5J0A

Crystal structure of PDZ-binding kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The crystal structure of an inactive dimer of PDZ-binding kinase

Dong, C.Tang, X.Xie, Y.Zou, Q.Yang, X.Zhou, H.

(2016) Biochem.Biophys.Res.Commun. 476: 586-593

  • DOI: 10.1016/j.bbrc.2016.05.166

  • PubMed Abstract: 
  • The overexpression of PDZ-binding kinase/T-LAK cell-originated protein kinase (PBK/TOPK) has been associated with hematologic tumors, breast cancer and various other cancers. However, the three-dimensional structure of PBK has not been solved. In thi ...

    The overexpression of PDZ-binding kinase/T-LAK cell-originated protein kinase (PBK/TOPK) has been associated with hematologic tumors, breast cancer and various other cancers. However, the three-dimensional structure of PBK has not been solved. In this study, we determined the crystal structure of human PBK, which has two phospho-mimicking mutations T9E and T198E. The structural data indicated that PBK may assemble into an inactive dimer in alkaline conditions. Analytical size-exclusion chromatography and analytical ultracentrifugation confirmed that PBK exists in a conformational transition between dimers and monomers at different pH conditions. Co-IP and kinase assays suggested that the active state of PBK is a monomer and does not form a dimer even under alkaline conditions. These results showed that the conformational transition of PBK is important for its kinase activity regulation. Collectively, our observations may provide a novel starting point for structure-based functional studies.


    Organizational Affiliation

    College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lymphokine-activated killer T-cell-originated protein kinase
A
300Homo sapiensMutation(s): 1 
Gene Names: PBK (TOPK)
EC: 2.7.12.2
Find proteins for Q96KB5 (Homo sapiens)
Go to Gene View: PBK
Go to UniProtKB:  Q96KB5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lymphokine-activated killer T-cell-originated protein kinase
B
304Homo sapiensMutation(s): 1 
Gene Names: PBK (TOPK)
EC: 2.7.12.2
Find proteins for Q96KB5 (Homo sapiens)
Go to Gene View: PBK
Go to UniProtKB:  Q96KB5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HC4
Query on HC4

Download SDF File 
Download CCD File 
A, B
4'-HYDROXYCINNAMIC ACID
PARA-COUMARIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.558α = 90.00
b = 97.905β = 90.00
c = 162.835γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release