5XQR
Crystal structure of Notched-fin eelpout type III antifreeze protein A20V mutant (NFE6, AFP), C2221 form
Summary for 5XQR
Entry DOI | 10.2210/pdb5xqr/pdb |
Descriptor | Ice-structuring protein, ACETATE ION (3 entities in total) |
Functional Keywords | type iii, notched-fin eelpout, antifreeze protein |
Biological source | Zoarces elongatus |
Total number of polymer chains | 2 |
Total formula weight | 14186.78 |
Authors | Adachi, M.,Shimizu, R.,Shibazaki, C.,Kondo, H.,Tsuda, S. (deposition date: 2017-06-07, release date: 2018-05-16, Last modification date: 2023-11-22) |
Primary citation | Mahatabuddin, S.,Fukami, D.,Arai, T.,Nishimiya, Y.,Shimizu, R.,Shibazaki, C.,Kondo, H.,Adachi, M.,Tsuda, S. Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein Proc. Natl. Acad. Sci. U.S.A., 115:5456-5461, 2018 Cited by PubMed Abstract: Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in ice-binding, we determined X-ray crystal structures of a 65-residue defective isoform of a -derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of ∼50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the [Formula: see text] first prism plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the [Formula: see text] pyramidal ice plane. The order of ice-binding strength was A20L < A20G < WT < A20T < A20V < A20I, where the top three mutants capable of binding to the first prism and the pyramidal ice planes commonly contained a bifurcated γ-CH group. These results suggest that a fine-tuning of the surface of -derived IBP assisted by a side-chain group regulates the holding property of its polypentagonal water network, the function of which is to freeze the host protein to specific ice planes. PubMed: 29735675DOI: 10.1073/pnas.1800635115 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (1.3 Å) |
Structure validation
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