Crystal structure of GCN5 PCAF N-terminal domain

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure.

Toma-Fukai, S.Hibi, R.Naganuma, T.Sakai, M.Saijo, S.Shimizu, N.Matsumoto, M.Shimizu, T.

(2020) J Biol Chem 295: 14630-14639

  • DOI: https://doi.org/10.1074/jbc.RA120.013431
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    General control nonderepressible 5 (GCN5, also known as Kat2a) and p300/CBP-associated factor (PCAF, also known as Kat2b) are two homologous acetyltransferases. Both proteins share similar domain architecture consisting of a PCAF N-terminal (PCAF_N) domain, acetyltransferase domain, and a bromodomain. PCAF also acts as a ubiquitin E3 ligase whose activity is attributable to the PCAF_N domain, but its structural aspects are largely unknown. Here, we demonstrated that GCN5 exhibited ubiquitination activity in a similar manner to PCAF and its activity was supported by the ubiquitin-conjugating enzyme UbcH5. Moreover, we determined the crystal structure of the PCAF_N domain at 1.8 Å resolution and found that PCAF_N domain folds into a helical structure with a characteristic binuclear zinc region, which was not predicted from sequence analyses. The zinc region is distinct from known E3 ligase structures, suggesting this region may form a new class of E3 ligase. Our biochemical and structural study provides new insight into not only the functional significance of GCN5 but also into ubiquitin biology.

  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2A
A, B
317Mus musculusMutation(s): 0 
Gene Names: Kat2aGcn5l2
Find proteins for Q9JHD2 (Mus musculus)
Explore Q9JHD2 
Go to UniProtKB:  Q9JHD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JHD2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.069α = 90
b = 148.857β = 101.03
c = 58.998γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2020-11-11
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Refinement description