4usc: Difference between revisions
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==Crystal structure of peroxidase from palm tree Chamaerops excelsa== | ==Crystal structure of peroxidase from palm tree Chamaerops excelsa== | ||
<StructureSection load='4usc' size='340' side='right' caption='[[4usc]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='4usc' size='340' side='right'caption='[[4usc]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4usc]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4usc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trachycarpus_fortunei Trachycarpus fortunei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4USC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4USC FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4 | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4usc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4usc OCA], [https://pdbe.org/4usc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4usc RCSB], [https://www.ebi.ac.uk/pdbsum/4usc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4usc ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0A0Y4H8_TRAFO A0A0A0Y4H8_TRAFO] Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress.[RuleBase:RU362060] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4usc" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Trachycarpus fortunei]] | [[Category: Trachycarpus fortunei]] | ||
[[Category: Bernardes | [[Category: Bernardes A]] | ||
[[Category: Cuadrado | [[Category: Cuadrado NH]] | ||
[[Category: Kostetsky | [[Category: Kostetsky EY]] | ||
[[Category: Muniz | [[Category: Muniz JRC]] | ||
[[Category: Polikarpov | [[Category: Polikarpov I]] | ||
[[Category: Roig | [[Category: Roig MG]] | ||
[[Category: Santos | [[Category: Santos JC]] | ||
[[Category: Shnyrov | [[Category: Shnyrov VL]] | ||
[[Category: Textor | [[Category: Textor LC]] | ||
Latest revision as of 13:35, 10 January 2024
Crystal structure of peroxidase from palm tree Chamaerops excelsaCrystal structure of peroxidase from palm tree Chamaerops excelsa
Structural highlights
FunctionA0A0A0Y4H8_TRAFO Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress.[RuleBase:RU362060] Publication Abstract from PubMedPalm tree peroxidases are known to be very stable enzymes and the peroxidase from the Chamaerops excelsa (CEP), which has a high pH and thermal stability, is no exception. To date, the structural and molecular events underscoring such biochemical behavior have not been explored in depth. In order to identify the structural characteristics accounting for the high stability of palm tree peroxidases, we solved and refined the X-ray structure of native CEP at a resolution of 2.6 A. The CEP structure has an overall fold typical of plant peroxidases and confirmed the conservation of characteristic structural elements such as the heme group and calcium ions. At the same time the structure revealed important modifications in the amino acid residues in the vicinity of the exposed heme edge region, involved in substrate binding, that could account for the morphological variations among palm tree peroxidases through the disruption of molecular interactions at the second binding site. These modifications could alleviate the inhibition of enzymatic activity caused by molecular interactions at the latter binding site. Comparing the CEP crystallographic model described here with other publicly available peroxidase structures allowed the identification of a noncovalent homodimer assembly held together by a number of ionic and hydrophobic interactions. We demonstrate, that this dimeric arrangement results in a more stable protein quaternary structure through stabilization of the regions that are highly dynamic in other peroxidases. In addition, we resolved five N-glycosylation sites, which might also contribute to enzyme stability and resistance against proteolytic cleavage. Crystal structure analysis of peroxidase from the palm tree Chamaerops excelsa.,Bernardes A, Textor LC, Santos JC, Cuadrado NH, Kostetsky EY, Roig MG, Bavro VN, Muniz JR, Shnyrov VL, Polikarpov I Biochimie. 2015 Apr;111:58-69. doi: 10.1016/j.biochi.2015.01.014. Epub 2015 Feb, 7. PMID:25660651[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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