4KDL

Crystal structure of p97/VCP N in complex with OTU1 UBXL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Ovarian Tumor Domain-containing Protein 1 (OTU1) Binding to p97/Valosin-containing Protein (VCP).

Kim, S.J.Cho, J.Song, E.J.Kim, S.J.Kim, H.M.Lee, K.E.Suh, S.W.Kim, E.E.

(2014) J Biol Chem 289: 12264-12274

  • DOI: 10.1074/jbc.M113.523936
  • Primary Citation of Related Structures:  
    4KDI, 4KDL

  • PubMed Abstract: 
  • Valosin-containing protein (VCP), also known as p97, is an AAA(+) ATPase that plays an essential role in a broad array of cellular processes including the endoplasmic reticulum-associated degradation (ERAD) pathway. Recently, ERAD-specific deubiquitinating enzymes have been reported to be physically associated with VCP, although the exact mechanism is not yet clear ...

    Valosin-containing protein (VCP), also known as p97, is an AAA(+) ATPase that plays an essential role in a broad array of cellular processes including the endoplasmic reticulum-associated degradation (ERAD) pathway. Recently, ERAD-specific deubiquitinating enzymes have been reported to be physically associated with VCP, although the exact mechanism is not yet clear. Among these enzymes is ovarian tumor domain-containing protein 1 (OTU1). Here, we report the structural basis for interaction between VCP and OTU1. The crystal structure of the ubiquitin regulatory X-like (UBXL) domain of OTU1 (UBXLOTU1) complexed to the N-terminal domain of VCP (NVCP) at 1.8-Å resolution reveals that UBXLOTU1 adopts a ubiquitin-like fold and binds at the interface of two subdomains of NVCP using the (39)GYPP(42) loop of UBXLOTU1 with the two prolines in cis- and trans-configurations, respectively. A mutagenesis study shows that this loop is not only critical for the interaction with VCP but also for its role in the ERAD pathway. Negative staining EM shows that one molecule of OTU1 binds to one VCP hexamer, and isothermal titration calorimetry suggests that the two proteins bind with a KD of 0.71 μM. Analytical size exclusion chromatography and isothermal titration calorimetry demonstrates that OTU1 can bind VCP in both the presence and absence of a heterodimer formed by ubiquitin fusion degradation protein 1 and nuclear localization protein 4.


    Organizational Affiliation

    From the Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPaseA193Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
NIH Common Fund Data Resources
PHAROS  P55072
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin thioesterase OTU1B90Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OTU1YFL044C
EC: 3.4.19.12
Find proteins for P43558 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43558 
Go to UniProtKB:  P43558
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.604α = 90
b = 60.803β = 90
c = 111.915γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-04-25 
  • Released Date: 2014-03-19 
  • Deposition Author(s): Kim, S.J., Kim, E.E.

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references