3H8K

Crystal structure of Ube2g2 complxed with the G2BR domain of gp78 at 1.8-A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78.

Das, R., Mariano, J., Tsai, Y.C., Kalathur, R.C., Kostova, Z., Li, J., Tarasov, S.G., McFeeters, R.L., Altieri, A.S., Ji, X., Byrd, R.A., Weissman, A.M.

(2009) Mol Cell 34: 674-685

  • DOI: 10.1016/j.molcel.2009.05.010
  • Primary Citation of Related Structures:  
    3H8K

  • PubMed Abstract: 

    • The activity of RING finger ubiquitin ligases (E3) is dependent on their ability to facilitate transfer of ubiquitin from ubiquitin-conjugating enzymes (E2) to substrates. The G2BR domain within the E3 gp78 binds selectively and with high affinity to the E2 Ube2g2 ...

    The activity of RING finger ubiquitin ligases (E3) is dependent on their ability to facilitate transfer of ubiquitin from ubiquitin-conjugating enzymes (E2) to substrates. The G2BR domain within the E3 gp78 binds selectively and with high affinity to the E2 Ube2g2. Through structural and functional analyses, we determine that this occurs on a region of Ube2g2 distinct from binding sites for ubiquitin-activating enzyme (E1) and RING fingers. Binding to the G2BR results in conformational changes in Ube2g2 that affect ubiquitin loading. The Ube2g2:G2BR interaction also causes an approximately 50-fold increase in affinity between the E2 and RING finger. This results in markedly increased ubiquitylation by Ube2g2 and the gp78 RING finger. The significance of this G2BR effect is underscored by enhanced ubiquitylation observed when Ube2g2 is paired with other RING finger E3s. These findings uncover a mechanism whereby allosteric effects on an E2 enhance E2-RING finger interactions and, consequently, ubiquitylation.

    Organizational Affiliation: 

    Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 G2A164Homo sapiensMutation(s): 0 
Gene Names: UBE2G2, UBC7
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P60604 (Homo sapiens)
Explore P60604 
Go to UniProtKB:  P60604
PHAROS:  P60604
GTEx:  ENSG00000184787 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60604
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Autocrine motility factor receptor, isoform 2B28Homo sapiensMutation(s): 1 
Gene Names: AMFR, RNF45
EC: 6.3.2 (PDB Primary Data), 2.3.2.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV5 (Homo sapiens)
Explore Q9UKV5 
Go to UniProtKB:  Q9UKV5
PHAROS:  Q9UKV5
GTEx:  ENSG00000159461 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKV5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.92α = 90
b = 60.15β = 90
c = 61.64γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-25
    Changes: Structure summary
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2021-10-13
    Changes: Database references