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| | <StructureSection load='3a2v' size='340' side='right'caption='[[3a2v]], [[Resolution|resolution]] 1.65Å' scene=''> | | <StructureSection load='3a2v' size='340' side='right'caption='[[3a2v]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a2v]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A2V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3a2v]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A2V FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PER:PEROXIDE+ION'>PER</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]] 1.65Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a2w|3a2w]], [[3a2x|3a2x]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APE_2278 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=3a2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2v OCA], [https://pdbe.org/3a2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a2v RCSB], [https://www.ebi.ac.uk/pdbsum/3a2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2v 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=3a2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2v OCA], [https://pdbe.org/3a2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a2v RCSB], [https://www.ebi.ac.uk/pdbsum/3a2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2v ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/TDXH_AERPE TDXH_AERPE] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aerpe]] | + | [[Category: Aeropyrum pernix K1]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Peroxiredoxin]]
| + | [[Category: Inoue T]] |
| - | [[Category: Inoue, T]] | + | [[Category: Ishikawa K]] |
| - | [[Category: Ishikawa, K]] | + | [[Category: Kado Y]] |
| - | [[Category: Kado, Y]] | + | [[Category: Matsumura H]] |
| - | [[Category: Matsumura, H]] | + | [[Category: Nakamura T]] |
| - | [[Category: Nakamura, T]] | + | [[Category: Yamaguchi F]] |
| - | [[Category: Yamaguchi, F]] | + | |
| - | [[Category: Antioxidant]]
| + | |
| - | [[Category: Hydrogen peroxide]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Redox-active center]]
| + | |
| - | [[Category: Thioredoxin peroxidase]]
| + | |
| Structural highlights
Function
TDXH_AERPE
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
Peroxiredoxin (Prx) reduces hydrogen peroxide and alkyl peroxides to water and corresponding alcohols, respectively. The reaction is dependent on a peroxidatic cysteine, whose sulphur atom nucleophilically attacks one of the oxygen atoms of the peroxide substrate. In spite of the many structural studies that have been carried out on this reaction, the tertiary structure of the hydrogen peroxide-bound form of Prx has not been elucidated. In this paper, we report the crystal structure of Prx from Aeropyrum pernix K1 in the peroxide-bound form. The conformation of the polypeptide chain is the same as that in the reduced apo-form. The hydrogen peroxide molecule is in close contact with the peroxidatic Cys50 and the neighbouring Thr47 and Arg126 side chain atoms, as well as with the main chain nitrogen atoms of Val49 and Cys50. Bound peroxide was also observed in the mutant C50S, in which the peroxidatic cysteine was replaced by serine. Therefore, the sulphur atom of the peroxidatic cysteine is not essential for peroxide binding, although it enhances the binding affinity. Hydrogen peroxide binds to the protein so that it fills the active site pocket. This study provides insight into the early stage of the Prx reaction.
Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide.,Nakamura T, Kado Y, Yamaguchi T, Matsumura H, Ishikawa K, Inoue T J Biochem. 2010 Jan;147(1):109-15. Epub 2009 Oct 9. PMID:19819903[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nakamura T, Kado Y, Yamaguchi T, Matsumura H, Ishikawa K, Inoue T. Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide. J Biochem. 2010 Jan;147(1):109-15. Epub 2009 Oct 9. PMID:19819903 doi:10.1093/jb/mvp154
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