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3ajh

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Crystal structure of PcyA V225D-biliverdin XIII alpha complex

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Retrieved from "http://52.214.119.220/wiki/index.php/3ajh"

Categories: Large Structures | Synechocystis sp. PCC 6803 | Fukuyama K | Hagiwara Y | Wada K

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 ==Crystal structure of PcyA V225D-biliverdin XIII alpha complex==
-<StructureSection load='3ajh' size='340' side='right' caption='[[3ajh]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+<StructureSection load='3ajh' size='340' side='right'caption='[[3ajh]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ajh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechocystis Synechocystis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AJH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AJH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ajh]] is a 2 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=3AJH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AJH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BL3:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(3-ETHENYL-4-METHYL-5-OXO-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-2-YLIDENE]METHYL]-5-[(Z)-(3-ETHENYL-4-METHYL-5-OXO-PYRROL-2-YLIDENE)METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>BL3</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]] 2.25&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ajg|3ajg]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BL3:3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-2-ylidene]methy+l]-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic+acid'>BL3</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pcyA, slr0116 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1142 Synechocystis])</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=3ajh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ajh OCA], [https://pdbe.org/3ajh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ajh RCSB], [https://www.ebi.ac.uk/pdbsum/3ajh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ajh ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ajh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ajh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ajh RCSB], [http://www.ebi.ac.uk/pdbsum/3ajh PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[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).
-Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the sequential reduction of the vinyl group of the D-ring and A-ring of biliverdin IXalpha (BV), using reducing equivalents provided by ferredoxin. This reaction produces phycocyanobilin, a pigment used for light-harvesting and light-sensing in red algae and cyanobacteria. The crystal structure of PcyA-BV reveals that BV is specifically bound in the PcyA active pocket through extensive hydrophobic and hydrophilic interactions. During the course of a mutational study of PcyA, we observed that mutation of the V225 position, apart from the processing sites, conferred an unusual property on PcyA; V225D mutant protein could bind BV and its analog BV13, but these complexes showed a distinct UV-vis absorption spectrum from that of the wild-type PcyA-BV complex. The crystal structures of BV- and BV13-bound forms of V225D protein revealed that gross structural changes occurred near the substrate-binding pocket, and that the BV/BV13 binding manner in the pocket was dramatically altered. Protein folding in V225D-BV/BV13 was more similar to that of substrate-free PcyA than that in PcyA-BV; the "induced-fit" did not occur when BV/BV13 was bound to the V225D protein. The unexpected structural change presented here provides a cautionary note about interpreting functional data derived from a mutated protein in the absence of its exact structure.
-One residue substitution in PcyA leads to unexpected changes in tetrapyrrole substrate binding.,Wada K, Hagiwara Y, Yutani Y, Fukuyama K Biochem Biophys Res Commun. 2010 Nov 12;402(2):373-7. Epub 2010 Oct 12. PMID:20946883<ref>PMID:20946883</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
 *[[Phycocyanobilin:ferredoxin oxidoreductase|Phycocyanobilin:ferredoxin oxidoreductase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Phycocyanobilin:ferredoxin oxidoreductase]]
+[[Category: Large Structures]]
-[[Category: Synechocystis]]
+[[Category: Synechocystis sp. PCC 6803]]
-[[Category: Fukuyama, K.]]
+[[Category: Fukuyama K]]
-[[Category: Hagiwara, Y.]]
+[[Category: Hagiwara Y]]
-[[Category: Wada, K.]]
+[[Category: Wada K]]
-[[Category: Alpha/beta/alpha sandwich]]
-[[Category: Oxidoreductase]]

3ajh

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Crystal structure of PcyA V225D-biliverdin XIII alpha complex

Structural highlights

Function

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