1eir: Difference between revisions

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-[[Image:1eir.jpg|left|200px]]<br /><applet load="1eir" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1eir, resolution 2.0&Aring;" />
-'''2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE'''<br />
-==Overview==
+==2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE==
-BphC derived from Pseudomonas sp. strain KKS102, an extradiol type catecholic dioxygenase, is a non-heam iron-containing enzyme, playing an important role in the degradation of biphenyl/PCB (Poly Chlorinated Biphenyls) in the microbe. Although we had earlier solved the crystal structure of KKS102 BphC, it was the inactive form with Fe(III) in the active site. In order to determine the active form structure, BphC was re-activated by anaerobic incubation with Fe(II) and ascorbate, and crystallized anaerobically. The crystal structures of activated BphC and its substrate complex (E x S complex) were determined at 2.0 A resolution under cryogenic condition. In addition, crystal structures of unactivated BphC in substrate free and complex forms were also re-determined. Comparison of activated and unactivated E x S complexes reveals that the orientation of the bound substrate in the active site is significantly different between the two. The structural comparison of the substrate free and complex forms of activated BphC show certain small conformational shifts around the active site upon substrate binding. As a result of the conformational shifts, His194, which has been suggested as the catalytic base, takes part in a weak hydrogen bond with hydroxyl group of the substrate.
+<StructureSection load='1eir' size='340' side='right'caption='[[1eir]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1eir]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._KKS102 Pseudomonas sp. KKS102]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIR 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]] 2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [https://pdbe.org/1eir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [https://www.ebi.ac.uk/pdbsum/1eir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eir ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BPHC_PSES1 BPHC_PSES1]
+== 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/ei/1eir_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=1eir ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-EIR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=BPY:'>BPY</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA].
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase., Uragami Y, Senda T, Sugimoto K, Sato N, Nagarajan V, Masai E, Fukuda M, Mitsu Y, J Inorg Biochem. 2001 Feb;83(4):269-79. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11293547 11293547]
+[[Category: Large Structures]]
-[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
+[[Category: Pseudomonas sp. KKS102]]
-[[Category: Pseudomonas sp.]]
+[[Category: Senda T]]
-[[Category: Single protein]]
-[[Category: Senda, T.]]
-[[Category: BPY]]
-[[Category: FE]]
-[[Category: four repetitions of beta-alpha-beta-beta-beta motifs]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:28:09 2008''