1f09: Difference between revisions

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<StructureSection load='1f09' size='340' side='right'caption='[[1f09]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
<StructureSection load='1f09' size='340' side='right'caption='[[1f09]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1f09]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeqvi Aeqvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F09 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1f09]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F09 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.14&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yfp|1yfp]], [[2yfp|2yfp]], [[1f0b|1f0b]]</div></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=1f09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f09 OCA], [https://pdbe.org/1f09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f09 RCSB], [https://www.ebi.ac.uk/pdbsum/1f09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f09 ProSAT]</span></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=1f09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f09 OCA], [https://pdbe.org/1f09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f09 RCSB], [https://www.ebi.ac.uk/pdbsum/1f09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f09 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.  
[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1f09 ConSurf].
</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=1f09 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The fluorescence emission of yellow fluorescent proteins (YFPs) has been shown to respond rapidly and reversibly to changes in the concentration of some small anions such as halides; this allows for the use of YFPs as genetically encodable Cl(-) sensors that may be targeted to specific organelles in living cells. Fluorescence is suppressed due to protonation of the chromophore upon anion binding, with a stronger level of interaction at low pH values. At pH 6.0, the apparent dissociation constant (K(app)) for Cl(-) is 32 mM for YFP and 22 mM for YFP-H148Q, whereas at pH 7.5, K(app) is 777 mM and 154 mM, respectively. In the cytosol, YFP-H148Q appears most promising as a halide sensor due to its high degree of sensitivity towards I(-) (K(app)=23 mM at pH 7.5). To aid in the design of variants with improved levels of specificity and affinity for Cl(-), we solved apo and I(-)-bound crystal structures of YFP-H148Q to 2.1 A resolution. The halide-binding site is found near van der Waals contact with the chromophore imidazolinone oxygen atom, in a small buried cavity adjacent to Arg96, which provides electrostatic stabilization. The halide ion is hydrogen bonded to the phenol group of T203Y, consistent with a mutational analysis that indicates that T203Y is indispensible for tight binding. A series of conformational changes occurs in the amphiphilic site upon anion binding, which appear to be propagated to the beta-bulge region around residue 148 on the protein surface. Anion binding raises the chromophore pK(a) values, since delocalization of the phenolate negative charge over the chromophore skeleton is suppressed. Extraction of microscopic binding constants for the linked equilibrium between anion and proton binding indicates that anion selectivity by YFP is related to hydration forces. Specific suggestions to improve Cl(-) binding to YFP-H148Q based on size and hydration energy are proposed.
Crystallographic and energetic analysis of binding of selected anions to the yellow variants of green fluorescent protein.,Wachter RM, Yarbrough D, Kallio K, Remington SJ J Mol Biol. 2000 Aug 4;301(1):157-71. PMID:10926499<ref>PMID:10926499</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1f09" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Aeqvi]]
[[Category: Aequorea victoria]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Kallio, K]]
[[Category: Kallio K]]
[[Category: Remington, S J]]
[[Category: Remington SJ]]
[[Category: Wachter, R M]]
[[Category: Wachter RM]]
[[Category: Yarbrough, D]]
[[Category: Yarbrough D]]
[[Category: Beta barrel]]
[[Category: Bioluminescence]]
[[Category: Green fluorescent protein]]
[[Category: Luminescence]]
[[Category: Luminescent protein]]
[[Category: Photoactive protein]]

Revision as of 10:08, 20 March 2024

CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT YFP-H148Q WITH TWO BOUND IODIDES

1f09, resolution 2.14Å

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