5LKX | pdb_00005lkx

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

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.239 (Depositor), 0.204 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nchembio.2217
Primary Citation 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.

Organizational Affiliation

European Molecular Biology Laboratory, Grenoble, France.

Macromolecule Content

Total Structure Weight: 68.45 kDa
Atom Count: 4,748
Modeled Residue Count: 554
Deposited Residue Count: 578
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 GTEx: ENSG00000100393
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q09472
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1VU Query on 1VU Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	propionyl Coenzyme A C₂₄ H₄₀ N₇ O₁₇ P₃ S QAQREVBBADEHPA-IEXPHMLFSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.239 (Depositor), 0.204 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.208 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Revision History (Full details and data files)

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
Version 2.0: 2024-01-10
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
Version 2.1: 2024-11-06
Changes: Structure summary