2vae: Difference between revisions

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-[[Image:2vae.jpg|left|200px]]<br /><applet load="2vae" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2vae, resolution 1.64&Aring;" />
-'''FAST MATURING RED FLUORESCENT PROTEIN, DSRED.T4'''<br />
-==Overview==
+==Fast maturing red fluorescent protein, DsRed.T4==
-The red fluorescent protein DsRed has been extensively engineered for use, as an in vivo research tool. In fast maturing DsRed variants, the, chromophore maturation half-time is approximately 40 min, compared to, approximately 12 h for wild-type DsRed. Further, DsRed has been converted, from a tetramer into a monomer, a task that entailed mutating, approximately 20% of the amino acids. These engineered variants of DsRed, have proven extremely valuable for biomedical research, but the structural, basis for the improved characteristics has not been thoroughly, investigated. Here we present a 1.7 A crystal structure of the fast, maturing tetrameric variant DsRed.T4. We also present a biochemical, characterization and 1.6 A crystal structure of the monomeric variant, DsRed.M1, also known as DsRed-Monomer. Analysis of the crystal structures, suggests that rearrangements of Ser69 and Glu215 contribute to fast, maturation, and that positioning of the Lys70 side chain modulates, fluorescence quantum yield. Despite the 45 mutations in DsRed.M1 relative, to wild-type DsRed, there is a root-mean-square deviation of only 0.3 A, between the two structures. We propose that novel intramolecular, interactions in DsRed.M1 partially compensate for the loss of, intermolecular interactions found in the tetramer.
+<StructureSection load='2vae' size='340' side='right'caption='[[2vae]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2vae]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Discosoma_sp. Discosoma sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VAE 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]] 1.64&#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=EDO:1,2-ETHANEDIOL'>EDO</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=2vae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vae OCA], [https://pdbe.org/2vae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vae RCSB], [https://www.ebi.ac.uk/pdbsum/2vae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vae ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RFP_DISSP RFP_DISSP] Thought to play a role in photoprotection of the coral's resident symbiont microalgae's photosystems from photoinhibition caused by high light levels found near the surface of coral reefs. In deeper water, the fluorescence may be to convert blue light into longer wavelengths more suitable for use in photosynthesis by the microalgal symbionts.<ref>PMID:10504696</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/va/2vae_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=2vae ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The red fluorescent protein DsRed has been extensively engineered for use as an in vivo research tool. In fast maturing DsRed variants, the chromophore maturation half-time is approximately 40 min, compared to approximately 12 h for wild-type DsRed. Further, DsRed has been converted from a tetramer into a monomer, a task that entailed mutating approximately 20% of the amino acids. These engineered variants of DsRed have proven extremely valuable for biomedical research, but the structural basis for the improved characteristics has not been thoroughly investigated. Here we present a 1.7 A crystal structure of the fast maturing tetrameric variant DsRed.T4. We also present a biochemical characterization and 1.6 A crystal structure of the monomeric variant DsRed.M1, also known as DsRed-Monomer. Analysis of the crystal structures suggests that rearrangements of Ser69 and Glu215 contribute to fast maturation, and that positioning of the Lys70 side chain modulates fluorescence quantum yield. Despite the 45 mutations in DsRed.M1 relative to wild-type DsRed, there is a root-mean-square deviation of only 0.3 A between the two structures. We propose that novel intramolecular interactions in DsRed.M1 partially compensate for the loss of intermolecular interactions found in the tetramer.
