5NFU

The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with LHSpTA peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

A cryptic hydrophobic pocket in the polo-box domain of the polo-like kinase PLK1 regulates substrate recognition and mitotic chromosome segregation.

Sharma, P.Mahen, R.Rossmann, M.Stokes, J.E.Hardwick, B.Huggins, D.J.Emery, A.Kunciw, D.L.Hyvonen, M.Spring, D.R.McKenzie, G.J.Venkitaraman, A.R.

(2019) Sci Rep 9: 15930-15930

  • DOI: 10.1038/s41598-019-50702-2
  • Primary Citation of Related Structures:  
    5NFU, 5NJE

  • PubMed Abstract: 
  • The human polo-like kinase PLK1 coordinates mitotic chromosome segregation by phosphorylating multiple chromatin- and kinetochore-binding proteins. How PLK1 activity is directed to specific substrates via phosphopeptide recognition by its carboxyl-terminal polo-box domain (PBD) is poorly understood ...

    The human polo-like kinase PLK1 coordinates mitotic chromosome segregation by phosphorylating multiple chromatin- and kinetochore-binding proteins. How PLK1 activity is directed to specific substrates via phosphopeptide recognition by its carboxyl-terminal polo-box domain (PBD) is poorly understood. Here, we combine molecular, structural and chemical biology to identify a determinant for PLK1 substrate recognition that is essential for proper chromosome segregation. We show that mutations ablating an evolutionarily conserved, Tyr-lined pocket in human PLK1 PBD trigger cellular anomalies in mitotic progression and timing. Tyr pocket mutations selectively impair PLK1 binding to the kinetochore phosphoprotein substrate PBIP1, but not to the centrosomal substrate NEDD1. Through a structure-guided approach, we develop a small-molecule inhibitor, Polotyrin, which occupies the Tyr pocket. Polotyrin recapitulates the mitotic defects caused by mutations in the Tyr pocket, further evidencing its essential function, and exemplifying a new approach for selective PLK1 inhibition. Thus, our findings support a model wherein substrate discrimination via the Tyr pocket in the human PLK1 PBD regulates mitotic chromosome segregation to preserve genome integrity.


    Organizational Affiliation

    The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom. arv22@mrc-cu.cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK1A236Homo sapiensMutation(s): 0 
Gene Names: PLK1PLK
EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for P53350 (Homo sapiens)
Explore P53350 
Go to UniProtKB:  P53350
PHAROS:  P53350
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53350
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ac-LEU-HIS-SER-(TPO)-ALAB [auth C]5Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LAY
Query on LAY
B [auth C]L-PEPTIDE LINKINGC8 H15 N O3LEU
TPO
Query on TPO
B [auth C]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.197α = 90
b = 59.808β = 102.69
c = 58.256γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 2.0: 2019-05-15
    Changes: Data collection, Polymer sequence
  • Version 2.1: 2019-07-10
    Changes: Data collection
  • Version 2.2: 2019-11-27
    Changes: Database references
  • Version 3.0: 2022-04-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary