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| | <StructureSection load='5jpr' size='340' side='right'caption='[[5jpr]], [[Resolution|resolution]] 1.81Å' scene=''> | | <StructureSection load='5jpr' size='340' side='right'caption='[[5jpr]], [[Resolution|resolution]] 1.81Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5jpr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JPR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5jpr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JPR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.806Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">apx1, GLYMA_U021900 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-ascorbate_peroxidase L-ascorbate peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.11 1.11.1.11] </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=5jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jpr OCA], [https://pdbe.org/5jpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jpr RCSB], [https://www.ebi.ac.uk/pdbsum/5jpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jpr ProSAT]</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=5jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jpr OCA], [http://pdbe.org/5jpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jpr RCSB], [http://www.ebi.ac.uk/pdbsum/5jpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jpr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q43758_SOYBN Q43758_SOYBN] |
| | <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: Glycine hispida]] | + | [[Category: Glycine max]] |
| - | [[Category: L-ascorbate peroxidase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Blakeley, M P]] | + | [[Category: Blakeley MP]] |
| - | [[Category: Kwon, H]] | + | [[Category: Kwon H]] |
| - | [[Category: Moody, P C.E]] | + | [[Category: Moody PCE]] |
| - | [[Category: Raven, E L]] | + | [[Category: Raven EL]] |
| - | [[Category: Compound ii]]
| + | |
| - | [[Category: Cryo-trapping]]
| + | |
| - | [[Category: Ferryle heme]]
| + | |
| - | [[Category: Heme peroxidase]]
| + | |
| - | [[Category: Intermediate]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
5jpr is a 1 chain structure with sequence from Glycine max. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | Hybrid , Neutron Diffraction , X-ray diffraction, Resolution 1.806Å |
| Ligands: | , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q43758_SOYBN
Publication Abstract from PubMed
Catalytic heme enzymes carry out a wide range of oxidations in biology. They have in common a mechanism that requires formation of highly oxidized ferryl intermediates. It is these ferryl intermediates that provide the catalytic engine to drive the biological activity. Unravelling the nature of the ferryl species is of fundamental and widespread importance. The essential question is whether the ferryl is best described as a Fe(IV)=O or a Fe(IV)-OH species, but previous spectroscopic and X-ray crystallographic studies have not been able to unambiguously differentiate between the two species. Here we use a different approach. We report a neutron crystal structure of the ferryl intermediate in Compound II of a heme peroxidase; the structure allows the protonation states of the ferryl heme to be directly observed. This, together with pre-steady state kinetic analyses, electron paramagnetic resonance spectroscopy and single crystal X-ray fluorescence, identifies a Fe(IV)-OH species as the reactive intermediate. The structure establishes a precedent for the formation of Fe(IV)-OH in a peroxidase.
Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme.,Kwon H, Basran J, Casadei CM, Fielding AJ, Schrader TE, Ostermann A, Devos JM, Aller P, Blakeley MP, Moody PC, Raven EL Nat Commun. 2016 Nov 29;7:13445. doi: 10.1038/ncomms13445. PMID:27897163[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kwon H, Basran J, Casadei CM, Fielding AJ, Schrader TE, Ostermann A, Devos JM, Aller P, Blakeley MP, Moody PC, Raven EL. Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme. Nat Commun. 2016 Nov 29;7:13445. doi: 10.1038/ncomms13445. PMID:27897163 doi:http://dx.doi.org/10.1038/ncomms13445
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