4XB0

Structure of the Plk2 polo-box domain

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2014-12-16 Released: 2015-05-06 
  • Deposition Author(s): Kim, J.H., Ku, B., Kim, S.J.
  • Funding Organization(s): National Research Foundation of Korea, Korea Research Institute of Bioscience and Biotechnology Research Initiative Program

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of the polo-box domain of human Polo-like kinase 2

Kim, J.H.Ku, B.Lee, K.S.Kim, S.J.

(2015) Proteins 83: 1201-1208

  • DOI: https://doi.org/10.1002/prot.24804
  • Primary Citation of Related Structures:  
    4XB0

  • PubMed Abstract: 

    Polo-like kinases (Plks) are the key regulators of cell cycle progression, the members of which share a kinase domain and a polo-box domain (PBD) that serves as a protein-binding module. While Plk1 is a promising target for antitumor therapy, Plk2 is regarded as a tumor suppressor even though the two Plks commonly recognize the S-pS/T-P motif through their PBD. Herein, we report the crystal structure of the PBD of Plk2 at 2.7 Å. Despite the overall structural similarity with that of Plk1 reflecting their high sequence homology, the crystal structure also contains its own features including the highly ordered loop connecting two subdomains and the absence of 310 -helices in the N-terminal region unlike the PBD of Plk1. Based on the three-dimensional structure, we furthermore could model its interaction with two types of phosphopeptides, one of which was previously screened as the optimal peptide for the PBD of Plk2.


  • Organizational Affiliation

    Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PLK2
A, B
218Homo sapiensMutation(s): 0 
Gene Names: PLK2SNK
EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYY3 (Homo sapiens)
Explore Q9NYY3 
Go to UniProtKB:  Q9NYY3
PHAROS:  Q9NYY3
GTEx:  ENSG00000145632 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYY3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.292α = 90
b = 152.292β = 90
c = 152.292γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2011-0030027
Korea Research Institute of Bioscience and Biotechnology Research Initiative ProgramKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description