4kdv: Difference between revisions

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 ==Crystal structure of a bacterial immunoglobulin-like domain from the M. primoryensis ice-binding adhesin==
-<StructureSection load='4kdv' size='340' side='right' caption='[[4kdv]], [[Resolution|resolution]] 2.42&Aring;' scene=''>
+<StructureSection load='4kdv' size='340' side='right'caption='[[4kdv]], [[Resolution|resolution]] 2.42&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4kdv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Jcm_11775 Jcm 11775]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KDV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4kdv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Marinomonas_primoryensis Marinomonas primoryensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KDV 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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.42&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3p4g|3p4g]], [[4kdw|4kdw]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MpAFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=178399 JCM 11775])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4kdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdv OCA], [https://pdbe.org/4kdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kdv RCSB], [https://www.ebi.ac.uk/pdbsum/4kdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kdv ProSAT]</span></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=4kdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kdv OCA], [http://pdbe.org/4kdv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kdv RCSB], [http://www.ebi.ac.uk/pdbsum/4kdv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kdv ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/A1YIY3_9GAMM A1YIY3_9GAMM]
-A Ca2+ -dependent 1.5-MDa antifreeze protein present in an Antarctic Gram-negative bacterium, Marinomonas primoryensis (MpAFP), has recently been re-assessed as an ice-binding adhesin. The non-ice-binding region II (RII), one of five distinct domains in MpAFP, comprises ~90% of the protein. RII consists of approximately 120 tandem copies of an identical 104-aa (amino acid) sequence. We used the Protein Homology/analogy Recognition Engine server to define the boundaries of a single 104-aa RII construct (RII-monomer). Circular dichroism demonstrates that Ca2+ is required for RII-monomer folding and that the monomer is fully structured at a Ca2+ : protein molar ratio of 10:1. The crystal structure of the RII-monomer was solved to a resolution of 1.35 A by SAD and MR methods using Ca2+ as the heavy atom to obtain phase information. The RII-monomer folds as a Ca2+ -bound immunoglobulin-like beta-sandwich. Ca2+ ions are coordinated at the interfaces between each RII-monomer and its symmetry-related molecules, suggesting these ions may be involved in the stabilization of the tandemly repeated RII. We hypothesize that &gt;600 Ca2+ help rigidify the chain of 104-aa repeats in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed role of RII is to help the strictly aerobic bacterium bind surface ice in an Antarctic lake for better access to oxygen and nutrients. This work may give insights about other bacterial proteins that resemble MpAFP, especially those of the large Repeats-In-Toxin family that have been characterized as adhesins exported via the Type I secretion pathway. This article is protected by copyright. All rights reserved.
-Role of Ca in folding the tandem beta-sandwich extender domains of a bacterial ice-binding adhesin.,Guo S, Garnham CP, Karunan SP, Campbell RL, Allingham JS, Davies PL FEBS J. 2013 Sep 11. doi: 10.1111/febs.12518. PMID:24024640<ref>PMID:24024640</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4kdv" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Antifreeze protein|Antifreeze protein]]
+*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Jcm 11775]]
+[[Category: Large Structures]]
-[[Category: Allingham, J S]]
+[[Category: Marinomonas primoryensis]]
-[[Category: Campbell, R L]]
+[[Category: Allingham JS]]
-[[Category: Davies, P L]]
+[[Category: Campbell RL]]
-[[Category: Garnham, C P]]
+[[Category: Davies PL]]
-[[Category: Guo, S]]
+[[Category: Garnham CP]]
-[[Category: Karunan, S P]]
+[[Category: Guo S]]
-[[Category: Adhesion protein]]
+[[Category: Karunan SP]]
-[[Category: Bacterial immunoglobulin-like beta-sandwich]]
-[[Category: Ca2+ -dependent]]
-[[Category: Cell adhesion]]
-[[Category: Extender domain]]