-==About this Structure==
+Structural rearrangements near the chromophore influence the maturation speed and brightness of DsRed variants.,Strongin DE, Bevis B, Khuong N, Downing ME, Strack RL, Sundaram K, Glick BS, Keenan RJ Protein Eng Des Sel. 2007 Nov;20(11):525-34. Epub 2007 Oct 25. PMID:17962222<ref>PMID:17962222</ref>
-VAE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Discosoma_sp. Discosoma sp.] with <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Sites: <scene name='pdbsite=AC1:Edo+Binding+Site+For+Chain+D'>AC1</scene>, <scene name='pdbsite=AC2:Edo+Binding+Site+For+Chain+C'>AC2</scene>, <scene name='pdbsite=AC3:Edo+Binding+Site+For+Chain+H'>AC3</scene>, <scene name='pdbsite=AC4:Edo+Binding+Site+For+Chain+B'>AC4</scene>, <scene name='pdbsite=AC5:Edo+Binding+Site+For+Chain+G'>AC5</scene>, <scene name='pdbsite=AC6:Edo+Binding+Site+For+Chain+C'>AC6</scene>, <scene name='pdbsite=AC7:Edo+Binding+Site+For+Chain+F'>AC7</scene>, <scene name='pdbsite=AC8:Edo+Binding+Site+For+Chain+A'>AC8</scene>, <scene name='pdbsite=AC9:Edo+Binding+Site+For+Chain+D'>AC9</scene>, <scene name='pdbsite=BC1:Edo+Binding+Site+For+Chain+D'>BC1</scene>, <scene name='pdbsite=BC2:Edo+Binding+Site+For+Chain+C'>BC2</scene>, <scene name='pdbsite=BC3:Edo+Binding+Site+For+Chain+E'>BC3</scene>, <scene name='pdbsite=BC4:Edo+Binding+Site+For+Chain+C'>BC4</scene>, <scene name='pdbsite=BC5:Edo+Binding+Site+For+Chain+F'>BC5</scene>, <scene name='pdbsite=BC6:Edo+Binding+Site+For+Chain+G'>BC6</scene>, <scene name='pdbsite=BC7:Edo+Binding+Site+For+Chain+H'>BC7</scene>, <scene name='pdbsite=BC8:Edo+Binding+Site+For+Chain+H'>BC8</scene>, <scene name='pdbsite=BC9:Edo+Binding+Site+For+Chain+A'>BC9</scene>, <scene name='pdbsite=CC1:Edo+Binding+Site+For+Chain+B'>CC1</scene>, <scene name='pdbsite=CC2:Edo+Binding+Site+For+Chain+F'>CC2</scene>, <scene name='pdbsite=CC3:Edo+Binding+Site+For+Chain+H'>CC3</scene>, <scene name='pdbsite=CC4:Edo+Binding+Site+For+Chain+B'>CC4</scene>, <scene name='pdbsite=CC5:Edo+Binding+Site+For+Chain+H'>CC5</scene>, <scene name='pdbsite=CC6:Edo+Binding+Site+For+Chain+F'>CC6</scene>, <scene name='pdbsite=CC7:Edo+Binding+Site+For+Chain+E'>CC7</scene>, <scene name='pdbsite=CC8:Edo+Binding+Site+For+Chain+A'>CC8</scene> and <scene name='pdbsite=CC9:Edo+Binding+Site+For+Chain+B'>CC9</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAE OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural rearrangements near the chromophore influence the maturation speed and brightness of DsRed variants., Strongin DE, Bevis B, Khuong N, Downing ME, Strack RL, Sundaram K, Glick BS, Keenan RJ, Protein Eng Des Sel. 2007 Oct 25;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17962222 17962222]
+</div>
-[[Category: Discosoma sp.]]
+<div class="pdbe-citations 2vae" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
-[[Category: Bevis, B.]]
-[[Category: Downing, M.E.]]
-[[Category: Glick, B.S.]]
-[[Category: Keenan, R.J.]]
-[[Category: Khuong, N.]]
-[[Category: Strack, R.L.]]
-[[Category: Strongin, D.E.]]
-[[Category: Sundaram, K.]]
-[[Category: EDO]]
-[[Category: chromophore]]
-[[Category: dsred]]
-[[Category: fast maturing]]
-[[Category: fluorescent protein]]
-[[Category: gfp-like]]
-[[Category: luminescence]]
-[[Category: photoprotein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 10:50:53 2008''
+==See Also==
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Discosoma sp]]
+[[Category: Large Structures]]
+[[Category: Bevis B]]
+[[Category: Downing ME]]
+[[Category: Glick BS]]
+[[Category: Keenan RJ]]
+[[Category: Khuong N]]
+[[Category: Strack RL]]
+[[Category: Strongin DE]]
+[[Category: Sundaram K]]