1kwc: Difference between revisions

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-[[Image:1kwc.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1kwc", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1kwc|  PDB=1kwc  |  SCENE=  }}
-'''The His145Ala mutant of 2,3-dihydroxybiphenyl dioxygenase in complex with 2,3-dihydroxybiphenyl'''
+==The His145Ala mutant of 2,3-dihydroxybiphenyl dioxygenase in complex with 2,3-dihydroxybiphenyl==
+<StructureSection load='1kwc' size='340' side='right'caption='[[1kwc]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kwc]] 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=1KWC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWC 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]] 2.1&#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></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=1kwc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwc OCA], [https://pdbe.org/1kwc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwc RCSB], [https://www.ebi.ac.uk/pdbsum/1kwc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwc 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/kw/1kwc_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=1kwc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BphC derived from Pseudomonas sp. strain KKS102 is an extradiol-cleaving catecholic dioxygenase. This enzyme contains a non-heme iron atom and plays an important role in degrading biphenyl/polychlorinated biphenyls (PCBs) in the microbe. To elucidate detailed structures of BphC reaction intermediates, crystal structures of the substrate-free form, the BphC-substrate complex, and the BphC-substrate-NO (nitric oxide) complex were determined. These crystal structures revealed (1) the binding site of the O(2) molecule in the coordination sphere and (2) conformational changes of His194 during the catalytic reaction. On the basis of these findings, we propose a catalytic mechanism for the extradiol-cleaving catecholic dioxygenase in which His194 seems to play three distinct roles. At the early stage of the catalytic reaction, His194 appears to act as a catalytic base, which likely deprotonates the hydroxyl group of the substrate. At the next stage, the protonated His194 seems to stabilize a negative charge on the O2 molecule located in the hydrophobic O2-binding cavity. Finally, protonated His194 seems to function as a proton donor, whose existence has been proposed.
-==Overview==
+Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase.,Sato N, Uragami Y, Nishizaki T, Takahashi Y, Sazaki G, Sugimoto K, Nonaka T, Masai E, Fukuda M, Senda T J Mol Biol. 2002 Aug 23;321(4):621-36. PMID:12206778<ref>PMID:12206778</ref>
-BphC derived from Pseudomonas sp. strain KKS102 is an extradiol-cleaving catecholic dioxygenase. This enzyme contains a non-heme iron atom and plays an important role in degrading biphenyl/polychlorinated biphenyls (PCBs) in the microbe. To elucidate detailed structures of BphC reaction intermediates, crystal structures of the substrate-free form, the BphC-substrate complex, and the BphC-substrate-NO (nitric oxide) complex were determined. These crystal structures revealed (1) the binding site of the O(2) molecule in the coordination sphere and (2) conformational changes of His194 during the catalytic reaction. On the basis of these findings, we propose a catalytic mechanism for the extradiol-cleaving catecholic dioxygenase in which His194 seems to play three distinct roles. At the early stage of the catalytic reaction, His194 appears to act as a catalytic base, which likely deprotonates the hydroxyl group of the substrate. At the next stage, the protonated His194 seems to stabilize a negative charge on the O2 molecule located in the hydrophobic O2-binding cavity. Finally, protonated His194 seems to function as a proton donor, whose existence has been proposed.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-KWC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWC OCA].
+</div>
+<div class="pdbe-citations 1kwc" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase., Sato N, Uragami Y, Nishizaki T, Takahashi Y, Sazaki G, Sugimoto K, Nonaka T, Masai E, Fukuda M, Senda T, J Mol Biol. 2002 Aug 23;321(4):621-36. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12206778 12206778]
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
+== References ==
-[[Category: Pseudomonas sp.]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Fukuda, M.]]
+</StructureSection>
-[[Category: Masai, E.]]
+[[Category: Large Structures]]
-[[Category: Nishizaki, T.]]
+[[Category: Pseudomonas sp. KKS102]]
-[[Category: Nonaka, T.]]
+[[Category: Fukuda M]]
-[[Category: Sato, N.]]
+[[Category: Masai E]]
-[[Category: Sazaki, G.]]
+[[Category: Nishizaki T]]
-[[Category: Senda, T.]]
+[[Category: Nonaka T]]
-[[Category: Sugimoto, K.]]
+[[Category: Sato N]]
-[[Category: Takahashi, Y.]]
+[[Category: Sazaki G]]
-[[Category: Uragami, Y.]]
+[[Category: Senda T]]
-[[Category: Four time repetitions of the beta-alpha-beta-beta-beta motif]]
+[[Category: Sugimoto K]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 23:14:53 2008''
+[[Category: Takahashi Y]]
+[[Category: Uragami Y]]