2zib: Difference between revisions

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-{{Seed}}
-[[Image:2zib.png|left|200px]]
-<!--
+==Crystal structure analysis of calcium-independent type II antifreeze protein==
-The line below this paragraph, containing "STRUCTURE_2zib", creates the "Structure Box" on the page.
+<StructureSection load='2zib' size='340' side='right'caption='[[2zib]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2zib]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Brachyopsis_segaliensis Brachyopsis segaliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZIB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZIB FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.34&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2zib|  PDB=2zib  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zib OCA], [https://pdbe.org/2zib PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zib RCSB], [https://www.ebi.ac.uk/pdbsum/2zib PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zib ProSAT]</span></td></tr>
+</table>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/2zib_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zib ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We recently found that longsnout poacher (Brachyosis rostratus) produces a Ca(2+)-independent type II antifreeze protein (lpAFP) and succeeded in expressing recombinant lpAFP using Phichia pastoris. Here, we report, for the first time, the X-ray crystal structure of lpAFP at 1.34 A resolution. The lpAFP structure displayed a relatively planar surface, which encompasses two loop regions (Cys86-Lys89 and Asn91-Cys97) and a short beta-strand (Trp109-Leu112) with three unstructured segments (Gly57-Ile58, Ala103-Ala104, and Pro113-His118). Electrostatic calculation of the protein surface showed that the relatively planar surface was divided roughly into a hydrophobic area (composed of the three unstructured segments lacking secondary structure) and a hydrophilic area (composed of the loops and beta-strand). Site-directed mutation of Ile58 with Phe at the center of the hydrophobic area decreased activity significantly, whereas mutation of Leu112 with Phe at an intermediate area between the hydrophobic and hydrophilic areas retained complete activity. In the hydrophilic area, a peptide-swap mutant in the loops retained 60% activity despite simultaneous mutations of eight residues. We conclude that the epicenter of the ice-binding site of lpAFP is the hydrophobic region, which is centered by Ile58, in the relatively planar surface. We built an ice-binding model for lpAFP on the basis of a lattice match of ice and constrained water oxygen atoms surrounding the hydrophobic area in the lpAFP structure. The model in which lpAFP has been docked to a secondary prism (2-1-10) plane, which is different from the one determined for Ca(2+)-independent type II AFP from sea raven (11-21), appears to explain the results of the mutagenesis analysis.
-===Crystal structure analysis of calcium-independent type II antifreeze protein===
+Crystal structure and mutational analysis of Ca2+-independent type II antifreeze protein from longsnout poacher, Brachyopsis rostratus.,Nishimiya Y, Kondo H, Takamichi M, Sugimoto H, Suzuki M, Miura A, Tsuda S J Mol Biol. 2008 Oct 10;382(3):734-46. Epub 2008 Jul 22. PMID:18674542<ref>PMID:18674542</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2zib" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18674542}}, adds the Publication Abstract to the page
+*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18674542 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18674542}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Brachyopsis segaliensis]]
-ZIB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Brachyopsis_rostratus Brachyopsis rostratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZIB OCA].
+[[Category: Large Structures]]
+[[Category: Kondo H]]
-==Reference==
+[[Category: Nishimiya Y]]
-Crystal Structure and Mutational Analysis of Ca(2+)-Independent Type II Antifreeze Protein from Longsnout Poacher, Brachyopsis rostratus., Nishimiya Y, Kondo H, Takamichi M, Sugimoto H, Suzuki M, Miura A, Tsuda S, J Mol Biol. 2008 Jul 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18674542 18674542]
+[[Category: Noro N]]
-[[Category: Brachyopsis rostratus]]
+[[Category: Sato R]]
-[[Category: Single protein]]
+[[Category: Sugimoto H]]
-[[Category: Kondo, H.]]
+[[Category: Suzuki M]]
-[[Category: Nishimiya, Y.]]
+[[Category: Tsuda S]]
-[[Category: Noro, N.]]
-[[Category: Sato, R.]]
-[[Category: Sugimoto, H.]]
-[[Category: Suzuki, M.]]
-[[Category: Tsuda, S.]]
-[[Category: Antifreeze protein]]
-[[Category: Lectin]]
-[[Category: Thermal hysteresis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov  5 10:37:44 2008''