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New page: left|200px<br /><applet load="1xae" size="450" color="white" frame="true" align="right" spinBox="true" caption="1xae, resolution 2.7Å" /> '''Crystal structure of ... |
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== | ==Crystal structure of wild type yellow fluorescent protein zFP538 from Zoanthus== | ||
Crystal structures of the tetrameric yellow-fluorescent protein zFP538 | <StructureSection load='1xae' size='340' side='right'caption='[[1xae]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</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> | |||
<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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1xae" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Zoanthus sp]] | |||
[[Category: Anderson DC]] | |||
[[Category: Branchaud B]] | |||
[[Category: Kallio K]] | |||
[[Category: Lukyanov KA]] | |||
[[Category: Remington SJ]] | |||
[[Category: Wachter RM]] | |||
[[Category: Yarbrough DK]] | |||
Latest revision as of 09:43, 23 August 2023
Crystal structure of wild type yellow fluorescent protein zFP538 from ZoanthusCrystal structure of wild type yellow fluorescent protein zFP538 from Zoanthus
Structural highlights
FunctionGFPL2_ZOASP Pigment protein that is yellow in color.[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedCrystal 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. 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[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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