4JJQ

Crystal structure of usp7-ntd with an e2 enzyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Ubiquitin-specific protease 7 is a regulator of ubiquitin-conjugating enzyme UbE2E1.

Sarkari, F., Wheaton, K., La Delfa, A., Mohamed, M., Shaikh, F., Khatun, R., Arrowsmith, C.H., Frappier, L., Saridakis, V., Sheng, Y.

(2013) J Biol Chem 288: 16975-16985

  • DOI: 10.1074/jbc.M113.469262
  • Primary Citation of Related Structures:  
    4JJQ

  • PubMed Abstract: 

    • Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme found in all eukaryotes that catalyzes the removal of ubiquitin from specific target proteins. Here, we report that UbE2E1, an E2 ubiquitin conjugation enzyme with a unique N-terminal extension, is a novel USP7-interacting protein ...

    Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme found in all eukaryotes that catalyzes the removal of ubiquitin from specific target proteins. Here, we report that UbE2E1, an E2 ubiquitin conjugation enzyme with a unique N-terminal extension, is a novel USP7-interacting protein. USP7 forms a complex with UbE2E1 in vitro and in vivo through the ASTS USP7 binding motif within its N-terminal extension in an identical manner with other known USP7 binding proteins. We show that USP7 attenuates UbE2E1-mediated ubiquitination, an effect that requires the N-terminal ASTS sequence of UbE2E1 as well as the catalytic activity of USP7. Additionally, USP7 is critical in maintaining the steady state levels of UbE2E1 in cells. This study reveals a new cellular mechanism that couples the opposing activities of the ubiquitination machinery and a deubiquitinating enzyme to maintain and modulate the dynamic balance of the ubiquitin-proteasome system.

    Organizational Affiliation: 

    Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 7A159Homo sapiensMutation(s): 1 
Gene Names: HAUSP, USP7, USP7/HAUSP
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens)
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Go to UniProtKB:  Q93009
PHAROS:  Q93009
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UniProt GroupQ93009
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 E1B10Homo sapiensMutation(s): 0 
Gene Names: UBE2E1, UBCH6
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P51965 (Homo sapiens)
Explore P51965 
Go to UniProtKB:  P51965
PHAROS:  P51965
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51965
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.901α = 90
b = 69.901β = 90
c = 45.733γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-03-08 
  • Released Date: 2013-05-01 
    • Deposition Author(s): Saridakis, V.

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references