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1lkd

From Proteopedia

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[[Image:1lkd.jpg|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)==
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|PDB= 1lkd |SIZE=350|CAPTION= <scene name='initialview01'>1lkd</scene>, resolution 1.70&Aring;
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<StructureSection load='1lkd' size='340' side='right'caption='[[1lkd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=BP6:2&#39;,6&#39;-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene> and <scene name='pdbligand=P6G:HEXAETHYLENE GLYCOL'>P6G</scene>
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<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKD FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 1.7&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
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}}
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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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [https://pdbe.org/1lkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [https://www.ebi.ac.uk/pdbsum/1lkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BPHC_PARXL BPHC_PARXL] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.
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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/lk/1lkd_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=1lkd ConSurf].
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<div style="clear:both"></div>
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'''CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)'''
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==See Also==
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The microbial degradation of polychlorinated biphenyls (PCBs) provides the potential to destroy these widespread, toxic and persistent environmental pollutants. For example, the four-step upper bph pathway transforms some of the more than 100 different PCBs found in commercial mixtures and is being engineered for more effective PCB degradation. In the critical third step of this pathway, 2,3-dihydroxybiphenyl (DHB) 1,2-dioxygenase (DHBD; EC 1.13.11.39) catalyzes aromatic ring cleavage. Here we demonstrate that ortho-chlorinated PCB metabolites strongly inhibit DHBD, promote its suicide inactivation and interfere with the degradation of other compounds. For example, k(cat)(app) for 2',6'-diCl DHB was reduced by a factor of approximately 7,000 relative to DHB, and it bound with sufficient affinity to competitively inhibit DHB cleavage at nanomolar concentrations. Crystal structures of two complexes of DHBD with ortho-chlorinated metabolites at 1.7 A resolution reveal an explanation for these phenomena, which have important implications for bioremediation strategies.
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[[Category: Large Structures]]
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[[Category: Paraburkholderia xenovorans LB400]]
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==About this Structure==
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[[Category: Bolin JT]]
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1LKD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_sp. Burkholderia sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA].
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[[Category: Dai S]]
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==Reference==
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Identification and analysis of a bottleneck in PCB biodegradation., Dai S, Vaillancourt FH, Maaroufi H, Drouin NM, Neau DB, Snieckus V, Bolin JT, Eltis LD, Nat Struct Biol. 2002 Dec;9(12):934-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12415290 12415290]
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[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
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[[Category: Burkholderia sp.]]
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[[Category: Single protein]]
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[[Category: Bolin, J T.]]
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[[Category: Dai, S.]]
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[[Category: BP6]]
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[[Category: FE2]]
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[[Category: P6G]]
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[[Category: 2]]
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[[Category: 3-dihydroxybiphenyl]]
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[[Category: anaerobic]]
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[[Category: extradiol dioxygenase]]
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[[Category: non-heme iron]]
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[[Category: pcb biodegradation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 12:38:14 2008''
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Current revision

CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)

PDB ID 1lkd

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