2ZZP

The crystal structure of human Atg4B(C74S)- LC3(1-124) complex

Summary for 2ZZP

• Entry DOI: 10.2210/pdb2zzp/pdb
• Descriptor: Cysteine protease ATG4B, Microtubule-associated proteins 1A/1B light chain 3B (3 entities in total)
• Functional Keywords: papain-like fold, ubiquitin fold, alternative splicing, autophagy, cytoplasm, hydrolase, phosphoprotein, polymorphism, protease, protein transport, thiol protease, transport, ubl conjugation pathway, cytoplasmic vesicle, lipoprotein, membrane, microtubule, hydrolase-structural protein complex, hydrolase/structural protein
• Biological source: Homo sapiens (human); More
• Cellular location: Cytoplasm (Probable): Q9Y4P1; Cytoplasm, cytoskeleton: Q62625
• Total number of polymer chains: 2
• Total formula weight: 55094.77

Authors

Satoo, K.,Noda, N.N.,Inagaki, F. (deposition date: 2009-02-22, release date: 2009-03-03, Last modification date: 2023-11-01)

Primary citation

Satoo, K.,Noda, N.N.,Kumeta, H.,Fujioka, Y.,Mizushima, N.,Ohsumi, Y.,Inagaki, F.
The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy.
Embo J., 28:1341-1350, 2009

PubMed Abstract: Atg8 is conjugated to phosphatidylethanolamine (PE) by ubiquitin-like conjugation reactions. Atg8 has at least two functions in autophagy: membrane biogenesis and target recognition. Regulation of PE conjugation and deconjugation of Atg8 is crucial for these functions in which Atg4 has a critical function by both processing Atg8 precursors and deconjugating Atg8-PE. Here, we report the crystal structures of catalytically inert human Atg4B (HsAtg4B) in complex with processed and unprocessed forms of LC3, a mammalian orthologue of yeast Atg8. On LC3 binding, the regulatory loop and the N-terminal tail of HsAtg4B undergo large conformational changes. The regulatory loop masking the entrance of the active site of free HsAtg4B is lifted by LC3 Phe119, so that a groove is formed along which the LC3 tail enters the active site. At the same time, the N-terminal tail masking the exit of the active site of HsAtg4B in the free form is detached from the enzyme core and a large flat surface is exposed, which might enable the enzyme to access the membrane-bound LC3-PE.

PubMed: 19322194
DOI: 10.1038/emboj.2009.80

Experimental method

X-RAY DIFFRACTION (2.05 Å)