6MF5

Crystal structure of budding yeast Cdc5 polo-box domain in complex with Spc72 phosphopeptide.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

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, 6MF5, 6MF6

  • 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 interacts with the polo-box domain of Cdc5 (the sole Plk in Saccharomyces cerevisiae) in a phosphorylation-independent manner ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell cycle serine/threonine-protein kinase CDC5/MSD2A, B290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC5, MSD2, PKX2, YMR001C, YM8270.03C
EC: 2.7.11.21
UniProt
Find proteins for P32562 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32562 
Go to UniProtKB:  P32562
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32562
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spc72C, D11Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39723 
Go to UniProtKB:  P39723
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39723
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		C, D L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.47α = 90
b = 68.19β = 102.59
c = 86.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

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