2PY2
Structure of Herring Type II Antifreeze Protein
Summary for 2PY2
| Entry DOI | 10.2210/pdb2py2/pdb |
| Descriptor | Antifreeze protein type II, CALCIUM ION (3 entities in total) |
| Functional Keywords | type ii antifreeze protein, antifreeze protein |
| Biological source | Clupea harengus (Atlantic herring) |
| Total number of polymer chains | 6 |
| Total formula weight | 92990.82 |
| Authors | Liu, Y.,Li, Z.,Lin, Q.,Seetharaman, J.,Sivaraman, J.,Hew, C.-L. (deposition date: 2007-05-15, release date: 2007-06-26, Last modification date: 2024-11-20) |
| Primary citation | Liu, Y.,Li, Z.,Lin, Q.,Kosinski, J.,Seetharaman, J.,Bujnicki, J.M.,Sivaraman, J.,Hew, C.L. Structure and Evolutionary Origin of Ca-Dependent Herring Type II Antifreeze Protein. PLoS ONE, 2:e548-e548, 2007 Cited by PubMed Abstract: In order to survive under extremely cold environments, many organisms produce antifreeze proteins (AFPs). AFPs inhibit the growth of ice crystals and protect organisms from freezing damage. Fish AFPs can be classified into five distinct types based on their structures. Here we report the structure of herring AFP (hAFP), a Ca(2+)-dependent fish type II AFP. It exhibits a fold similar to the C-type (Ca(2+)-dependent) lectins with unique ice-binding features. The 1.7 A crystal structure of hAFP with bound Ca(2+) and site-directed mutagenesis reveal an ice-binding site consisting of Thr96, Thr98 and Ca(2+)-coordinating residues Asp94 and Glu99, which initiate hAFP adsorption onto the [10-10] prism plane of the ice lattice. The hAFP-ice interaction is further strengthened by the bound Ca(2+) through the coordination with a water molecule of the ice lattice. This Ca(2+)-coordinated ice-binding mechanism is distinct from previously proposed mechanisms for other AFPs. However, phylogenetic analysis suggests that all type II AFPs evolved from the common ancestor and developed different ice-binding modes. We clarify the evolutionary relationship of type II AFPs to sugar-binding lectins. PubMed: 17579720DOI: 10.1371/journal.pone.0000548 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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