Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.82 kDa 
• Atom Count: 2683 
• Modelled Residue Count: 313 
• Deposited Residue Count: 334 
• Unique protein chains: 1

4BFM

The crystal structure of mouse PK38

• PDB DOI: 10.2210/pdb4BFM/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-03-21 Released: 2014-02-12 
• Deposition Author(s): Yoo, J.H., Cho, Y.S., Park, S.M., Cho, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

The Structures of the Kinase Domain and Uba Domain of Mpk38 Suggest the Activation Mechanism for Kinase Activity.

Cho, Y.S., Yoo, J., Park, S., Cho, H.S.

(2014) Acta Crystallogr D Biol Crystallogr 70: 514

• PubMed: 24531485 
• DOI: 10.1107/S1399004713027806
• Primary Citation of Related Structures:  
  4BFM


• PubMed Abstract: 
  

Murine protein serine/threonine kinase 38 (MPK38) is the murine orthologue of human maternal embryonic leucine-zipper kinase (MELK), which belongs to the SNF1/AMPK family. MELK is considered to be a promising drug target for anticancer therapy because overexpression and hyperactivation of MELK is correlated with several human cancers. Activation of MPK38 requires the extended sequence (ExS) containing the ubiquitin-associated (UBA) linker and UBA domain and phosphorylation of the activation loop. However, the activation mechanism of MPK38 is unknown. This paper reports the crystal structure of MPK38 (T167E), which mimics a phosphorylated state of the activation loop, in complex with AMP-PNP. In the MPK38 structure, the UBA linker forces an inward movement of the αC helix. Phosphorylation of the activation loop then induces movement of the activation loop towards the C-lobe and results in interlobar cleft closure. These processes generate a fully active state of MPK38. This structure suggests that MPK38 has a similar molecular mechanism regulating activation as in other kinases of the SNF1/AMPK family.

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Organizational Affiliation: 

Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MATERNAL EMBRYONIC LEUCINE ZIPPER KINASE	A	334	Mus musculus	Mutation(s): 1  Gene Names: Melk, Kiaa0175, Pk38 EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt
Find proteins for Q61846 (Mus musculus) Explore Q61846  Go to UniProtKB:  Q61846

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.799	α = 90
b = 75.711	β = 90
c = 128.088	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-21 
• Released Date: 2014-02-12 
Deposition Author(s): Yoo, J.H., Cho, Y.S., Park, S.M., Cho, H.S.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Database references