2ZD7

The structure of VPS75 (Vacuolar protein sorting-associated protein 75)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Histone chaperone specificity in Rtt109 activation.

Park, Y.J.Sudhoff, K.B.Andrews, A.J.Stargell, L.A.Luger, K.

(2008) Nat Struct Mol Biol 15: 957-964

  • DOI: 10.1038/nsmb.1480
  • Primary Citation of Related Structures:  
    2ZD7

  • PubMed Abstract: 
  • Rtt109 is a histone acetyltransferase that requires a histone chaperone for the acetylation of histone 3 at lysine 56 (H3K56). Rtt109 forms a complex with the chaperone Vps75 in vivo and is implicated in DNA replication and repair. Here we show that both Rtt109 and Vps75 bind histones with high affinity, but only the complex is efficient for catalysis ...

    Rtt109 is a histone acetyltransferase that requires a histone chaperone for the acetylation of histone 3 at lysine 56 (H3K56). Rtt109 forms a complex with the chaperone Vps75 in vivo and is implicated in DNA replication and repair. Here we show that both Rtt109 and Vps75 bind histones with high affinity, but only the complex is efficient for catalysis. The C-terminal acidic domain of Vps75 contributes to activation of Rtt109 and is necessary for in vivo functionality of Vps75, but it is not required for interaction with either Rtt109 or histones. We demonstrate that Vps75 is a structural homolog of yeast Nap1 by solving its crystal structure. Nap1 and Vps75 interact with histones and Rtt109 with comparable affinities. However, only Vps75 stimulates Rtt109 enzymatic activity. Our data highlight the functional specificity of Vps75 in Rtt109 activation.


    Related Citations: 
    • Histone chaperone specificity in Rtt109 activation
      Park, Y.J., Sudhoff, K.B., Andrews, A.J., Stargell, L.A., Luger, K.
      (2008) Nat Struct Mol Biol --: --

    Organizational Affiliation

    Howard Hughes Medical Institute, Colorado State University, Fort Collins, Colorado 80523-1870, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 75A, B264Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS75
UniProt
Find proteins for P53853 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53853 
Go to UniProtKB:  P53853
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53853
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EVDLPLSDEEPSSC13synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.692α = 90
b = 84.58β = 90
c = 86.224γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-11-20 
  • Released Date: 2008-08-12 
  • Deposition Author(s): Park, Y.J., Luger, K.

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-12-25
    Changes: Database references, Source and taxonomy