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 
  • R-Value Observed: 0.182 

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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:  
    4C57, 4C58, 4C59

  • 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 clinical kinase inhibitors associated with respiratory side effects of these drugs ...

    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: 

    *University of Oxford, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Old Road Campus Research Building, Oxford OX3 7DQ, U.K.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-G-associated kinaseA340Homo sapiensMutation(s): 0 
Gene Names: GAK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14976 (Homo sapiens)
Explore O14976 
Go to UniProtKB:  O14976
PHAROS:  O14976
GTEx:  ENSG00000178950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14976
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
nanobodyB140Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
824
Query on 824
Download Ideal Coordinates CCD File 
E [auth A]9-HYDROXY-4-PHENYLPYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE
C20 H12 N2 O3
IAUZTOZLTFSMIE-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B]		1,2-ETHANEDIOL
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 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.866α = 90
b = 37.43β = 108.48
c = 76.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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