6J7F

Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP

Summary for 6J7F

• Entry DOI: 10.2210/pdb6j7f/pdb
• Descriptor: Protein prenyltransferase alpha subunit repeat-containing protein 1, Geranylgeranyl transferase type-2 subunit beta, Synaptobrevin homolog YKT6, ... (7 entities in total)
• Functional Keywords: lipid transferase, lipid binding protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 98308.30

Authors

Goto-Ito, S.,Yamagata, A.,Sato, Y.,Fukai, S. (deposition date: 2019-01-18, release date: 2020-01-22, Last modification date: 2025-05-28)

Primary citation

Shirakawa, R.,Goto-Ito, S.,Goto, K.,Wakayama, S.,Kubo, H.,Sakata, N.,Trinh, D.A.,Yamagata, A.,Sato, Y.,Masumoto, H.,Cheng, J.,Fujimoto, T.,Fukai, S.,Horiuchi, H.
A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus.
Embo J., 39:e104120-e104120, 2020

PubMed Abstract: Protein prenylation is essential for many cellular processes including signal transduction, cytoskeletal reorganization, and membrane trafficking. Here, we identify a novel type of protein prenyltransferase, which we named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of RabGGTase. Using a biotinylated geranylgeranyl analogue, we identified the Golgi SNARE protein Ykt6 as a substrate of GGTase-III. GGTase-III transfers a geranylgeranyl group to mono-farnesylated Ykt6, generating doubly prenylated Ykt6. The crystal structure of GGTase-III in complex with Ykt6 provides structural basis for Ykt6 double prenylation. In GGTase-III-deficient cells, Ykt6 remained in a singly prenylated form, and the Golgi SNARE complex assembly was severely impaired. Consequently, the Golgi apparatus was structurally disorganized, and intra-Golgi protein trafficking was delayed. Our findings reveal a fourth type of protein prenyltransferase that generates geranylgeranyl-farnesyl Ykt6. Double prenylation of Ykt6 is essential for the structural and functional organization of the Golgi apparatus.

PubMed: 32128853
DOI: 10.15252/embj.2019104120

Experimental method

X-RAY DIFFRACTION (2.883 Å)