5XQP

Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), P212121 form

Summary for 5XQP

• Entry DOI: 10.2210/pdb5xqp/pdb
• Descriptor: Ice-structuring protein, SULFATE ION (3 entities in total)
• Functional Keywords: antifreeze protein
• Biological source: Zoarces elongatus
• Total number of polymer chains: 4
• Total formula weight: 28409.42

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

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: 29735675
DOI: 10.1073/pnas.1800635115

Experimental method

X-RAY DIFFRACTION (1 Å)