5hpf: Difference between revisions
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==Crystal Structure of the Double Mutant of PobR Transcription Factor Inducer Binding Domain from Acinetobacter== | |||
<StructureSection load='5hpf' size='340' side='right'caption='[[5hpf]], [[Resolution|resolution]] 2.31Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5hpf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baylyi_ADP1 Acinetobacter baylyi ADP1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HPF 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]] 2.309Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5hpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hpf OCA], [https://pdbe.org/5hpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hpf RCSB], [https://www.ebi.ac.uk/pdbsum/5hpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hpf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/POBR_ACIAD POBR_ACIAD] Positive regulator of the pobA gene for p-hydroxybenzoate hydroxylase. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to 'sense' a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10(7) variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection ( approximately 2 muM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work. | |||
A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.,Jha RK, Kern TL, Kim Y, Tesar C, Jedrzejczak R, Joachimiak A, Strauss CE Nucleic Acids Res. 2016 Sep 30;44(17):8490-500. doi: 10.1093/nar/gkw687. Epub, 2016 Aug 17. PMID:27536006<ref>PMID:27536006</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5hpf" style="background-color:#fffaf0;"></div> | ||
[[Category: Joachimiak | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Acinetobacter baylyi ADP1]] | |||
[[Category: Large Structures]] | |||
[[Category: Jedrejczak R]] | |||
[[Category: Jha R]] | |||
[[Category: Joachimiak A]] | |||
[[Category: Kim Y]] | |||
[[Category: Strauss CEM]] | |||
[[Category: Tesar C]] | |||
Latest revision as of 13:49, 16 August 2023
Crystal Structure of the Double Mutant of PobR Transcription Factor Inducer Binding Domain from AcinetobacterCrystal Structure of the Double Mutant of PobR Transcription Factor Inducer Binding Domain from Acinetobacter
Structural highlights
FunctionPOBR_ACIAD Positive regulator of the pobA gene for p-hydroxybenzoate hydroxylase. Publication Abstract from PubMedA whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to 'sense' a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10(7) variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection ( approximately 2 muM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work. A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.,Jha RK, Kern TL, Kim Y, Tesar C, Jedrzejczak R, Joachimiak A, Strauss CE Nucleic Acids Res. 2016 Sep 30;44(17):8490-500. doi: 10.1093/nar/gkw687. Epub, 2016 Aug 17. PMID:27536006[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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