Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.45 kDa 
• Atom Count: 4748 
• Modelled Residue Count: 554 
• Deposited Residue Count: 578 
• Unique protein chains: 1

5LKX

Crystal structure of the p300 acetyltransferase catalytic core with propionyl-coenzyme A.

• PDB DOI: 10.2210/pdb5LKX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2016-07-25 Released: 2016-11-02 
• Deposition Author(s): Kaczmarska, Z., Ortega, E., Marquez, J.A., Panne, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.239 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Structure of p300 in complex with acyl-CoA variants.

Kaczmarska, Z., Ortega, E., Goudarzi, A., Huang, H., Kim, S., Marquez, J.A., Zhao, Y., Khochbin, S., Panne, D.

(2017) Nat Chem Biol 13: 21-29

• PubMed: 27820805 
• DOI: 10.1038/nchembio.2217
• Primary Citation of Related Structures:  
  5LKT, 5LKU, 5LKX, 5LKZ


• PubMed Abstract: 
  

Histone acetylation plays an important role in transcriptional activation. Histones are also modified by chemically diverse acylations that are frequently deposited by p300, a transcriptional coactivator that uses a number of different acyl-CoA cofactors. Here we report that while p300 is a robust acetylase, its activity gets weaker with increasing acyl-CoA chain length. Crystal structures of p300 in complex with propionyl-, crotonyl-, or butyryl-CoA show that the aliphatic portions of these cofactors are bound in the lysine substrate-binding tunnel in a conformation that is incompatible with substrate transfer. Lysine substrate binding is predicted to remodel the acyl-CoA ligands into a conformation compatible with acyl-chain transfer. This remodeling requires that the aliphatic portion of acyl-CoA be accommodated in a hydrophobic pocket in the enzymes active site. The size of the pocket and its aliphatic nature exclude long-chain and charged acyl-CoA variants, presumably explaining the cofactor preference for p300.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Grenoble, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase p300,Histone acetyltransferase p300	A	578	Homo sapiens	Mutation(s): 1  Gene Names: EP300, P300 EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens) Explore Q09472  Go to UniProtKB:  Q09472
PHAROS:  Q09472

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1VU	F [auth A]	propionyl Coenzyme A C24 H40 N7 O17 P3 S QAQREVBBADEHPA-IEXPHMLFSA-N
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-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: 2.52 Å
• R-Value Free: 0.239 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.81	α = 90
b = 155.26	β = 90
c = 109.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-07-25 
• Released Date: 2016-11-02 
Deposition Author(s): Kaczmarska, Z., Ortega, E., Marquez, J.A., Panne, D.

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Database references
• Version 1.2: 2016-12-28
  Changes: Database references