4PSX

Crystal structure of histone acetyltransferase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.509 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Hat2p recognizes the histone H3 tail to specify the acetylation of the newly synthesized H3/H4 heterodimer by the Hat1p/Hat2p complex

Li, Y.Zhang, L.Liu, T.Chai, C.Fang, Q.Wu, H.Agudelo garcia, P.A.Han, Z.Zong, S.Yu, Y.Zhang, X.Parthun, M.R.Chai, J.Xu, R.M.Yang, M.

(2014) Genes Dev. 28: 1217-1227

  • DOI: 10.1101/gad.240531.114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Post-translational modifications of histones are significant regulators of replication, transcription, and DNA repair. Particularly, newly synthesized histone H4 in H3/H4 heterodimers becomes acetylated on N-terminal lysine residues prior to its inco ...

    Post-translational modifications of histones are significant regulators of replication, transcription, and DNA repair. Particularly, newly synthesized histone H4 in H3/H4 heterodimers becomes acetylated on N-terminal lysine residues prior to its incorporation into chromatin. Previous studies have established that the histone acetyltransferase (HAT) complex Hat1p/Hat2p medicates this modification. However, the mechanism of how Hat1p/Hat2p recognizes and facilitates the enzymatic activities on the newly assembled H3/H4 heterodimer remains unknown. Furthermore, Hat2p is a WD40 repeat protein, which is found in many histone modifier complexes. However, how the WD40 repeat proteins facilitate enzymatic activities of histone modification enzymes is unclear. In this study, we first solved the high-resolution crystal structure of a Hat1p/Hat2p/CoA/H4 peptide complex and found that the H4 tail interacts with both Hat1p and Hat2p, by which substrate recruitment is facilitated. We further discovered that H3 N-terminal peptides can bind to the Hat2p WD40 domain and solved the structure of the Hat1p/Hat2p/CoA/H4/H3 peptide complex. Moreover, the interaction with Hat2p requires unmodified Arg2/Lys4 and Lys9 on the H3 tail, suggesting a novel model to specify the activity of Hat1p/Hat2p toward newly synthesized H3/H4 heterodimers. Together, our study demonstrated the substrate recognition mechanism by the Hat1p/Hat2p complex, which is critical for DNA replication and other chromatin remodeling processes.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase type B catalytic subunit
A, D
320Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HAT1
EC: 2.3.1.48
Find proteins for Q12341 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: HAT1
Go to UniProtKB:  Q12341
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase type B subunit 2
B, E
401Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: HAT2
Find proteins for P39984 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39984
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
C, F
48Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: HHF1, HHF2
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02309
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H3
Y, P
15Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HHT1, HHT2 (SIN2)
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P61830
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, D
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.509 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 78.548α = 75.97
b = 85.331β = 72.40
c = 114.510γ = 66.06
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
Blu-Icedata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-08 
  • Released Date: 2014-07-09 
  • Deposition Author(s): Yang, M., Li, Y.

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release