6JK5

Ca2+-dependent type II antifreeze protein (Ca2+-free form)

Summary for 6JK5

• Entry DOI: 10.2210/pdb6jk5/pdb
• Related: 6JK4
• Descriptor: Type II antifreeze protein, SULFATE ION (3 entities in total)
• Functional Keywords: antifreeze protein, c-type lectin, ice-binding protein
• Biological source: Hypomesus nipponensis (Japanese smelt)
• Total number of polymer chains: 1
• Total formula weight: 15417.12

Authors

Arai, T.,Tsuda, S.,Kondo, H.,Nishimiya, Y. (deposition date: 2019-02-27, release date: 2019-06-26, Last modification date: 2024-10-30)

Primary citation

Arai, T.,Nishimiya, Y.,Ohyama, Y.,Kondo, H.,Tsuda, S.
Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface.
Biomolecules, 9:-, 2019

PubMed Abstract: Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca-dependent species of AFP, however, it has not been clarified how 1 mol of Ca-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca-dependent AFP (jsAFP) from Japanese smelt, , in both Ca-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca-binding site. Firstly, the side-chains of four of the five Ca-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca-bound state. Second, a Ca-binding loop consisting of a segment D94-E99 becomes less flexible by the Ca-binding. Third, the Ca-binding induces a generation of ice-like clathrate waters around the Ca-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca-binding enables the ice-binding of this protein.

PubMed: 31035615
DOI: 10.3390/biom9050162

Experimental method

X-RAY DIFFRACTION (1.25 Å)