2d1e

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[[Image:2d1e.gif|left|200px]]
 
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{{Structure
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==Crystal structure of PcyA-biliverdin complex==
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|PDB= 2d1e |SIZE=350|CAPTION= <scene name='initialview01'>2d1e</scene>, resolution 1.510&Aring;
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<StructureSection load='2d1e' size='340' side='right'caption='[[2d1e]], [[Resolution|resolution]] 1.51&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
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<table><tr><td colspan='2'>[[2d1e]] 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=2D1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1E FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phycocyanobilin:ferredoxin_oxidoreductase Phycocyanobilin:ferredoxin oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.5 1.3.7.5] </span>
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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]] 1.51&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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|DOMAIN=
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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=2d1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1e OCA], [https://pdbe.org/2d1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1e RCSB], [https://www.ebi.ac.uk/pdbsum/2d1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1e ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1e OCA], [http://www.ebi.ac.uk/pdbsum/2d1e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d1e RCSB]</span>
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== Function ==
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}}
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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/d1/2d1e_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=2d1e ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of PcyA-biliverdin complex'''
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==See Also==
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*[[Phycocyanobilin:ferredoxin oxidoreductase|Phycocyanobilin:ferredoxin oxidoreductase]]
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__TOC__
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==Overview==
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</StructureSection>
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Phytobilins (light harvesting and photoreceptor pigments in higher plants, algae, and cyanobacteria) are synthesized from biliverdin IXalpha (BV) by ferredoxin-dependent bilin reductases (FDBRs). Phycocyanobilin:ferredoxin oxidoreductase (PcyA), one such FDBR, is a new class of radical enzymes that require neither cofactors nor metals and serially reduces the vinyl group of the D-ring and A-ring of BV using four electrons from ferredoxin to produce phycocyanobilin, one of the phytobilins. We have determined the crystal structure of PcyA from Synechocystis sp. PCC 6803 in complex with BV, revealing the first tertiary structure of an FDBR family member. PcyA is folded in a three-layer alpha/beta/alpha sandwich structure, in which BV in a cyclic conformation is positioned between the beta-sheet and C-terminal alpha-helices. The basic patch on the PcyA surface near the BV molecule may provide a binding site for acidic ferredoxin, allowing direct transfer of electrons to BV. The orientation of BV is definitely fixed in PcyA by several hydrophilic interactions and the shape of the BV binding pocket of PcyA. We propose the mechanism by which the sequential reduction of the D- and A-rings is controlled, where Asp-105, located between the two reduction sites, would play the central role by changing its conformation during the reaction. Homology modeling of other FDBRs based on the PcyA structure fits well with previous genetic and biochemical data, thereby providing a structural basis for the reaction mechanism of FDBRs.
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[[Category: Large Structures]]
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[[Category: Synechocystis sp. PCC 6803]]
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==About this Structure==
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[[Category: Fukuyama K]]
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2D1E 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=2D1E OCA].
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[[Category: Hagiwara Y]]
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[[Category: Sugishima M]]
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==Reference==
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[[Category: Takahashi Y]]
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Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phycocyanobilin., Hagiwara Y, Sugishima M, Takahashi Y, Fukuyama K, Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):27-32. Epub 2005 Dec 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16380422 16380422]
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[[Category: Phycocyanobilin:ferredoxin oxidoreductase]]
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[[Category: Single protein]]
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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: enzyme-substrate complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:28:57 2008''
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Current revision

Crystal structure of PcyA-biliverdin complex

PDB ID 2d1e

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