Institute and Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, Michigan 48109.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein VTA1 homolog
A, B, C
163Homo sapiensMutation(s): 0 
Gene Names: VTA1 (C6orf55)
Find proteins for Q9NP79 (Homo sapiens)
Go to Gene View: VTA1
Go to UniProtKB:  Q9NP79
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.248 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.381α = 90.00
b = 76.381β = 90.00
c = 355.938γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-07-04 
  • Released Date: 2015-02-11 
  • Deposition Author(s): Vild, C.J., Xu, Z.

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesF027259

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-02-18
    Type: Database references
  • Version 1.2: 2015-03-25
    Type: Database references