3eck: Difference between revisions
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<StructureSection load='3eck' size='340' side='right' caption='[[3eck]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='3eck' size='340' side='right' caption='[[3eck]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3eck]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3eck]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/'brevibacterium_fuscum' 'brevibacterium fuscum']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ECK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ECK FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=XXG:3,3-DIHYDROXY-4-OXOCYCLOHEXA-1,5-DIENE-1-SULFONIC+ACID'>XXG</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=XXG:3,3-DIHYDROXY-4-OXOCYCLOHEXA-1,5-DIENE-1-SULFONIC+ACID'>XXG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ecj|3ecj]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ecj|3ecj]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hpcd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47914 Brevibacterium fuscum])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hpcd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47914 'Brevibacterium fuscum'])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=3eck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eck OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eck RCSB], [http://www.ebi.ac.uk/pdbsum/3eck PDBsum]</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=3eck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eck OCA], [http://pdbe.org/3eck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eck RCSB], [http://www.ebi.ac.uk/pdbsum/3eck PDBsum]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=3eck ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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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 3eck" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Brevibacterium fuscum]] | |||
[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]] | [[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]] | ||
[[Category: Kovaleva, E G]] | [[Category: Kovaleva, E G]] | ||
[[Category: Lipscomb, J D]] | [[Category: Lipscomb, J D]] | ||
Revision as of 16:07, 8 February 2016
Structure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrationsStructure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrations
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe reactive oxy intermediate of the catalytic cycle of extradiol aromatic ring-cleaving dioxygenases is formed by binding the catecholic substrate and O2 in adjacent ligand positions of the active site metal [usually Fe(II)]. This intermediate and the following Fe(II)-alkylperoxo intermediate resulting from oxygen attack on the substrate have been previously characterized in a crystal of homoprotocatechuate 2,3-dioxygenase (HPCD). Here a subsequent intermediate in which the O-O bond is broken to yield a gem diol species is structurally characterized. This new intermediate is stabilized in the crystal by using the alternative substrate, 4-sulfonylcatechol, and the Glu323Leu variant of HPCD, which alters the crystal packing. Intermediate in the O-O bond cleavage reaction of an extradiol dioxygenase.,Kovaleva EG, Lipscomb JD Biochemistry. 2008 Oct 28;47(43):11168-70. Epub 2008 Oct 1. PMID:18826259[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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