3QBZ

Crystal structure of the Rad53-recognition domain of Saccharomyces cerevisiae Dbf4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Saccharomyces cerevisiae Dbf4 has unique fold necessary for interaction with Rad53 kinase.

Matthews, L.A., Jones, D.R., Prasad, A.A., Duncker, B.P., Guarne, A.

(2012) J Biol Chem 287: 2378-2387

  • DOI: 10.1074/jbc.M111.233973
  • Primary Citation of Related Structures:  
    3QBZ

  • PubMed Abstract: 

    • Dbf4 is a conserved eukaryotic protein that functions as the regulatory subunit of the Dbf4-dependent kinase (DDK) complex. DDK plays essential roles in DNA replication initiation and checkpoint activation. During the replication checkpoint, Saccharomyce ...

    Dbf4 is a conserved eukaryotic protein that functions as the regulatory subunit of the Dbf4-dependent kinase (DDK) complex. DDK plays essential roles in DNA replication initiation and checkpoint activation. During the replication checkpoint, Saccharomyces cerevisiae Dbf4 is phosphorylated in a Rad53-dependent manner, and this, in turn, inhibits initiation of replication at late origins. We have determined the minimal region of Dbf4 required for the interaction with the checkpoint kinase Rad53 and solved its crystal structure. The core of this fragment of Dbf4 folds as a BRCT domain, but it includes an additional N-terminal helix unique to Dbf4. Mutation of the residues that anchor this helix to the domain core abolish the interaction between Dbf4 and Rad53, indicating that this helix is an integral element of the domain. The structure also reveals that previously characterized Dbf4 mutants with checkpoint phenotypes destabilize the domain, indicating that its structural integrity is essential for the interaction with Rad53. Collectively, these results allow us to propose a model for the association between Dbf4 and Rad53.

    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of motif N from Saccharomyces cerevisiae Dbf4
      Matthews, L.A., Duong, A., Prasad, A.A., Duncker, B.P., Guarne, A.
      (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun F65: 890
    Organizational Affiliation: 

    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DDK kinase regulatory subunit DBF4 A160Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: D4205, DBF4, DNA52, YD9609.07C, YDR052C
Find proteins for P32325 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32325 
Go to UniProtKB:  P32325
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.74α = 90
b = 83.74β = 90
c = 103.669γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2011-12-21
    Changes: Database references
  • Version 1.2: 2013-02-20
    Changes: Database references