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2dke

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Revision as of 10:32, 8 December 2021

Crystal structure of substrate-free form of PcyA

Structural highlights

2dke is a 1 chain structure with sequence from Aphanocapsa sp. (strain n-1). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2d1e
Activity:	Phycocyanobilin:ferredoxin oxidoreductase, with EC number 1.3.7.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hagiwara Y, Sugishima M, Takahashi Y, Fukuyama K. Induced-fitting and electrostatic potential change of PcyA upon substrate binding demonstrated by the crystal structure of the substrate-free form. FEBS Lett. 2006 Jul 10;580(16):3823-8. Epub 2006 Jun 12. PMID:16782089 doi:10.1016/j.febslet.2006.05.075

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dke"

@@ Line 3: / Line 3: @@
 <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 [http://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dke]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2d1e|2d1e]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d1e|2d1e]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phycocyanobilin:ferredoxin_oxidoreductase Phycocyanobilin:ferredoxin oxidoreductase], with EC number [https://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=2dke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dke OCA], [http://pdbe.org/2dke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dke RCSB], [http://www.ebi.ac.uk/pdbsum/2dke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dke 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=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 ==
-[[http://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).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 30: @@
 </div>
 <div class="pdbe-citations 2dke" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phycocyanobilin:ferredoxin oxidoreductase|Phycocyanobilin:ferredoxin oxidoreductase]]
 == References ==
 <references/>

2dke

From Proteopedia

Revision as of 10:32, 8 December 2021

Crystal structure of substrate-free form of PcyA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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