5c2i: Difference between revisions

Line 1:

'''~~Unreleased~~ structure'''

==Crystal structure of Anabaena sp. DyP-type peroxidese (AnaPX)==

== Structural highlights ==

<table><tr><td colspan='2'>[[5c2i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C2I FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=5c2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c2i OCA], [http://pdbe.org/5c2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c2i RCSB], [http://www.ebi.ac.uk/pdbsum/5c2i PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

DyP-type peroxidases are a newly discovered family of heme peroxidases distributed from prokaryotes to eukaryotes. Recently, using a structure-based sequence alignment, we proposed the new classes, P, I and V, as substitutes for classes A, B, C, and D [Arch Biochem Biophys 2015;574:49-55]. Although many class V enzymes from eukaryotes have been characterized, only two from prokaryotes have been reported. Here, we show the crystal structure of one of these two enzymes, Anabaena sp. DyP-type peroxidase (AnaPX). AnaPX is tetramer formed from Cys224-Cys224 disulfide-linked dimers. The tetramer of wild-type AnaPX was stable at all salt concentrations tested. In contrast, the C224A mutant showed salt concentration-dependent oligomeric states: in 600 mM NaCl, it maintained a tetrameric structure, whereas in the absence of salt, it dissociated into monomers, leading to a reduction in thermostability. Although the tetramer exhibits non-crystallographic, 2-fold symmetry in the asymmetric unit, two subunits forming the Cys224-Cys224 disulfide-linked dimer are related by 165 degrees rotation. This asymmetry creates an opening to cavities facing the inside of the tetramer, providing a pathway for hydrogen peroxide access. Finally, a phylogenetic analysis using structure-based sequence alignments showed that class V enzymes from prokaryotes, including AnaPX, are phylogenetically closely related to class V enzymes from eukaryotes. This article is protected by copyright. All rights reserved.

~~The entry 5c2i~~ is ~~ON HOLD until Paper Publication~~

Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers.,Yoshida T, Ogola HJ, Amano Y, Hisabori T, Ashida H, Sawa Y, Tsuge H, Sugano Y Proteins. 2015 Oct 22. doi: 10.1002/prot.24952. PMID:26492416<ref>PMID:26492416</ref>

~~Authors: Yoshida, T., Amano~~, Y.~~, Tsuge, H~~.~~, Sugano, Y~~.

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

</div>

~~Description~~:

~~[[Category: Unreleased Structures]]~~

== References ==

__TOC__

</StructureSection>

[[Category: Amano, Y]]

[[Category: Sugano, Y]]

[[Category: Tsuge, H]]

[[Category: Yoshida, T]]

[[Category: ~~Tsuge, H~~]]

[[Category: Dye-decolorizing peroxidase]]

[[Category: ~~Sugano, Y~~]]

[[Category: Dyp-type peroxidase]]

[[Category: Oxidoreductase]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+==Crystal structure of Anabaena sp. DyP-type peroxidese (AnaPX)==
+<StructureSection load='5c2i' size='340' side='right' caption='[[5c2i]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5c2i]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C2I FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=5c2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c2i OCA], [http://pdbe.org/5c2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c2i RCSB], [http://www.ebi.ac.uk/pdbsum/5c2i PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DyP-type peroxidases are a newly discovered family of heme peroxidases distributed from prokaryotes to eukaryotes. Recently, using a structure-based sequence alignment, we proposed the new classes, P, I and V, as substitutes for classes A, B, C, and D [Arch Biochem Biophys 2015;574:49-55]. Although many class V enzymes from eukaryotes have been characterized, only two from prokaryotes have been reported. Here, we show the crystal structure of one of these two enzymes, Anabaena sp. DyP-type peroxidase (AnaPX). AnaPX is tetramer formed from Cys224-Cys224 disulfide-linked dimers. The tetramer of wild-type AnaPX was stable at all salt concentrations tested. In contrast, the C224A mutant showed salt concentration-dependent oligomeric states: in 600 mM NaCl, it maintained a tetrameric structure, whereas in the absence of salt, it dissociated into monomers, leading to a reduction in thermostability. Although the tetramer exhibits non-crystallographic, 2-fold symmetry in the asymmetric unit, two subunits forming the Cys224-Cys224 disulfide-linked dimer are related by 165 degrees rotation. This asymmetry creates an opening to cavities facing the inside of the tetramer, providing a pathway for hydrogen peroxide access. Finally, a phylogenetic analysis using structure-based sequence alignments showed that class V enzymes from prokaryotes, including AnaPX, are phylogenetically closely related to class V enzymes from eukaryotes. This article is protected by copyright. All rights reserved.
-The entry 5c2i is ON HOLD  until Paper Publication
+Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers.,Yoshida T, Ogola HJ, Amano Y, Hisabori T, Ashida H, Sawa Y, Tsuge H, Sugano Y Proteins. 2015 Oct 22. doi: 10.1002/prot.24952. PMID:26492416<ref>PMID:26492416</ref>
-Authors: Yoshida, T., Amano, Y., Tsuge, H., Sugano, Y.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description:
+<div class="pdbe-citations 5c2i" style="background-color:#fffaf0;"></div>
-[[Category: Unreleased Structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Amano, Y]]
+[[Category: Sugano, Y]]
+[[Category: Tsuge, H]]
 [[Category: Yoshida, T]]
-[[Category: Tsuge, H]]
+[[Category: Dye-decolorizing peroxidase]]
-[[Category: Sugano, Y]]
+[[Category: Dyp-type peroxidase]]
+[[Category: Oxidoreductase]]