3bza: Difference between revisions

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-[[Image:3bza.png|left|200px]]
-{{STRUCTURE_3bza|  PDB=3bza  |  SCENE=  }}
+==Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.7 Ang resolution==
+<StructureSection load='3bza' size='340' side='right'caption='[[3bza]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3bza]] 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=3BZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BZA 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]] 1.7&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=3bza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bza OCA], [https://pdbe.org/3bza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bza RCSB], [https://www.ebi.ac.uk/pdbsum/3bza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bza 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/bz/3bza_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=3bza ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Biological O(2) activation often occurs after binding to a reduced metal [e.g., M(II)] in an enzyme active site. Subsequent M(II)-to-O(2) electron transfer results in a reactive M(III)-superoxo species. For the extradiol aromatic ring-cleaving dioxygenases, we have proposed a different model where an electron is transferred from substrate to O(2) via the M(II) center to which they are both bound, thereby obviating the need for an integral change in metal redox state. This model is tested by using homoprotocatechuate 2,3-dioxygenases from Brevibacterium fuscum (Fe-HPCD) and Arthrobacter globiformis (Mn-MndD) that share high sequence identity and very similar structures. Despite these similarities, Fe-HPCD binds Fe(II) whereas Mn-MndD incorporates Mn(II). Methods are described to incorporate the nonphysiological metal into each enzyme (Mn-HPCD and Fe-MndD). The x-ray crystal structure of Mn-HPCD at 1.7 A is found to be indistinguishable from that of Fe-HPCD, while EPR studies show that the Mn(II) sites of Mn-MndD and Mn-HPCD, and the Fe(II) sites of the NO complexes of Fe-HPCD and Fe-MndD, are very similar. The uniform metal site structures of these enzymes suggest that extradiol dioxygenases cannot differentially compensate for the 0.7-V gap in the redox potentials of free iron and manganese. Nonetheless, all four enzymes exhibit nearly the same K(M) and V(max) values. These enzymes constitute an unusual pair of metallo-oxygenases that remain fully active after a metal swap, implicating a different way by which metals are used to promote oxygen activation without an integral change in metal redox state.
-===Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.7 Ang resolution===
+Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state.,Emerson JP, Kovaleva EG, Farquhar ER, Lipscomb JD, Que L Jr Proc Natl Acad Sci U S A. 2008 May 27;105(21):7347-52. Epub 2008 May 20. PMID:18492808<ref>PMID:18492808</ref>
-{{ABSTRACT_PUBMED_18492808}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3bza" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3bza]] 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=3BZA OCA].
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018492808</ref><references group="xtra"/>
+__TOC__
-[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
+</StructureSection>
 [[Category: Brevibacterium fuscum]]
-[[Category: Kovaleva, E G.]]
+[[Category: Large Structures]]
-[[Category: Lipscomb, J D.]]
+[[Category: Kovaleva EG]]
-[[Category: Dioxygenase]]
+[[Category: Lipscomb JD]]
-[[Category: Extradiol]]
-[[Category: Metal substitution]]
-[[Category: Mn ii]]
-[[Category: Oxidoreductase]]
-[[Category: Oxygenase]]