4C58

Structure of GAK kinase in complex with nanobody (NbGAK_4)

Summary for 4C58

• Entry DOI: 10.2210/pdb4c58/pdb
• Related: 4C57 4C59
• Descriptor: Cyclin-G-associated kinase, nanobody, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: transferase, kinase, conformational plasticity, activation
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 53783.59

Authors

Chaikuad, A.,Keates, T.,Allerston, C.K.,Gileadi, O.,von Delft, F.,Arrowsmith, C.H.,Edwards, A.M.,Bountra, C.,Knapp, S.,Muller-Knapp, S. (deposition date: 2013-09-10, release date: 2013-10-09, Last modification date: 2024-11-13)

Primary citation

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.
Structure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies.
Biochem. J., 459:59-69, 2014

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. 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.

PubMed: 24438162
DOI: 10.1042/BJ20131399

Experimental method

X-RAY DIFFRACTION (2.16 Å)