6edh: Difference between revisions
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<StructureSection load='6edh' size='340' side='right'caption='[[6edh]], [[Resolution|resolution]] 1.73Å' scene=''> | <StructureSection load='6edh' size='340' side='right'caption='[[6edh]], [[Resolution|resolution]] 1.73Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6edh]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EDH FirstGlance]. <br> | <table><tr><td colspan='2'>[[6edh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EDH FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TAU:2-AMINOETHANESULFONIC+ACID'>TAU</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tauD, ssiD, yaiG, b0368, JW0360 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Taurine_dioxygenase Taurine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.17 1.14.11.17] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Taurine_dioxygenase Taurine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.17 1.14.11.17] </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=6edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edh OCA], [http://pdbe.org/6edh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6edh RCSB], [http://www.ebi.ac.uk/pdbsum/6edh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6edh 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=6edh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6edh OCA], [http://pdbe.org/6edh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6edh RCSB], [http://www.ebi.ac.uk/pdbsum/6edh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6edh ProSAT]</span></td></tr> | ||
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== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/TAUD_ECOLI TAUD_ECOLI]] Catalyzes the conversion of taurine and alpha ketoglutarate to sulfite, aminoacetaldehyde and succinate. Required for the utilization of taurine (2-aminoethanesulfonic acid) as an alternative sulfur source. Pentane-sulfonic acid, 3-(N-morpholino)propanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid are also substrates for this enzyme. | [[http://www.uniprot.org/uniprot/TAUD_ECOLI TAUD_ECOLI]] Catalyzes the conversion of taurine and alpha ketoglutarate to sulfite, aminoacetaldehyde and succinate. Required for the utilization of taurine (2-aminoethanesulfonic acid) as an alternative sulfur source. Pentane-sulfonic acid, 3-(N-morpholino)propanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid are also substrates for this enzyme. | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Iron(II)- and 2-(oxo)-glutarate-dependent (Fe/2OG) oxygenases catalyze a diverse array of oxidation reactions via a common iron(IV)-oxo (ferryl) intermediate. Although the intermediate has been characterized spectroscopically, its short lifetime has precluded crystallograhic characterization. In solution, the ferryl was first observed directly in the archetypal Fe/2OG hydroxylase, taurine:2OG dioxygenase (TauD). Here, we substitute the iron cofactor of TauD with the stable vanadium(IV)-oxo (vanadyl) ion to obtain crystal structures mimicking the key ferryl complex. Intriguingly, whereas the structure of the TauD.(V(IV)-oxo).succinate.taurine complex exhibits the expected orientation of the V identical withO bond-trans to the His255 ligand and toward the C-H bond to be cleaved, in what has been termed the in-line configuration-the TauD.(V(IV)-oxo) binary complex is best modeled with its oxo ligand trans to Asp101. This off-line-like configuration is similar to one recently posited as a means to avoid hydroxylation in Fe/2OG enzymes that direct other outcomes, though neither has been visualized in an Fe/2OG structure to date. Whereas an off-line (trans to the proximal His) or off-line-like (trans to the carboxylate ligand) ferryl is unlikely to be important in the hydroxylation reaction of TauD, the observation that the ferryl may deviate from an in-line orientation in the absence of the primary substrate may explain the enzyme's mysterious self-hydroxylation behavior, should the oxo ligand lie trans to His99. This finding reinforces the potential for analogous functional off-line oxo configurations in halogenases, desaturases, and/or cyclases. | |||
Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD.,Davis KM, Altmyer M, Martinie RJ, Schaperdoth I, Krebs C, Bollinger JM Jr, Boal AK Biochemistry. 2019 Oct 15;58(41):4218-4223. doi: 10.1021/acs.biochem.9b00598., Epub 2019 Oct 2. PMID:31503454<ref>PMID:31503454</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6edh" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Ecoli]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Taurine dioxygenase]] | [[Category: Taurine dioxygenase]] | ||
Revision as of 10:50, 23 October 2019
Taurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine, and succinateTaurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine, and succinate
Structural highlights
Function[TAUD_ECOLI] Catalyzes the conversion of taurine and alpha ketoglutarate to sulfite, aminoacetaldehyde and succinate. Required for the utilization of taurine (2-aminoethanesulfonic acid) as an alternative sulfur source. Pentane-sulfonic acid, 3-(N-morpholino)propanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid are also substrates for this enzyme. Publication Abstract from PubMedIron(II)- and 2-(oxo)-glutarate-dependent (Fe/2OG) oxygenases catalyze a diverse array of oxidation reactions via a common iron(IV)-oxo (ferryl) intermediate. Although the intermediate has been characterized spectroscopically, its short lifetime has precluded crystallograhic characterization. In solution, the ferryl was first observed directly in the archetypal Fe/2OG hydroxylase, taurine:2OG dioxygenase (TauD). Here, we substitute the iron cofactor of TauD with the stable vanadium(IV)-oxo (vanadyl) ion to obtain crystal structures mimicking the key ferryl complex. Intriguingly, whereas the structure of the TauD.(V(IV)-oxo).succinate.taurine complex exhibits the expected orientation of the V identical withO bond-trans to the His255 ligand and toward the C-H bond to be cleaved, in what has been termed the in-line configuration-the TauD.(V(IV)-oxo) binary complex is best modeled with its oxo ligand trans to Asp101. This off-line-like configuration is similar to one recently posited as a means to avoid hydroxylation in Fe/2OG enzymes that direct other outcomes, though neither has been visualized in an Fe/2OG structure to date. Whereas an off-line (trans to the proximal His) or off-line-like (trans to the carboxylate ligand) ferryl is unlikely to be important in the hydroxylation reaction of TauD, the observation that the ferryl may deviate from an in-line orientation in the absence of the primary substrate may explain the enzyme's mysterious self-hydroxylation behavior, should the oxo ligand lie trans to His99. This finding reinforces the potential for analogous functional off-line oxo configurations in halogenases, desaturases, and/or cyclases. Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD.,Davis KM, Altmyer M, Martinie RJ, Schaperdoth I, Krebs C, Bollinger JM Jr, Boal AK Biochemistry. 2019 Oct 15;58(41):4218-4223. doi: 10.1021/acs.biochem.9b00598., Epub 2019 Oct 2. PMID:31503454[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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