6jk4: Difference between revisions

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'''Unreleased structure'''


The entry 6jk4 is ON HOLD  until Paper Publication
==Ca2+-dependent type II antifreeze protein==
<StructureSection load='6jk4' size='340' side='right'caption='[[6jk4]], [[Resolution|resolution]] 1.06&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6jk4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JK4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6jk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jk4 OCA], [http://pdbe.org/6jk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jk4 RCSB], [http://www.ebi.ac.uk/pdbsum/6jk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jk4 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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(2+)-dependent species of AFP, however, it has not been clarified how 1 mol of Ca(2+)-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca(2+)-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca(2+)-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Calpha = 0.31 A), while they exhibited a significant difference around their Ca(2+)-binding site. Firstly, the side-chains of four of the five Ca(2+)-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca(2+)-bound state. Second, a Ca(2+)-binding loop consisting of a segment D94-E99 becomes less flexible by the Ca(2+)-binding. Third, the Ca(2+)-binding induces a generation of ice-like clathrate waters around the Ca(2+)-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(2+)-binding enables the ice-binding of this protein.


Authors:  
Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface.,Arai T, Nishimiya Y, Ohyama Y, Kondo H, Tsuda S Biomolecules. 2019 Apr 27;9(5). pii: biom9050162. doi: 10.3390/biom9050162. PMID:31035615<ref>PMID:31035615</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 6jk4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Arai, T]]
[[Category: Kondo, H]]
[[Category: Nishimiya, Y]]
[[Category: Tsuda, S]]
[[Category: Antifreeze protein]]
[[Category: C-type lectin]]
[[Category: Ice-binding protein]]
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