2ib5: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2ib5.png|left|200px]]
-<!--
+==Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus==
-The line below this paragraph, containing "STRUCTURE_2ib5", creates the "Structure Box" on the page.
+<StructureSection load='2ib5' size='340' side='right'caption='[[2ib5]], [[Resolution|resolution]] 1.80&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'>[[2ib5]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Epiactis_japonica Epiactis japonica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IB5 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRQ:[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC+ACID'>CRQ</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_2ib5|  PDB=2ib5  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ib5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ib5 OCA], [https://pdbe.org/2ib5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ib5 RCSB], [https://www.ebi.ac.uk/pdbsum/2ib5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ib5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0AQQ7_EPIJA A0AQQ7_EPIJA]
+== 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/ib/2ib5_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=2ib5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Green fluorescent protein (GFP) and its relatives (GFP protein family) have been isolated from marine organisms such as jellyfish and corals that belong to the phylum Cnidaria (stinging aquatic invertebrates). They are intrinsically fluorescent proteins. In search of new members of the family of green fluorescent protein family, we identified a non-fluorescent chromoprotein from the Cnidopus japonicus species of sea anemone that possesses 45% sequence identity to dsRed (a red fluorescent protein). This newly identified blue color protein has an absorbance maximum of 610 nm and is hereafter referred to as cjBlue. Determination of the cjBlue 1.8 A crystal structure revealed a chromophore comprised of Gln(63)-Tyr(64)-Gly(65). The ring stacking between Tyr(64) and His(197) stabilized the cjBlue trans chromophore conformation along the Calpha2-Cbeta2 bond of 5-[(4-hydroxyphenyl)methylene]-imidazolinone, which closely resembled that of the "Kindling Fluorescent Protein" and Rtms5. Replacement of Tyr(64) with Leu in wild-type cjBlue produced a visible color change from blue to yellow with a new absorbance maximum of 417 nm. Interestingly, the crystal structure of the yellow mutant Y64L revealed two His(197) imidazole ring orientations, suggesting a flip-flop interconversion between the two conformations in solution. We conclude that the dynamics and structure of the chromophore are both essential for the optical appearance of these color proteins.
-===Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus===
+Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone Cnidopus japonicus.,Chan MC, Karasawa S, Mizuno H, Bosanac I, Ho D, Prive GG, Miyawaki A, Ikura M J Biol Chem. 2006 Dec 8;281(49):37813-9. Epub 2006 Oct 6. PMID:17028187<ref>PMID:17028187</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17028187}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ib5" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17028187 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17028187}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Epiactis japonica]]
-IB5 is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Cnidopus_japonicus Cnidopus japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IB5 OCA].
+[[Category: Large Structures]]
+[[Category: Bosanac I]]
-==Reference==
+[[Category: Chan MCY]]
-<ref group="xtra">PMID:17028187</ref><references group="xtra"/>
+[[Category: Ikura M]]
-[[Category: Cnidopus japonicus]]
-[[Category: Bosanac, I.]]
-[[Category: Chan, M C.Y.]]
-[[Category: Ikura, M.]]
-[[Category: Alpha helix]]
-[[Category: Beta barrel]]
-[[Category: Blue]]
-[[Category: Chromophore]]
-[[Category: Chromoprotein]]
-[[Category: Gfp-like protein]]
-[[Category: Luminescent protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May  6 09:17:46 2009''