 | Acta Crystallographica Section F Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS |
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![[Figure 4]](nj5303fig4mag.jpg)
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Figure 4
Comparison of phenylalanine-directed crystal contacts between HP1 of neighbouring molecules with canonical and noncanonical LIR peptides. (a) The interface between Phe117 (red) of GABARAPL2 (deep purple) and the HP1 pocket (yellow) of a neighbouring molecule in PDB entry 7lk3 and (b) the interface of an alternative crystal contact that can form between Phe115 (red) of GABARAPL2 (purple) and HP1 of a neighbouring molecule (PDB entry 1eo6). (c) The only structure of GABARAPL2 (magenta) bound to a LIR peptide (green) is noncanonical and binds in an atypical manner (PDB entry 6h8c). The UBA5 LIR peptide contains two extra residues within the core LIR, flanked by the typical aromatic residue at position 0 (Trp341), which binds to a novel HP0 pocket (olive). However, the aliphatic residue (Val346) that typically occurs at the +3 position in canonical LIR motifs is in the +6 position and binds to the HP2 pocket (purple), modifying the topology of the HP1 pocket. (d) GABARAPL1 (pink) bound to the Atg4B LIR (blue) (PDB entry 5lxh; Skytte Rasmussen et al., 2017  ) provides an example of how a canonical LIR peptide binds to the Atg8 HP1 pocket and adopts a similar conformation to the GABARAPL2 Phe117–HP1 crystal contact seen in PDB entry 7lk3. PDB entry 5lxh was used as an example as there are no GABARAPL2 structures bound to canonical LIR peptides available in the PDB, and the 0 residue of the Atg4B LIR peptide is a phenylalanine, as per the interface of PDB entry 7lk3. This Phe388 residue inserts into the HP1 pocket (yellow) of GABARAPL1, and Leu391 at the +3 position inserts into the HP2 pocket (light purple). |
![[Figure 4]](nj5303fig4.jpg)
| STRUCTURAL BIOLOGY COMMUNICATIONS |
ISSN: 2053-230X
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