4C58

Structure of GAK kinase in complex with nanobody (NbGAK_4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies.

Chaikuad, A.Keates, T.Vincke, C.Kaufholz, M.Zenn, M.Zimmermann, B.Gutierrez, C.Zhang, R.G.Hatzos-Skintges, C.Joachimiak, A.Muyldermans, S.Herberg, F.W.Knapp, S.Muller, S.

(2014) Biochem. J. 459: 59-69

  • DOI: 10.1042/BJ20131399
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GAK (cyclin G-associated kinase) is a key regulator of clathrin-coated vesicle trafficking and plays a central role during development. Additionally, due to the unusually high plasticity of its catalytic domain, it is a frequent 'off-target' of clini ...

    GAK (cyclin G-associated kinase) is a key regulator of clathrin-coated vesicle trafficking and plays a central role during development. Additionally, due to the unusually high plasticity of its catalytic domain, it is a frequent 'off-target' of clinical kinase inhibitors associated with respiratory side effects of these drugs. In the present paper, we determined the crystal structure of the GAK catalytic domain alone and in complex with specific single-chain antibodies (nanobodies). GAK is constitutively active and weakly associates in solution. The GAK apo structure revealed a dimeric inactive state of the catalytic domain mediated by an unusual activation segment interaction. Co-crystallization with the nanobody NbGAK_4 trapped GAK in a dimeric arrangement similar to the one observed in the apo structure, whereas NbGAK_1 captured the activation segment of monomeric GAK in a well-ordered conformation, representing features of the active kinase. The presented structural and biochemical data provide insight into the domain plasticity of GAK and demonstrate the utility of nanobodies to gain insight into conformational changes of dynamic molecules. In addition, we present structural data on the binding mode of ATP mimetic inhibitors and enzyme kinetic data, which will support rational inhibitor design of inhibitors to reduce the off-target effect on GAK.


    Organizational Affiliation

    ‡Department of Biochemistry, University of Kassel, Heinrich-Plett Strasse 40, 34132 Kassel, Germany.,§Biaffin GmbH & CoKG, Heinrich-Plett Strasse 40, 34132 Kassel, Germany.,∥Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, U.S.A.,*University of Oxford, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Old Road Campus Research Building, Oxford OX3 7DQ, U.K.,¶Department of Animal Medicine and Surgery, Veterinary Faculty, University of Las Palmas de Gran Canaria, 35416, Arucas, Las Palmas, Spain.,†Research Unit of Cellular and Molecular Immunology and Department of Structural Biology, VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-G-associated kinase
A
340Homo sapiensMutation(s): 0 
Gene Names: GAK
EC: 2.7.11.1
Find proteins for O14976 (Homo sapiens)
Go to Gene View: GAK
Go to UniProtKB:  O14976
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
nanobody
B
140N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
824
Query on 824

Download SDF File 
Download CCD File 
A
9-HYDROXY-4-PHENYLPYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE
9-HYDROXY-4-PHENYL-6H-PYRROLO[3,4-C]CARBAZOLE-1,3-DIONE
C20 H12 N2 O3
IAUZTOZLTFSMIE-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.866α = 90.00
b = 37.430β = 108.48
c = 76.010γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references
  • Version 1.2: 2019-02-06
    Type: Data collection, Database references, Experimental preparation, Source and taxonomy, Structure summary