6MF6

Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4 polo-interacting region.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division.

Almawi, A.W.Langlois-Lemay, L.Boulton, S.Rodriguez Gonzalez, J.Melacini, G.D'Amours, D.Guarne, A.

(2020) Sci Rep 10: 3379-3379

  • DOI: 10.1038/s41598-020-60344-4
  • Primary Citation of Related Structures:  
    6MF4, 6MF6, 6MF5

  • PubMed Abstract: 
  • Polo-like kinases (Plks) are key cell cycle regulators. They contain a kinase domain followed by a polo-box domain that recognizes phosphorylated substrates and enhances their phosphorylation. The regulatory subunit of the Dbf4-dependent kinase complex i ...

    Polo-like kinases (Plks) are key cell cycle regulators. They contain a kinase domain followed by a polo-box domain that recognizes phosphorylated substrates and enhances their phosphorylation. The regulatory subunit of the Dbf4-dependent kinase complex interacts with the polo-box domain of Cdc5 (the sole Plk in Saccharomyces cerevisiae) in a phosphorylation-independent manner. We have solved the crystal structures of the polo-box domain of Cdc5 on its own and in the presence of peptides derived from Dbf4 and a canonical phosphorylated substrate. The structure bound to the Dbf4-peptide reveals an additional density on the surface opposite to the phospho-peptide binding site that allowed us to propose a model for the interaction. We found that the two peptides can bind simultaneously and non-competitively to the polo-box domain in solution. Furthermore, point mutations on the surface opposite to the phosphopeptide binding site of the polo-box domain disrupt the interaction with the Dbf4 peptide in solution and cause an early anaphase arrest phenotype distinct from the mitotic exit defect typically observed in cdc5 mutants. Collectively, our data illustrates the importance of non-canonical interactions mediated by the polo-box domain and provide key mechanistic insights into the combinatorial recognition of substrates by Polo-like kinases.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, QC, Canada. alba.guarne@mcgill.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell cycle serine/threonine-protein kinase CDC5/MSD2 AB290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC5MSD2PKX2YMR001CYM8270.03C
EC: 2.7.11.21
Find proteins for P32562 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32562 
Go to UniProtKB:  P32562
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DDK kinase regulatory subunit DBF4 CD21Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DBF4DNA52YDR052CD4205YD9609.07C
Find proteins for P32325 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32325 
Go to UniProtKB:  P32325
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.054α = 90
b = 135.054β = 90
c = 75.163γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History 

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references