4qcd
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4qcd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QCD FirstGlance]. <br> | <table><tr><td colspan='2'>[[4qcd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QCD FirstGlance]. <br> | ||
| - | </td></tr><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=D3O:TRIDEUTERIOOXIDANIUM'>D3O</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.932Å</td></tr> |
| + | <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=D3O:TRIDEUTERIOOXIDANIUM'>D3O</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=4qcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qcd OCA], [https://pdbe.org/4qcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qcd RCSB], [https://www.ebi.ac.uk/pdbsum/4qcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qcd 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=4qcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qcd OCA], [https://pdbe.org/4qcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qcd RCSB], [https://www.ebi.ac.uk/pdbsum/4qcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qcd ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == 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). | [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). | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXalpha (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Ndelta was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis. | ||
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| - | Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography.,Unno M, Ishikawa-Suto K, Kusaka K, Tamada T, Hagiwara Y, Sugishima M, Wada K, Yamada T, Tomoyori K, Hosoya T, Tanaka I, Niimura N, Kuroki R, Inaka K, Ishihara M, Fukuyama K J Am Chem Soc. 2015 Apr 29;137(16):5452-60. doi: 10.1021/jacs.5b00645. Epub 2015 , Apr 15. PMID:25872660<ref>PMID:25872660</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4qcd" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Phycocyanobilin:ferredoxin oxidoreductase|Phycocyanobilin:ferredoxin oxidoreductase]] | *[[Phycocyanobilin:ferredoxin oxidoreductase|Phycocyanobilin:ferredoxin oxidoreductase]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Neutron crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha at room temperature.
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