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4iet

From Proteopedia

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Cys-persulfenate bound Cysteine Dioxygenase at pH 6.8 in the presence of Cys

Structural highlights

4iet is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4iet"

Categories: Large Structures | Rattus norvegicus | Cooley RB | Driggers CM | Karplus PA

@@ Line 1: / Line 1: @@
 ==Cys-persulfenate bound Cysteine Dioxygenase at pH 6.8 in the presence of Cys==
-<StructureSection load='4iet' size='340' side='right' caption='[[4iet]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+<StructureSection load='4iet' size='340' side='right'caption='[[4iet]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4iet]] 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=4IET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IET FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4iet]] 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=4IET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IET 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=FE2:FE+(II)+ION'>FE2</scene></td></tr>
+</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=FE2:FE+(II)+ION'>FE2</scene></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]], [[4ies|4ies]], [[4ieu|4ieu]], [[4iev|4iev]], [[4iew|4iew]], [[4iex|4iex]], [[4iey|4iey]], [[4iez|4iez]], [[4if0|4if0]], [[4if1|4if1]]</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=4iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iet OCA], [https://pdbe.org/4iet PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iet RCSB], [https://www.ebi.ac.uk/pdbsum/4iet PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iet ProSAT]</span></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='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>
-<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=4iet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iet OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4iet RCSB], [http://www.ebi.ac.uk/pdbsum/4iet PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CDO1_RAT CDO1_RAT]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 17: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4iet" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Dioxygenase|Dioxygenase]]
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cysteine dioxygenase]]
+[[Category: Large Structures]]
 [[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: C93-y157 crosslink]]
-[[Category: Catalyzes oxidation]]
-[[Category: Cupin fold]]
-[[Category: Cysteine to cysteine sulfinate]]
-[[Category: Cytosol]]
-[[Category: Oxidoreductase]]

4iet

From Proteopedia

Current revision

Cys-persulfenate bound Cysteine Dioxygenase at pH 6.8 in the presence of Cys

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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