1tmx: Difference between revisions

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 <StructureSection load='1tmx' size='340' side='right'caption='[[1tmx]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1tmx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"corynebacterium_simplex"_jensen_1934 "corynebacterium simplex" jensen 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TMX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1tmx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pimelobacter_simplex Pimelobacter simplex]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TMX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HGX:1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL+CHOLINE'>HGX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.75&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxyquinol_1,2-dioxygenase Hydroxyquinol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.37 1.13.11.37] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HGX:1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL+CHOLINE'>HGX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1tmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmx OCA], [http://pdbe.org/1tmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tmx RCSB], [http://www.ebi.ac.uk/pdbsum/1tmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmx ProSAT]</span></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=1tmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tmx OCA], [https://pdbe.org/1tmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tmx RCSB], [https://www.ebi.ac.uk/pdbsum/1tmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tmx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CHQB_NOCSI CHQB_NOCSI]] Catalyzes the ortho-cleavage of the aromatic ring of hydroxyquinol.
+[https://www.uniprot.org/uniprot/CHQB_NOCSI CHQB_NOCSI] Catalyzes the ortho-cleavage of the aromatic ring of hydroxyquinol.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1tmx ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Hydroxyquinol 1,2-dioxygenase (1,2-HQD) catalyzes the ring cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), a central intermediate in the degradation of aromatic compounds including a variety of particularly recalcitrant polychloro- and nitroaromatic pollutants. We report here the primary sequence determination and the analysis of the crystal structure of the 1,2-HQD from Nocardioides simplex 3E solved at 1.75 A resolution using the multiple wavelength anomalous dispersion of the two catalytic irons (1 Fe/293 amino acids). The catalytic Fe(III) coordination polyhedron composed by the side chains of Tyr164, Tyr197, His221, and His223 resembles that of the other known intradiol-cleaving dioxygenases, but several of the tertiary structure features are notably different. One of the most distinctive characteristics of the present structure is the extensive openings and consequent exposure to solvent of the upper part of the catalytic cavity arranged to favor the binding of hydroxyquinols but not catechols. A co-crystallized benzoate-like molecule is also found bound to the metal center forming a distinctive hydrogen bond network as observed previously also in 4-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP. This is the first structure of an intradiol dioxygenase specialized in hydroxyquinol ring cleavage to be investigated in detail.
-Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation.,Ferraroni M, Seifert J, Travkin VM, Thiel M, Kaschabek S, Scozzafava A, Golovleva L, Schlomann M, Briganti F J Biol Chem. 2005 Jun 3;280(22):21144-54. Epub 2005 Mar 16. PMID:15772073<ref>PMID:15772073</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1tmx" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Corynebacterium simplex jensen 1934]]
-[[Category: Hydroxyquinol 1,2-dioxygenase]]
 [[Category: Large Structures]]
-[[Category: Briganti, F]]
+[[Category: Pimelobacter simplex]]
-[[Category: Ferraroni, M]]
+[[Category: Briganti F]]
-[[Category: Golovleva, L]]
+[[Category: Ferraroni M]]
-[[Category: Schlomann, M]]
+[[Category: Golovleva L]]
-[[Category: Scozzafava, A]]
+[[Category: Schlomann M]]
-[[Category: Seifert, J]]
+[[Category: Scozzafava A]]
-[[Category: Travkin, V M]]
+[[Category: Seifert J]]
-[[Category: Beta barrel]]
+[[Category: Travkin VM]]
-[[Category: Oxidoreductase]]