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5XQR

Crystal structure of Notched-fin eelpout type III antifreeze protein A20V mutant (NFE6, AFP), C2221 form

Summary for 5XQR
Entry DOI10.2210/pdb5xqr/pdb
DescriptorIce-structuring protein, ACETATE ION (3 entities in total)
Functional Keywordstype iii, notched-fin eelpout, antifreeze protein
Biological sourceZoarces elongatus
Total number of polymer chains2
Total formula weight14186.78
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 citationMahatabuddin, 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: 29735675
DOI: 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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