9H0K | pdb_00009h0k

Crystal structure of human CREBBP histone acetyltransferase domain in complex with Propionyl- Coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural and functional characterization of CREB-binding protein (CREBBP) as a histone propionyltransferase.

Cui, G.Ley, M.Mechaly, A.E.Bui, L.C.Michail, C.Berthelet, J.Dairou, J.Yang, H.Chevreux, G.Moroy, G.Green, M.R.Haouz, A.Rodrigues Lima, F.

(2025) J Biological Chem 301: 110444-110444

  • DOI: https://doi.org/10.1016/j.jbc.2025.110444
  • Primary Citation Related Structures: 
    9H02, 9H0K

  • PubMed Abstract: 

    In addition to histone acetylation, histone lysine propionylation (such as the H3K18Pr mark) has recently attracted significant attention as a common and abundant modification linking the cellular metabolic state and gene expression. CREB-binding protein (CREBBP) and EP300 are key histone acetyltransferases that play a critical role in gene expression through their catalytic activity. Although CREBBP and EP300 are homologous enzymes with high structural similarities, they exhibit both redundant and specific functions. Dissecting the shared and divergent properties of CREBBP and EP300 is thus important to understand their roles. However, despite the importance of CREBBP, most mechanistic and structural studies have focused on EP300, leaving much less information about CREBBP. Interestingly, recent enzymatic and structural studies have demonstrated that EP300 can also function as a histone propionyltransferase. Using a combination of acyltransferase assays with different acyl-CoA cofactors and with peptides, recombinant histone, or recombinant nucleosomes as substrates, we provide enzymatic evidence that, in addition to its well-documented acetyltransferase activity, CREBBP readily propionylates histone H3 in vitro, notably generating the H3K18Pr mark. Importantly, subsequent cellular studies using CRISPR-Cas9-edited cells further support that CREBBP can act as a histone propionyltransferase in vivo, notably depositing the H3K18Pr mark. Finally, the crystal structures of the human CREBBP histone acetyltransferase domain in complex with propionyl-CoA or in complex with Lys-CoA provide the structural basis for the histone propionyltransferase properties of CREBBP. Taken together, these findings provide new insights into the enzymatic functions of CREBBP and a better understanding of the mechanisms linking cellular metabolism and epigenetic regulation.


  • Organizational Affiliation
    • Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 82.72 kDa 
  • Atom Count: 5,896 
  • Modeled Residue Count: 639 
  • Deposited Residue Count: 696 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CREB-binding protein
A, B
348Homo sapiensMutation(s): 1 
Gene Names: CREBBPCBP
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
PHAROS:  Q92793
GTEx:  ENSG00000005339 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92793
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.240 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.408α = 90
b = 88.513β = 90
c = 112.455γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--
Chinese Scholarship CouncilChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2026-06-03
    Changes: Database references