Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 33.92 kDa 
• Atom Count: 2143 
• Modelled Residue Count: 256 
• Deposited Residue Count: 298 
• Unique protein chains: 1

2ZV2

Crystal structure of human calcium/calmodulin-dependent protein kinase kinase 2, beta, CaMKK2 kinase domain in complex with STO-609

• DOI: 10.2210/pdb2ZV2/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2008-10-31 Released: 2009-11-03 
• Deposition Author(s): Yoshikawa, S., Kukimoto-niino, M., Shirouzu, M., Suzuki, A., Lee, S., Minokoshi, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.203 

Literature

Crystal structure of the Ca2+/calmodulin-dependent protein kinase kinase in complex with the inhibitor STO-609

Kukimoto-Niino, M., Yoshikawa, S., Takagi, T., Ohsawa, N., Tomabechi, Y., Terada, T., Shirouzu, M., Suzuki, A., Lee, S., Yamauchi, T., Okada-Iwabu, M., Iwabu, M., Kadowaki, T., Minokoshi, Y., Yokoyama, S.

(2011) J Biol Chem 286: 22570-22579

• PubMed: 21504895 
• DOI: 10.1074/jbc.M111.251710
• Primary Citation of Related Structures:  
  2ZV2


• PubMed Abstract: 
  

Ca(2+)/calmodulin (CaM)-dependent protein kinase (CaMK) kinase (CaMKK) is a member of the CaMK cascade that mediates the response to intracellular Ca(2+) elevation. CaMKK phosphorylates and activates CaMKI and CaMKIV, which directly activate transcription factors. In this study, we determined the 2.4 Å crystal structure of the catalytic kinase domain of the human CaMKKβ isoform complexed with its selective inhibitor, STO-609. The structure revealed that CaMKKβ lacks the αD helix and that the equivalent region displays a hydrophobic molecular surface, which may reflect its unique substrate recognition and autoinhibition. Although CaMKKβ lacks the activation loop phosphorylation site, the activation loop is folded in an active-state conformation, which is stabilized by a number of interactions between amino acid residues conserved among the CaMKK isoforms. An in vitro analysis of the kinase activity confirmed the intrinsic activity of the CaMKKβ kinase domain. Structure and sequence analyses of the STO-609-binding site revealed amino acid replacements that may affect the inhibitor binding. Indeed, mutagenesis demonstrated that the CaMKKβ residue Pro(274), which replaces the conserved acidic residue of other protein kinases, is an important determinant for the selective inhibition by STO-609. Therefore, the present structure provides a molecular basis for clarifying the known biochemical properties of CaMKKβ and for designing novel inhibitors targeting CaMKKβ and the related protein kinases.

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Organizational Affiliation: 

RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CAMKK2, CAMKKB, KIAA0787 EC: 2.7.11.17
Find proteins for Q96RR4 (Homo sapiens) Explore Q96RR4  Go to UniProtKB:  Q96RR4
NIH Common Fund Data Resources
PHAROS:  Q96RR4 GTEx:  ENSG00000110931

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
609	B [auth A]	7-oxo-7H-benzimidazo[2,1-a]benz[de]isoquinoline-3-carboxylic acid C19 H10 N2 O3 MYKOWOGZBMOVBJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
609	IC50:  500   nM  BindingDB
609	IC50 :  500   nM  PDBBind
609	IC50:  24200   nM  BindingDB
609	IC50:  10   nM  BindingDB
609	IC50:  40   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.368	α = 90
b = 77.153	β = 90
c = 84.332	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-31 
• Released Date: 2009-11-03 
Deposition Author(s): Yoshikawa, S., Kukimoto-niino, M., Shirouzu, M., Suzuki, A., Lee, S., Minokoshi, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-11-20
  Changes: Database references