1kwb: Difference between revisions

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-[[Image:1kwb.jpg|left|200px]]<br /><applet load="1kwb" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1kwb, resolution 2.000&Aring;" />
-'''Crystal structure of the His145Ala mutant of 2,3-dihydroxybipheny dioxygenase (BphC)'''<br />
-==Overview==
+==Crystal structure of the His145Ala mutant of 2,3-dihydroxybipheny dioxygenase (BphC)==
-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.
+<StructureSection load='1kwb' size='340' side='right'caption='[[1kwb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kwb]] 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=1KWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWB 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwb OCA], [https://pdbe.org/1kwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwb RCSB], [https://www.ebi.ac.uk/pdbsum/1kwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwb 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/1kwb_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=1kwb 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.
-==About this Structure==
+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>
-KWB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KWB OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12206778 12206778]
+</div>
-[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
+<div class="pdbe-citations 1kwb" style="background-color:#fffaf0;"></div>
-[[Category: Pseudomonas sp.]]
-[[Category: Single protein]]
-[[Category: Fukuda, M.]]
-[[Category: Masai, E.]]
-[[Category: Nishizaki, T.]]
-[[Category: Nonaka, T.]]
-[[Category: Sato, N.]]
-[[Category: Sazaki, G.]]
-[[Category: Senda, T.]]
-[[Category: Sugimoto, K.]]
-[[Category: Takahashi, Y.]]
-[[Category: Uragami, Y.]]
-[[Category: four time repetitions of the beta-alpha-beta-beta-beta motif]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:01:02 2007''
+==See Also==
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pseudomonas sp. KKS102]]
+[[Category: Fukuda M]]
+[[Category: Masai E]]
+[[Category: Nishizaki T]]
+[[Category: Nonaka T]]
+[[Category: Sato N]]
+[[Category: Sazaki G]]
+[[Category: Senda T]]
+[[Category: Sugimoto K]]
+[[Category: Takahashi Y]]
+[[Category: Uragami Y]]