1kw9

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(New page: 200px<br /><applet load="1kw9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kw9, resolution 1.95&Aring;" /> '''Crystal structure of...)
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[[Image:1kw9.jpg|left|200px]]<br /><applet load="1kw9" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kw9, resolution 1.95&Aring;" />
 
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'''Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution'''<br />
 
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==Overview==
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==Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution==
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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.
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<StructureSection load='1kw9' size='340' side='right'caption='[[1kw9]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kw9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._KKS102 Pseudomonas sp. KKS102]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1eim 1eim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KW9 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
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<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=FE2:FE+(II)+ION'>FE2</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kw9 OCA], [https://pdbe.org/1kw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kw9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kw9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BPHC_PSES1 BPHC_PSES1]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/1kw9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1kw9 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1KW9 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 FE2 and BPY as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1EIM. 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=1KW9 OCA].
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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]
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[[Category: Large Structures]]
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[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
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[[Category: Pseudomonas sp. KKS102]]
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[[Category: Pseudomonas sp.]]
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[[Category: Fukuda M]]
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[[Category: Single protein]]
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[[Category: Masai E]]
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[[Category: Fukuda, M.]]
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[[Category: Nishizaki T]]
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[[Category: Masai, E.]]
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[[Category: Nonaka T]]
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[[Category: Nishizaki, T.]]
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[[Category: Sato N]]
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[[Category: Nonaka, T.]]
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[[Category: Sazaki G]]
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[[Category: Sato, N.]]
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[[Category: Senda T]]
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[[Category: Sazaki, G.]]
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[[Category: Sugimoto K]]
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[[Category: Senda, T.]]
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[[Category: Takahashi Y]]
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[[Category: Sugimoto, K.]]
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[[Category: Uragami Y]]
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[[Category: Takahashi, Y.]]
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[[Category: Uragami, Y.]]
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[[Category: BPY]]
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[[Category: FE2]]
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[[Category: four time repetitions of the beta-alpha-beta-beta-beta motif]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:00:55 2007''
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Current revision

Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution

PDB ID 1kw9

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