3UYV: Crystal Structure Of A Glycosylated Ice-Binding Protein (Leibp) From Arctic Yeast

Arctic yeast Leucosporidium sp. produces a glycosylated ice-binding protein (LeIBP) with a molecular mass of approximately 25 kDa, which can lower the freezing point below the melting point once it binds to ice. LeIBP is a member of a large class of ice-binding proteins, the structures of which are unknown. Here, we report the crystal structures of non-glycosylated LeIBP and glycosylated LeIBP at 1.57 A and 2.43 A resolution, respectively. Structural analysis of the LeIBPs revealed a dimeric right-handed beta-helix fold, which is composed of three parts: a large coiled structural domain, a long helix region (residues 96-115 form a long alpha-helix that packs along one face of the beta-helix) and a C-terminal hydrophobic loop region (243-PFVPAPEVV-251). Unexpectedly, the C-terminal hydrophobic loop region has an extended conformation pointing away from the body of the coiled structural domain and forms intertwined dimer interactions. In addition, structural analysis of glycosylated LeIBP with sugar moieties attached to Asn185 provides a basis for interpreting previous biochemical analyses as well as the increased stability and secretion of glycosylated LeIBP. We also determined that the aligned Thr/Ser/Ala residues are critical for ice binding within the B face of LeIBP using site-directed mutagenesis. Although LeIBP has a common beta-helical fold similar to that of canonical hyperactive antifreeze proteins, the ice-binding site is more complex and does not have a simple ice-binding motif. In conclusion, we could identify the ice-binding site of LeIBP and discuss differences in the ice-binding modes compared to other known AFPs and IBPs.
PDB ID: 3UYVDownload
MMDB ID: 97639
PDB Deposition Date: 2011/12/6
Updated in MMDB: 2012/03
Experimental Method:
x-ray diffraction
Resolution: 2.43  Å
Source Organism:
Similar Structures:
Biological Unit for 3UYV: dimeric; determined by author and by software (PISA)
Molecular Components in 3UYV
Label Count Molecule
Proteins (2 molecules)
Antifreeze Protein
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB