8CMZ | pdb_00008cmz

Crystal structure of CREBBP-R1446C histone acetyltransferase domain in complex with Coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb8CMZ/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-02-21 Released: 2024-03-06 
• Deposition Author(s): Mechaly, A.E., Zhang, W., Haouz, A., Green, M., Rodrigues-Lima, F.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.297 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Structural and functional divergence of cancer hotspot mutations in CREBBP.

Zhang, W., Yang, H., Mechaly, A., Li, Z., Cui, G., Regad, L., Duval, R., Dairou, J., Haouz, A., Green, M.R., Rodrigues Lima, F.

(2026) Proc Natl Acad Sci U S A 123: e2605702123-e2605702123

• PubMed: 42771512 
• DOI: https://doi.org/10.1073/pnas.2605702123
• Primary Citation Related Structures: 
  8CMZ, 8CN0, 8CNB, 8OG2, 9TZ6


• PubMed Abstract: 
  

  CREBBP is among the most frequently mutated genes in human cancer and encodes a lysine acetyltransferase (KAT) protein that acetylates histones and nonhistone proteins to drive transcriptional activation. Mutations of CREBBP most frequently result in missense changes affecting the active site within the KAT domain. However, there has not yet been comprehensive biochemical, structural, and functional studies to determine the impact of recurrent KAT-domain variants. Here we show that the most frequently mutated residue of CREBBP , arginine 1446, alters the stability of acetyl-CoA binding within the cofactor-binding pocket but retains detectable acetyltransferase activity for a variety of substrates including histones. In contrast, other recurrently mutated residues affect the catalytic center within the KAT domain and result in a catalytically dead protein with a profound loss of histone acetylation and enhancer activity. These results highlight functionally divergent classes of CREBBP mutations depending on the position of the mutated residue within KAT domain.

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Organizational Affiliation: 
• Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.
Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Plate-forme de Cristallographie-C2RT, Paris F-75015, France.
Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris F-75013, France.
INSERM U1133, Computational Modeling of Protein-Ligand Interactions, Paris F-75013, France.
Université Paris Cité and Université des Antilles, INSERM, UMRS 1134, Paris F-75015, France.
Centre National de Référence pour les Groupes Sanguins, Établissement Français du Sang Ile-de-France, Paris F-75522, France.
Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Paris F-75006, France.
Department of Hematopoietic Biology & Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 76.03 kDa 
• Atom Count: 4,481 
• Modeled Residue Count: 532 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histone acetyltransferase	A	640	Mus musculus	Mutation(s): 1  Gene Names: Crebbp EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for P45481 (Mus musculus) Explore P45481  Go to UniProtKB:  P45481

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	F [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.297 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.181	α = 90
b = 145.095	β = 90
c = 154.783	γ = 90

Software Package:

Software Name	Purpose
autoBUSTER	refinement
PHASER	phasing
autoPROC	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Mechaly, A.E., Zhang, W., Haouz, A., Green, M., Rodrigues-Lima, F.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary
• Version 1.2: 2026-10-21
  Changes: Database references