2vad: Difference between revisions

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-{{Seed}}
-[[Image:2vad.png|left|200px]]
-<!--
+==Monomeric red fluorescent protein, DsRed.M1==
-The line below this paragraph, containing "STRUCTURE_2vad", creates the "Structure Box" on the page.
+<StructureSection load='2vad' size='340' side='right'caption='[[2vad]], [[Resolution|resolution]] 1.59&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'>[[2vad]] is a 1 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=2VAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VAD 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]] 1.59&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2vad|  PDB=2vad  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vad OCA], [https://pdbe.org/2vad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vad RCSB], [https://www.ebi.ac.uk/pdbsum/2vad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vad 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/2vad_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=2vad 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.
-===MONOMERIC RED FLUORESCENT PROTEIN, DSRED.M1===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vad" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17962222}}, 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 17962222 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17962222}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Discosoma sp]]
-VAD is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Discosoma_sp. Discosoma sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAD OCA].
+[[Category: Large Structures]]
+[[Category: Bevis B]]
-==Reference==
+[[Category: Downing ME]]
-<ref group="xtra">PMID:17962222</ref><references group="xtra"/>
+[[Category: Glick BS]]
-[[Category: Discosoma sp.]]
+[[Category: Keenan RJ]]
-[[Category: Bevis, B.]]
+[[Category: Khuong N]]
-[[Category: Downing, M E.]]
+[[Category: Strack RL]]
-[[Category: Glick, B S.]]
+[[Category: Strongin DE]]
-[[Category: Keenan, R J.]]
+[[Category: Sundaram K]]
-[[Category: Khuong, N.]]
-[[Category: Strack, R L.]]
-[[Category: Strongin, D E.]]
-[[Category: Sundaram, K.]]
-[[Category: Chromophore]]
-[[Category: Dsred]]
-[[Category: Fluorescent protein]]
-[[Category: Gfp-like]]
-[[Category: Luminescence]]
-[[Category: Monomeric]]
-[[Category: Photoprotein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:31:33 2009''