5TRL

Crystal structure of human GCN5 histone acetyltransferase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

KAT2A coupled with the alpha-KGDH complex acts as a histone H3 succinyltransferase.

Wang, Y.Guo, Y.R.Liu, K.Yin, Z.Liu, R.Xia, Y.Tan, L.Yang, P.Lee, J.H.Li, X.J.Hawke, D.Zheng, Y.Qian, X.Lyu, J.He, J.Xing, D.Tao, Y.J.Lu, Z.

(2017) Nature 552: 273-277

  • DOI: 10.1038/nature25003
  • Primary Citation of Related Structures:  
    5TRL, 5TRM

  • PubMed Abstract: 
  • Histone modifications, such as the frequently occurring lysine succinylation, are central to the regulation of chromatin-based processes. However, the mechanism and functional consequences of histone succinylation are unknown. Here we show that the α ...

    Histone modifications, such as the frequently occurring lysine succinylation, are central to the regulation of chromatin-based processes. However, the mechanism and functional consequences of histone succinylation are unknown. Here we show that the α-ketoglutarate dehydrogenase (α-KGDH) complex is localized in the nucleus in human cell lines and binds to lysine acetyltransferase 2A (KAT2A, also known as GCN5) in the promoter regions of genes. We show that succinyl-coenzyme A (succinyl-CoA) binds to KAT2A. The crystal structure of the catalytic domain of KAT2A in complex with succinyl-CoA at 2.3 Å resolution shows that succinyl-CoA binds to a deep cleft of KAT2A with the succinyl moiety pointing towards the end of a flexible loop 3, which adopts different structural conformations in succinyl-CoA-bound and acetyl-CoA-bound forms. Site-directed mutagenesis indicates that tyrosine 645 in this loop has an important role in the selective binding of succinyl-CoA over acetyl-CoA. KAT2A acts as a succinyltransferase and succinylates histone H3 on lysine 79, with a maximum frequency around the transcription start sites of genes. Preventing the α-KGDH complex from entering the nucleus, or expression of KAT2A(Tyr645Ala), reduces gene expression and inhibits tumour cell proliferation and tumour growth. These findings reveal an important mechanism of histone modification and demonstrate that local generation of succinyl-CoA by the nuclear α-KGDH complex coupled with the succinyltransferase activity of KAT2A is instrumental in histone succinylation, tumour cell proliferation, and tumour development.


    Organizational Affiliation

    MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, Texas 77030, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2AABCDEFGH168Homo sapiensMutation(s): 0 
Gene Names: KAT2AGCN5GCN5L2HGCN5
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q92830 (Homo sapiens)
Explore Q92830 
Go to UniProtKB:  Q92830
NIH Common Fund Data Resources
PHAROS  Q92830
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCA
Query on SCA

Download CCD File 
A, B, C, D, E, F, G, H
SUCCINYL-COENZYME A
C25 H40 N7 O19 P3 S
VNOYUJKHFWYWIR-ITIYDSSPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.728α = 90
b = 175.728β = 90
c = 175.728γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
HKL-3000data scaling
HKLdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-10-26 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Guo, Y.R., Tao, Y.J.

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-20
    Changes: Database references
  • Version 1.2: 2017-12-27
    Changes: Database references