1xae: Difference between revisions

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-{{Seed}}
-[[Image:1xae.png|left|200px]]
-<!--
+==Crystal structure of wild type yellow fluorescent protein zFP538 from Zoanthus==
-The line below this paragraph, containing "STRUCTURE_1xae", creates the "Structure Box" on the page.
+<StructureSection load='1xae' size='340' side='right'caption='[[1xae]], [[Resolution|resolution]] 2.70&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'>[[1xae]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoanthus_sp. Zoanthus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XAE 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]] 2.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CH7:[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CH7</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</scene></td></tr>
-{{STRUCTURE_1xae|  PDB=1xae  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xae OCA], [https://pdbe.org/1xae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xae RCSB], [https://www.ebi.ac.uk/pdbsum/1xae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xae ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GFPL2_ZOASP GFPL2_ZOASP] Pigment protein that is yellow in color.<ref>PMID:10504696</ref> <ref>PMID:15628861</ref>
+== 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/xa/1xae_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1xae ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures of the tetrameric yellow-fluorescent protein zFP538 from the button polyp Zoanthus sp. and a green-emitting mutant (K66M) are presented. The atomic models have been refined at 2.7 and 2.5 A resolution, with final crystallographic R factors of 0.206 (R(free) = 0.255) and 0.190 (R(free) = 0.295), respectively, and have excellent stereochemistry. The fold of the protomer is very similar to that of green (GFP) and red (DsRed) fluorescent proteins; however, evidence from crystallography and mass spectrometry suggests that zFP538 contains a three-ring chromophore derived from that of GFP. The yellow-emitting species (lambda(em)(max) = 538 nm) is proposed to result from a transimination reaction in which a transiently appearing DsRed-like acylimine is attacked by the terminal amino group of lysine 66 to form a new six-membered ring, cleaving the polypeptide backbone at the 65-66 position. This extends the chromophore conjugation by an additional double bond compared to GFP, lowering the absorption and emission frequencies. Substitution of lysine 66 with aspartate or glutamate partially converts zFP538 into a red-fluorescent protein, providing additional support for an acylimine intermediate. The diverse and unexpected roles of the side chain at position 66 give new insight into the chemistry of chromophore maturation in the extended family of GFP-like proteins.
-===Crystal structure of wild type yellow fluorescent protein zFP538 from Zoanthus===
+zFP538, a yellow-fluorescent protein from Zoanthus, contains a novel three-ring chromophore.,Remington SJ, Wachter RM, Yarbrough DK, Branchaud B, Anderson DC, Kallio K, Lukyanov KA Biochemistry. 2005 Jan 11;44(1):202-12. PMID:15628861<ref>PMID:15628861</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1xae" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15628861}}, adds the Publication Abstract to the page
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15628861 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15628861}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-XAE is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Zoanthus_sp. Zoanthus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XAE OCA].
+[[Category: Zoanthus sp]]
+[[Category: Anderson DC]]
-==Reference==
+[[Category: Branchaud B]]
-<ref group="xtra">PMID:15628861</ref><references group="xtra"/>
+[[Category: Kallio K]]
-[[Category: Zoanthus sp.]]
+[[Category: Lukyanov KA]]
-[[Category: Anderson, D C.]]
+[[Category: Remington SJ]]
-[[Category: Branchaud, B.]]
+[[Category: Wachter RM]]
-[[Category: Kallio, K.]]
+[[Category: Yarbrough DK]]
-[[Category: Lukyanov, K A.]]
-[[Category: Remington, S J.]]
-[[Category: Wachter, R M.]]
-[[Category: Yarbrough, D K.]]
-[[Category: Beta-barrel]]
-[[Category: Beta-can]]
-[[Category: Fluorescent protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:28:10 2009''