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[[Image:2dke.gif|left|200px]]
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{{STRUCTURE_2dke|  PDB=2dke  |  SCENE=  }}
'''Crystal structure of substrate-free form of PcyA'''


==Crystal structure of substrate-free form of PcyA==
<StructureSection load='2dke' size='340' side='right'caption='[[2dke]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== Function ==
[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).
== 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/dk/2dke_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=2dke ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
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>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2DKE is a [[Single protein]] 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].
</div>
<div class="pdbe-citations 2dke" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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:[http://www.ncbi.nlm.nih.gov/pubmed/16782089 16782089]
*[[Phycocyanobilin:ferredoxin oxidoreductase|Phycocyanobilin:ferredoxin oxidoreductase]]
[[Category: Phycocyanobilin:ferredoxin oxidoreductase]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Synechocystis sp.]]
__TOC__
[[Category: Fukuyama, K.]]
</StructureSection>
[[Category: Hagiwara, Y.]]
[[Category: Large Structures]]
[[Category: Sugishima, M.]]
[[Category: Synechocystis sp. PCC 6803]]
[[Category: Takahashi, Y.]]
[[Category: Fukuyama K]]
[[Category: Alpha-beta-alpha sandwich]]
[[Category: Hagiwara Y]]
[[Category: Substrate free form]]
[[Category: Sugishima M]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 00:36:36 2008''
[[Category: Takahashi Y]]

Latest revision as of 08:27, 25 October 2023

Crystal structure of substrate-free form of PcyA

2dke, resolution 2.50Å

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