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| | ==Cys-persulfenate bound Cysteine Dioxygenase at pH 6.2 in the presence of Cys== | | ==Cys-persulfenate bound Cysteine Dioxygenase at pH 6.2 in the presence of Cys== |
| - | <StructureSection load='4ies' size='340' side='right' caption='[[4ies]], [[Resolution|resolution]] 1.40Å' scene=''> | + | <StructureSection load='4ies' size='340' side='right'caption='[[4ies]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ies]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IES FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ies]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IES FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2CO:S-HYDROPEROXYCYSTEINE'>2CO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 1.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ieo|4ieo]], [[4iep|4iep]], [[4ieq|4ieq]], [[4ier|4ier]], [[4iet|4iet]], [[4ieu|4ieu]], [[4iev|4iev]], [[4iew|4iew]], [[4iex|4iex]], [[4iey|4iey]], [[4iez|4iez]], [[4if0|4if0]], [[4if1|4if1]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2CO:S-HYDROPEROXYCYSTEINE'>2CO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cdo1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=4ies FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ies OCA], [https://pdbe.org/4ies PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ies RCSB], [https://www.ebi.ac.uk/pdbsum/4ies PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ies ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_dioxygenase Cysteine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.20 1.13.11.20] </span></td></tr>
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| - | <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=4ies FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ies OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ies RCSB], [http://www.ebi.ac.uk/pdbsum/4ies PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/CDO1_RAT CDO1_RAT] |
| | <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 4ies" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Dioxygenase|Dioxygenase]] | + | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cysteine dioxygenase]] | + | [[Category: Large Structures]] |
| | [[Category: Rattus norvegicus]] | | [[Category: Rattus norvegicus]] |
| - | [[Category: Cooley, R B]] | + | [[Category: Cooley RB]] |
| - | [[Category: Driggers, C M]] | + | [[Category: Driggers CM]] |
| - | [[Category: Karplus, P A]] | + | [[Category: Karplus PA]] |
| - | [[Category: Sankaran, B]] | + | [[Category: Sankaran B]] |
| - | [[Category: C93-y157 crosslink]]
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| - | [[Category: Catalyzes oxidation]]
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| - | [[Category: Cupin fold]]
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| - | [[Category: Cysteine to cysteine sulfinate]]
| + | |
| - | [[Category: Cytosol]]
| + | |
| - | [[Category: Oxidoreductase]]
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| Structural highlights
Function
CDO1_RAT
Publication Abstract from PubMed
Mammalian cysteine dioxygenase (CDO) is a mononuclear non-heme iron protein that catalyzes the conversion of cysteine (Cys) to cysteine sulfinic acid by an unclarified mechanism. One structural study revealed that a Cys-persulfenate (or Cys-persulfenic acid) formed in the active site, but quantum mechanical calculations have been used to support arguments that it is not an energetically feasible reaction intermediate. Here, we report a series of high-resolution structures of CDO soaked with Cys at pH values from 4 to 9. Cys binding is minimal at pH</=5 and persulfenate formation is consistently seen at pH values between 5.5 and 7. Also, a structure determined using laboratory-based X-ray diffraction shows that the persulfenate, with an apparent average O-O separation distance of ~1.8A, is not an artifact of synchrotron radiation. At pH>/=8, the active-site iron shifts from 4- to 5-coordinate, and Cys soaks reveal a complex with Cys, but no dioxygen, bound. This 'Cys-only' complex differs in detail from a previously published 'Cys-only' complex, which we reevaluate and conclude is not reliable. The high-resolution structures presented here do not resolve the CDO mechanism but do imply that an iron-bound persulfenate (or persulfenic acid) is energetically accessible in the CDO active site, and that CDO active-site chemistry in the crystals is influenced by protonation/deprotonation events with effective pKa values near ~5.5 and ~7.5 that influence Cys binding and oxygen binding/reactivity, respectively. Furthermore, this work provides reliable ligand-bound models for guiding future mechanistic considerations.
Cysteine Dioxygenase Structures from pH4 to 9: Consistent Cys-Persulfenate Formation at Intermediate pH and a Cys-Bound Enzyme at Higher pH.,Driggers CM, Cooley RB, Sankaran B, Hirschberger LL, Stipanuk MH, Karplus PA J Mol Biol. 2013 Jun 7. pii: S0022-2836(13)00358-6. doi:, 10.1016/j.jmb.2013.05.028. PMID:23747973[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Driggers CM, Cooley RB, Sankaran B, Hirschberger LL, Stipanuk MH, Karplus PA. Cysteine Dioxygenase Structures from pH4 to 9: Consistent Cys-Persulfenate Formation at Intermediate pH and a Cys-Bound Enzyme at Higher pH. J Mol Biol. 2013 Jun 7. pii: S0022-2836(13)00358-6. doi:, 10.1016/j.jmb.2013.05.028. PMID:23747973 doi:10.1016/j.jmb.2013.05.028
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