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| ==R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor after photoconversion== | | ==R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor after photoconversion== |
- | <StructureSection load='5omj' size='340' side='right' caption='[[5omj]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='5omj' size='340' side='right'caption='[[5omj]], [[Resolution|resolution]] 2.00Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[5omj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geoka Geoka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OMJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5omj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OMJ FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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]] 2.005Å</td></tr> |
- | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr> |
- | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4hr0|4hr0]], [[4hr4|4hr4]], [[4hr5|4hr5]], [[4xb9|4xb9]], [[4xbv|4xbv]], [[4xbw|4xbw]], [[5dco|5dco]], [[5dcr|5dcr]], [[5dcs|5dcs]], [[5ekb|5ekb]]</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=5omj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omj OCA], [https://pdbe.org/5omj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5omj RCSB], [https://www.ebi.ac.uk/pdbsum/5omj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5omj ProSAT]</span></td></tr> |
- | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GK2771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</td></tr>
| + | |
- | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </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=5omj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omj OCA], [http://pdbe.org/5omj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omj RCSB], [http://www.ebi.ac.uk/pdbsum/5omj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omj ProSAT]</span></td></tr> | + | |
| </table> | | </table> |
| + | == Function == |
| + | [https://www.uniprot.org/uniprot/Q5KW80_GEOKA Q5KW80_GEOKA] |
| <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| </div> | | </div> |
| <div class="pdbe-citations 5omj" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5omj" style="background-color:#fffaf0;"></div> |
| + | |
| + | ==See Also== |
| + | *[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] |
| == References == | | == References == |
| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
- | [[Category: Geoka]] | + | [[Category: Geobacillus kaustophilus HTA426]] |
- | [[Category: Ribonucleoside-diphosphate reductase]] | + | [[Category: Large Structures]] |
- | [[Category: Griese, J J]] | + | [[Category: Griese JJ]] |
- | [[Category: Hogbom, M]] | + | [[Category: Hogbom M]] |
- | [[Category: Diiron cofactor]]
| + | |
- | [[Category: Metalloprotein oxidoreductase]]
| + | |
- | [[Category: Oxidoreductase]]
| + | |
- | [[Category: R2-like ligand-binding oxidase]]
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- | [[Category: Ribonucleotide reductase r2 subunit fold]]
| + | |
| Structural highlights
Function
Q5KW80_GEOKA
Publication Abstract from PubMed
The heterobimetallic R2lox protein binds both manganese and iron ions in a site-selective fashion and activates oxygen, ultimately performing C-H bond oxidation to generate a tyrosine-valine crosslink near the active site. In this work, we demonstrate that following assembly, R2lox undergoes photoinduced changes to the active site geometry and metal coordination motif. Through spectroscopic, structural, and mass spectrometric characterization, the photoconverted species is found to consist of a tyrosinate-bound iron center following light-induced decarboxylation of a coordinating glutamate residue and cleavage of the tyrosine-valine crosslink. This process occurs with high quantum efficiencies (phi= 3%) using violet and near-ultraviolet light, suggesting that the photodecarboxylation is initiated via ligand-to-metal charge transfer excitation. Site-directed mutagenesis and structural analysis suggest that the crosslinked tyrosine-162 is the coordinating residue. One primary product is observed following irradiation, indicating potential use of this class of proteins, which contains a putative substrate channel, for controlled photoinduced decarboxylation processes, with relevance for in vivo functionality of R2lox as well as application in environmental remediation.
Driving protein conformational changes with light: Photoinduced structural rearrangement in a heterobimetallic oxidase.,Maugeri PT, Griese JJ, Branca RM, Miller EK, Smith ZR, Eirich J, Hogbom M, Shafaat HS J Am Chem Soc. 2017 Dec 22. doi: 10.1021/jacs.7b11966. PMID:29268610[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Maugeri PT, Griese JJ, Branca RM, Miller EK, Smith ZR, Eirich J, Hogbom M, Shafaat HS. Driving protein conformational changes with light: Photoinduced structural rearrangement in a heterobimetallic oxidase. J Am Chem Soc. 2017 Dec 22. doi: 10.1021/jacs.7b11966. PMID:29268610 doi:http://dx.doi.org/10.1021/jacs.7b11966
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