6CYR

Crystal structure of the UBE2A variant Q93E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1038/s41589-018-0177-2
  • Structures With Same Primary Citation

  • 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 determi ...

    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.


    Organizational Affiliation

    Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil. kleber.franchini@lnbio.cnpem.br.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 A
A
155Homo sapiensMutation(s): 1 
Gene Names: UBE2ARAD6A
EC: 2.3.2.23
Find proteins for P49459 (Homo sapiens)
Go to UniProtKB:  P49459
NIH Common Fund Data Resources
PHAROS  P49459
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.511α = 90
b = 52.419β = 90
c = 88.59γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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