1lkd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1lkd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1lkd, resolution 1.70&Aring;" /> '''CRYSTAL STRUCTURE OF...)
Current revision (07:33, 14 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1lkd.jpg|left|200px]]<br /><applet load="1lkd" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1lkd, resolution 1.70&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)==
-
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.
+
<StructureSection load='1lkd' size='340' side='right'caption='[[1lkd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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>
 +
</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>
 +
<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>
 +
<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>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/BPHC_PARXL BPHC_PARXL] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.
 +
== 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/lk/1lkd_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=1lkd ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1LKD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_sp. Burkholderia sp.] with FE2, BP6 and P6G 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA].
+
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12415290 12415290]
+
[[Category: Large Structures]]
-
[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
+
[[Category: Paraburkholderia xenovorans LB400]]
-
[[Category: Burkholderia sp.]]
+
[[Category: Bolin JT]]
-
[[Category: Single protein]]
+
[[Category: Dai S]]
-
[[Category: Bolin, J.T.]]
+
-
[[Category: Dai, S.]]
+
-
[[Category: BP6]]
+
-
[[Category: FE2]]
+
-
[[Category: P6G]]
+
-
[[Category: 2]]
+
-
[[Category: 3-dihydroxybiphenyl]]
+
-
[[Category: anaerobic]]
+
-
[[Category: extradiol dioxygenase]]
+
-
[[Category: non-heme iron]]
+
-
[[Category: pcb biodegradation]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:37:33 2007''
+

Current revision

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

PDB ID 1lkd

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1lkd"
Personal tools