Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.63 kDa 
• Atom Count: 1031 
• Residue Count: 122 
• Unique protein chains: 1

2AWF

Structure of human Ubiquitin-conjugating enzyme E2 G1

• DOI: 10.2210/pdb2AWF/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-01 Released: 2005-09-20 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Finerty, P., Mackenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.263 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.

Sheng, Y., Hong, J.H., Doherty, R., Srikumar, T., Shloush, J., Avvakumov, G.V., Walker, J.R., Xue, S., Neculai, D., Wan, J.W., Kim, S.K., Arrowsmith, C.H., Raught, B., Dhe-Paganon, S.

(2012) Mol Cell Proteomics 11: 329-341

• PubMed: 22496338 
• DOI: 10.1074/mcp.O111.013706
• Primary Citation of Related Structures:  
  2QGX, 2OB4, 1ZUO, 2A4D, 2A7L, 3BZH, 3CEG, 2F4W, 2AWF, 1Y6L


• PubMed Abstract: 
  

Here we describe a systematic structure-function analysis of the human ubiquitin (Ub) E2 conjugating proteins, consisting of the determination of 15 new high-resolution three-dimensional structures of E2 catalytic domains, and autoubiquitylation assays for 26 Ub-loading E2s screened against a panel of nine different HECT (homologous to E6-AP carboxyl terminus) E3 ligase domains. Integration of our structural and biochemical data revealed several E2 surface properties associated with Ub chain building activity; (1) net positive or neutral E2 charge, (2) an "acidic trough" located near the catalytic Cys, surrounded by an extensive basic region, and (3) similarity to the previously described HECT binding signature in UBE2L3 (UbcH7). Mass spectrometry was used to characterize the autoubiquitylation products of a number of functional E2-HECT pairs, and demonstrated that HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. Our data set represents the first comprehensive analysis of E2-HECT E3 interactions, and thus provides a framework for better understanding the molecular mechanisms of ubiquitylation.

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Organizational Affiliation: 

Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 G1	A	172	Homo sapiens	Mutation(s): 0  Gene Names: UBE2G1, UBE2G EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P62253 (Homo sapiens) Explore P62253  Go to UniProtKB:  P62253
NIH Common Fund Data Resources
PHAROS:  P62253 GTEx:  ENSG00000132388

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.263 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.444	α = 90
b = 59.444	β = 90
c = 186.812	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-01 
• Released Date: 2005-09-20 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Finerty, P., Mackenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-11-28
  Changes: Database references