Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 17.61 kDa 
• Atom Count: 1294 
• Modelled Residue Count: 152 
• Deposited Residue Count: 155 
• Unique protein chains: 1

6CYO

Crystal structure of human UBE2A (RAD6A)

• DOI: 10.2210/pdb6CYO/pdb

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


• Deposited: 2018-04-06 Released: 2018-12-12 
• Deposition Author(s): Ranzani, A.T., de Oliveira, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.214 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Literature

Mechanistic insights revealed by a UBE2A mutation linked to intellectual disability.

de Oliveira, J.F., do Prado, P.F.V., da Costa, S.S., Sforca, M.L., Canateli, C., Ranzani, A.T., Maschietto, M., de Oliveira, P.S.L., Otto, P.A., Klevit, R.E., Krepischi, A.C.V., Rosenberg, C., Franchini, K.G.

(2019) Nat Chem Biol 15: 62-70

• PubMed: 30531907 
• DOI: 10.1038/s41589-018-0177-2
• Primary Citation of Related Structures:  
  6CYO, 6CYR


• PubMed Abstract: 
  

Ubiquitin-conjugating enzymes (E2) enable protein ubiquitination by conjugating ubiquitin to their catalytic cysteine for subsequent transfer to a target lysine side chain. Deprotonation of the incoming lysine enables its nucleophilicity, but determinants of lysine activation remain poorly understood. We report a novel pathogenic mutation in the E2 UBE2A, identified in two brothers with mild intellectual disability. The pathogenic Q93E mutation yields UBE2A with impaired aminolysis activity but no loss of the ability to be conjugated with ubiquitin. Importantly, the low intrinsic reactivity of UBE2A Q93E was not overcome by a cognate ubiquitin E3 ligase, RAD18, with the UBE2A target PCNA. However, UBE2A Q93E was reactive at high pH or with a low-pK _a amine as the nucleophile, thus providing the first evidence of reversion of a defective UBE2A mutation. We propose that Q93E substitution perturbs the UBE2A catalytic microenvironment essential for lysine deprotonation during ubiquitin transfer, thus generating an enzyme that is disabled but not dead.

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Organizational Affiliation: 

Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 A	A	155	Homo sapiens	Mutation(s): 0  Gene Names: UBE2A, RAD6A EC: 2.3.2.23
Find proteins for P49459 (Homo sapiens) Explore P49459  Go to UniProtKB:  P49459
NIH Common Fund Data Resources
PHAROS:  P49459 GTEx:  ENSG00000077721

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.214 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.497	α = 90
b = 51.35	β = 90
c = 88.663	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-04-06 
• Released Date: 2018-12-12 
Deposition Author(s): Ranzani, A.T., de Oliveira, J.F.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references