2dke

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{{Seed}}
 
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[[Image:2dke.png|left|200px]]
 
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==Crystal structure of substrate-free form of PcyA==
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The line below this paragraph, containing "STRUCTURE_2dke", creates the "Structure Box" on the page.
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<StructureSection load='2dke' size='340' side='right'caption='[[2dke]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2dke]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803 Synechocystis sp. PCC 6803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKE FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
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{{STRUCTURE_2dke| PDB=2dke | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dke OCA], [https://pdbe.org/2dke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dke RCSB], [https://www.ebi.ac.uk/pdbsum/2dke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dke ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PCYA_SYNY3 PCYA_SYNY3] Catalyzes the four-electron reduction of biliverdin IX-alpha (2-electron reduction at both the A and D rings); the reaction proceeds via an isolatable 2-electron intermediate, 181,182-dihydrobiliverdin (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dke_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2dke ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the sequential reduction of the vinyl group of the D-ring and the A-ring of biliverdin IXalpha (BV) using ferredoxin to produce phycocyanobilin, a pigment used for light-harvesting and light-sensing in red algae and cyanobacteria. We have determined the crystal structure of the substrate-free form of PcyA from Synechocystis sp. PCC 6803 at 2.5 A resolution. Structural comparison of the substrate-free form and the PcyA-BV complex shows major changes around the entrance of the BV binding pocket; upon BV binding, two alpha-helices and nearby side-chains move to produce tight BV binding. Unexpectedly, these movements localize the positive charges around the BV binding site, which may contribute to the proper binding of ferredoxin to PcyA. In the substrate-free form, the side-chain of Asp105 was located at a site that would be underneath the BV A-ring in the PcyA-BV complex and hydrogen-bonded with His88. We propose that BV is protonated by a mechanism involving conformational changes of these two residues before reduction.
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===Crystal structure of substrate-free form of PcyA===
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Induced-fitting and electrostatic potential change of PcyA upon substrate binding demonstrated by the crystal structure of the substrate-free form.,Hagiwara Y, Sugishima M, Takahashi Y, Fukuyama K FEBS Lett. 2006 Jul 10;580(16):3823-8. Epub 2006 Jun 12. PMID:16782089<ref>PMID:16782089</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2dke" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16782089}}, adds the Publication Abstract to the page
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*[[Phycocyanobilin:ferredoxin oxidoreductase|Phycocyanobilin:ferredoxin oxidoreductase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16782089 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16782089}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2DKE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp. Synechocystis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKE OCA].
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[[Category: Synechocystis sp. PCC 6803]]
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[[Category: Fukuyama K]]
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==Reference==
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[[Category: Hagiwara Y]]
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<ref group="xtra">PMID:16782089</ref><references group="xtra"/>
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[[Category: Sugishima M]]
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[[Category: Phycocyanobilin:ferredoxin oxidoreductase]]
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[[Category: Takahashi Y]]
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[[Category: Synechocystis sp.]]
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[[Category: Fukuyama, K.]]
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[[Category: Hagiwara, Y.]]
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[[Category: Sugishima, M.]]
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[[Category: Takahashi, Y.]]
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[[Category: Alpha-beta-alpha sandwich]]
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[[Category: Substrate free form]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:48:08 2009''
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Current revision

Crystal structure of substrate-free form of PcyA

PDB ID 2dke

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