2iga: Difference between revisions

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New page: left|200px<br /><applet load="2iga" size="350" color="white" frame="true" align="right" spinBox="true" caption="2iga, resolution 1.95Å" /> '''Structure of Homopro...
 
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[[Image:2iga.gif|left|200px]]<br /><applet load="2iga" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2iga, resolution 1.95&Aring;" />
'''Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.'''<br />


==Overview==
==Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.==
We report the structures of three intermediates in the O2 activation and, insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal, of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the, slow substrate 4-nitrocatechol in a low O2 atmosphere. The x-ray crystal, structure shows that three different intermediates reside in different, subunits of a single homotetrameric enzyme molecule. One of these is the, key substrate-alkylperoxo-Fe2+ intermediate, which has been predicted, but, not structurally characterized, in an oxygenase. The intermediates define, the major chemical steps of the dioxygenase mechanism and point to a, general mechanistic strategy for the diverse 2-His-1-carboxylate enzyme, family.
<StructureSection load='2iga' size='340' side='right'caption='[[2iga]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2iga]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IGA FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=XX2:1-KETO,2-HYDROXY,4-NITROBENZENE,+1+ELECTRON+OXIDIZED'>XX2</scene>, <scene name='pdbligand=XX3:(1S)-1-HYDROPEROXY-1-HYDROXY-2-KETO-5-NITROCYCLOHEXA-3,5-DIENE'>XX3</scene>, <scene name='pdbligand=XXP:2-KETO,5-NITRO,6-HYDROXY-3,5-HEXADIENOIC+ACID'>XXP</scene></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=2iga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iga OCA], [https://pdbe.org/2iga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iga RCSB], [https://www.ebi.ac.uk/pdbsum/2iga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iga ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q45135_9MICO Q45135_9MICO]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/2iga_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2iga ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The x-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been predicted, but not structurally characterized, in an oxygenase. The intermediates define the major chemical steps of the dioxygenase mechanism and point to a general mechanistic strategy for the diverse 2-His-1-carboxylate enzyme family.


==About this Structure==
Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates.,Kovaleva EG, Lipscomb JD Science. 2007 Apr 20;316(5823):453-7. PMID:17446402<ref>PMID:17446402</ref>
2IGA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum] with <scene name='pdbligand=FE2:'>FE2</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=XXP:'>XXP</scene>, <scene name='pdbligand=XX3:'>XX3</scene>, <scene name='pdbligand=XX2:'>XX2</scene>, <scene name='pdbligand=OXY:'>OXY</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGA OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates., Kovaleva EG, Lipscomb JD, Science. 2007 Apr 20;316(5823):453-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17446402 17446402]
</div>
[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
<div class="pdbe-citations 2iga" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Brevibacterium fuscum]]
[[Category: Brevibacterium fuscum]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Kovaleva, E.G.]]
[[Category: Kovaleva EG]]
[[Category: Lipscomb, J.D.]]
[[Category: Lipscomb JD]]
[[Category: CA]]
[[Category: CL]]
[[Category: FE2]]
[[Category: GOL]]
[[Category: OXY]]
[[Category: XX2]]
[[Category: XX3]]
[[Category: XXP]]
[[Category: alkylperoxo intermediate]]
[[Category: extradiol]]
[[Category: fe(ii)]]
[[Category: homoprotocatechuate]]
[[Category: open-ring product]]
[[Category: oxygenase]]
[[Category: substrate-semiquinone]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:47:27 2008''

Latest revision as of 10:10, 30 August 2023

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.

2iga, resolution 1.95Å

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