5D94

Crystal structure of LC3-LIR peptide complex

Summary for 5D94

• Entry DOI: 10.2210/pdb5d94/pdb
• Descriptor: Microtubule-associated proteins 1A/1B light chain 3B, Peptide from FYVE and coiled-coil domain-containing protein 1 (3 entities in total)
• Functional Keywords: fyco1, autophagy, lc3, lir, protein binding-peptide complex, protein binding/peptide
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 16616.04

Authors

Takagi, K.,Mizushima, T.,Johansen, T. (deposition date: 2015-08-18, release date: 2015-10-21, Last modification date: 2024-03-20)

Primary citation

Olsvik, H.L.,Lamark, T.,Takagi, K.,Larsen, K.B.,Evjen, G.,vervatn, A.,Mizushima, T.,Johansen, T.
FYCO1 Contains a C-terminally Extended, LC3A/B-preferring LC3-interacting Region (LIR) Motif Required for Efficient Maturation of Autophagosomes during Basal Autophagy
J.Biol.Chem., 290:29361-29374, 2015

PubMed Abstract: FYCO1 (FYVE and coiled-coil protein 1) is a transport adaptor that binds to phosphatidylinositol 3-phosphate, to Rab7, and to LC3 (microtubule-associated protein 1 light chain 3) to mediate transport of late endosomes and autophagosomes along microtubules in the plus end direction. We have previously shown that FYCO1 binds to LC3B via a 19-amino acid sequence containing a putative core LC3-interacting region (LIR) motif. Here, we show that FYCO1 preferentially binds to LC3A and -B. By peptide array-based two-dimensional mutational scans of the binding to LC3B, we found FYCO1 to contain a C-terminally extended LIR domain. We determined the crystal structure of a complex between a 13-amino acid LIR peptide from FYCO1 and LC3B at 1.53 Å resolution. By combining the structural information with mutational analyses, both the basis for the C-terminally extended LIR and the specificity for LC3A/B binding were revealed. FYCO1 contains a 9-amino acid-long F-type LIR motif. In addition to the canonical aromatic residue at position 1 and the hydrophobic residue at position 3, an acidic residue and a hydrophobic residue at positions 8 and 9, respectively, are important for efficient binding to LC3B explaining the C-terminal extension. The specificity for binding to LC3A/B is due to the interaction between Asp(1285) in FYCO1 and His(57) in LC3B. To address the functional significance of the LIR motif of FYCO1, we generated FYCO1 knock-out cells that subsequently were reconstituted with GFP-FYCO1 WT and LIR mutant constructs. Our data show that FYCO1 requires a functional LIR motif to facilitate efficient maturation of autophagosomes under basal conditions, whereas starvation-induced autophagy was unaffected.

PubMed: 26468287
DOI: 10.1074/jbc.M115.686915

Experimental method

X-RAY DIFFRACTION (1.53 Å)