3Q35

Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation.

Tang, Y.Holbert, M.A.Delgoshaie, N.Wurtele, H.Guillemette, B.Meeth, K.Yuan, H.Drogaris, P.Lee, E.H.Durette, C.Thibault, P.Verreault, A.Cole, P.A.Marmorstein, R.

(2011) Structure 19: 221-231

  • DOI: 10.1016/j.str.2010.12.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Yeast Rtt109 promotes nucleosome assembly and genome stability by acetylating K9, K27, and K56 of histone H3 through interaction with either of two distinct histone chaperones, Vps75 or Asf1. We report the crystal structure of an Rtt109-AcCoA/Vps75 c ...

    Yeast Rtt109 promotes nucleosome assembly and genome stability by acetylating K9, K27, and K56 of histone H3 through interaction with either of two distinct histone chaperones, Vps75 or Asf1. We report the crystal structure of an Rtt109-AcCoA/Vps75 complex revealing an elongated Vps75 homodimer bound to two globular Rtt109 molecules to form a symmetrical holoenzyme with a ∼12 Å diameter central hole. Vps75 and Rtt109 residues that mediate complex formation in the crystals are also important for Rtt109-Vps75 interaction and H3K9/K27 acetylation both in vitro and in yeast cells. The same Rtt109 residues do not participate in Asf1-mediated Rtt109 acetylation in vitro or H3K56 acetylation in yeast cells, demonstrating that Asf1 and Vps75 dictate Rtt109 substrate specificity through distinct mechanisms. These studies also suggest that Vps75 binding stimulates Rtt109 catalytic activity by appropriately presenting the H3-H4 substrate within the central cavity of the holoenzyme to promote H3K9/K27 acetylation of new histones before deposition.


    Related Citations: 
    • Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP.
      Tang, Y.,Holbert, M.A.,Wurtele, H.,Meeth, K.,Rocha, W.,Gharib, M.,Jiang, E.,Thibault, P.,Verreault, A.,Verrault, A.,Cole, P.A.,Marmorstein, R.
      (2008) Nat.Struct.Mol.Biol. 15: 738
    • Structure of Vps75 and implications for histone chaperone function.
      Tang, Y.,Meeth, K.,Jiang, E.,Luo, C.,Marmorstein, R.
      (2008) Proc.Natl.Acad.Sci.USA 105: 12206


    Organizational Affiliation

    Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase
A
438Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RTT109 (KIM2, REM50)
EC: 2.3.1.48
Find proteins for Q07794 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07794
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 75
B
232Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPS75
Find proteins for P53853 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53853
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download SDF File 
Download CCD File 
A
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.085α = 90.00
b = 119.001β = 90.00
c = 80.292γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PHENIXrefinement
AMoREphasing
Blu-Icedata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance