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| | <StructureSection load='3sid' size='340' side='right'caption='[[3sid]], [[Resolution|resolution]] 1.40Å' scene=''> | | <StructureSection load='3sid' size='340' side='right'caption='[[3sid]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3sid]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cyapa Cyapa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SID FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3sid]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cyanophora_paradoxa Cyanophora paradoxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SID FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 1.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3qhb|3qhb]], [[3qhc|3qhc]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cyanelle ORF180 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2762 CYAPA])</td></tr>
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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=3sid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sid OCA], [https://pdbe.org/3sid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sid RCSB], [https://www.ebi.ac.uk/pdbsum/3sid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sid 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=3sid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sid OCA], [https://pdbe.org/3sid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sid RCSB], [https://www.ebi.ac.uk/pdbsum/3sid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sid ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/YCX8_CYAPA YCX8_CYAPA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cyapa]] | + | [[Category: Cyanophora paradoxa]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Arp, D J]] | + | [[Category: Arp DJ]] |
| - | [[Category: Cooley, R B]] | + | [[Category: Cooley RB]] |
| - | [[Category: Karplus, P A]] | + | [[Category: Karplus PA]] |
| - | [[Category: Ferritin-like superfamily]]
| + | |
| - | [[Category: Oxidoreductase]]
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| Structural highlights
Function
YCX8_CYAPA
Publication Abstract from PubMed
Rubrerythrins are diiron-containing peroxidases that belong to the ferritin-like superfamily (FLSF). Here, we describe the structures of symerythrin, a novel rubrerythrin variant from the oxygenic phototroph Cyanophora paradoxa, at 1.20-1.40 A resolution in three different states: diferric, azide-bound diferric and chemically reduced. The symerythrin metallocenter has a unique eighth ligating residue compared to rubrerythrin-an additional glutamate inserted into helix A of the four-helix bundle that resides on a pi-helical segment. Otherwise, the diferric metallocenter structure is highly similar to that of characterized rubrerythrins. Azide binds the diferric center in a mu-1,1 orientation similar to how peroxide binds to diferric rubrerythrin. The structure of the diferrous metallocenter shows heterogeneity that we ascribe to the acidic pH of the crystals. In what we consider the neutral pH conformation, reduction causes a 2.0-A shift in Fe1 and the toggling of a Glu to a His ligand, as seen with rubrerythrins. The function of symerythrin remains unknown, but preliminary tests showing oxidase and peroxidase activities and the similarities of its metallocenter to other rubrerythrins suggest similar functionalities between the two despite the additional ligating glutamate in symerythrin. Of particular interest is the high internal symmetry of symerythrin, which supports the notion that its core four-helix bundle was formed by the gene duplication and fusion of a two-helix peptide. Sequence comparisons with another family in the FLSF that also has notable internal symmetry provide compelling evidence that, contrary to previous assumptions, there have been multiple gene fusion events that have generated the single-chain FLSF fold.
Symerythrin structures at atomic resolution and the origins of rubrerythrins and the ferritin-like superfamily.,Cooley RB, Arp DJ, Karplus PA J Mol Biol. 2011 Oct 14;413(1):177-94. Epub 2011 Aug 19. PMID:21872605[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Cooley RB, Arp DJ, Karplus PA. Symerythrin structures at atomic resolution and the origins of rubrerythrins and the ferritin-like superfamily. J Mol Biol. 2011 Oct 14;413(1):177-94. Epub 2011 Aug 19. PMID:21872605 doi:10.1016/j.jmb.2011.08.019
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