4rpn: Difference between revisions
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==PcpR inducer binding domain complex with pentachlorophenol== | ==PcpR inducer binding domain complex with pentachlorophenol== | ||
<StructureSection load='4rpn' size='340' side='right' caption='[[4rpn]], [[Resolution|resolution]] 2.27Å' scene=''> | <StructureSection load='4rpn' size='340' side='right'caption='[[4rpn]], [[Resolution|resolution]] 2.27Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4rpn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RPN OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4rpn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingobium_chlorophenolicum Sphingobium chlorophenolicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RPN FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.272Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCI:PENTACHLOROPHENOL'>PCI</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4rpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rpn OCA], [https://pdbe.org/4rpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rpn RCSB], [https://www.ebi.ac.uk/pdbsum/4rpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rpn ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/PCPR_SPHCR PCPR_SPHCR] Transcriptional activator for the pcpA, pcpB and pcpE genes for pentachlorophenol (PCP) degradation. Essential for PCP degradation.<ref>PMID:12169590</ref> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4rpn" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Sphingobium chlorophenolicum]] | ||
[[Category: | [[Category: Hayes RP]] | ||
[[Category: | [[Category: Kang C]] | ||
[[Category: | [[Category: Lewis KM]] | ||
[[Category: | [[Category: Moural TW]] | ||
[[Category: | [[Category: Onofrei D]] | ||
[[Category: | [[Category: Xun L]] | ||
Latest revision as of 20:53, 20 September 2023
PcpR inducer binding domain complex with pentachlorophenolPcpR inducer binding domain complex with pentachlorophenol
Structural highlights
FunctionPCPR_SPHCR Transcriptional activator for the pcpA, pcpB and pcpE genes for pentachlorophenol (PCP) degradation. Essential for PCP degradation.[1] Publication Abstract from PubMedPcpR is a LysR-type transcription factor from Sphingobium chlorophenolicum L-1 that is responsible for the activation of several genes involved in polychlorophenol degradation. PcpR responds to several polychlorophenols in vivo. Here, we report the crystal structures of the inducer-binding domain of PcpR in the apo-form and binary complexes with pentachlorophenol (PCP) and 2,4,6-trichlorophenol (2,4,6-TCP). Both X-ray crystal structures and isothermal titration calorimetry data indicated the association of two PCP molecules per PcpR, but only one 2,4,6-TCP molecule. The hydrophobic nature and hydrogen bonds of one binding cavity allowed the tight association of both PCP (Kd = 110 nM) and 2,4,6-TCP (Kd = 22.8 nM). However, the other cavity was unique to PCP with much weaker affinity (Kd = 70 muM) and thus its significance was not clear. Neither phenol nor benzoic acid displayed any significant affinity to PcpR, indicating a role of chlorine substitution in ligand specificity. When PcpR is compared with TcpR, a LysR-type regulator controlling the expression of 2,4,6-trichlorophenol degradation in Cupriavidus necator JMP134, most of the residues constituting the two inducer-binding cavities of PcpR are different, except for their general hydrophobic nature. The finding concurs that PcpR uses various polychlorophenols as long as it includes 2,4,6-trichlorophenol, as inducers; whereas TcpR is only responsive to 2,4,6-trichlorophenol. Structures of the Inducer-Binding Domain of Pentachlorophenol-Degrading Gene Regulator PcpR from Sphingobium chlorophenolicum.,Hayes RP, Moural TW, Lewis KM, Onofrei D, Xun L, Kang C Int J Mol Sci. 2014 Nov 12;15(11):20736-52. doi: 10.3390/ijms151120736. PMID:25397598[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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