5kbi - Revision history

OCA at 12:39, 6 March 2024

2024-03-06T12:39:36Z

←Older revision		Revision as of 12:39, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MOPR_ACIGI MOPR_ACIGI] Involved in the regulation of the phenol degradation pathway. Activates phenol hydroxylase expression in the presence of phenol.<ref>PMID:9023219</ref>		[https://www.uniprot.org/uniprot/MOPR_ACIGI MOPR_ACIGI] Involved in the regulation of the phenol degradation pathway. Activates phenol hydroxylase expression in the presence of phenol.<ref>PMID:9023219</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Phenol and its derivatives are common pollutants that are present in industrial discharge and are major xenobiotics that lead to water pollution. To monitor as well as improve water quality, attempts have been made in the past to engineer bacterial in vivo biosensors. However, due to the paucity of structural information, there is insufficiency in gauging the factors that lead to high sensitivity and selectivity, thereby impeding development. Here, we present the crystal structure of the sensor domain of MopR (MopRAB) from Acinetobacter calcoaceticus in complex with phenol and its derivatives to a maximum resolution of 2.5 A. The structure reveals that the N-terminal residues 21-47 possess a unique fold, which are involved in stabilization of the biological dimer, and the central ligand binding domain belongs to the "nitric oxide signaling and golgi transport" fold, commonly present in eukaryotic proteins that bind long-chain fatty acids. In addition, MopRAB nests a zinc atom within a novel zinc binding motif, crucial for maintaining structural integrity. We propose that this motif is crucial for orchestrated motions associated with the formation of the effector binding pocket. Our studies reveal that residues W134 and H106 play an important role in ligand binding and are the key selectivity determinants. Furthermore, comparative analysis of MopR with XylR and DmpR sensor domains enabled the design of a MopR binding pocket that is competent in binding DmpR-specific ligands. Collectively, these findings pave way towards development of specific/broad based biosensors, which can act as useful tools for detection of this class of pollutants.
-
-	Structural Basis of Selective Aromatic Pollutant Sensing by the Effector Binding Domain of MopR, an NtrC Family Transcriptional Regulator.,Ray S, Gunzburg MJ, Wilce M, Panjikar S, Anand R ACS Chem Biol. 2016 Jun 30. PMID:27362503<ref>PMID:27362503</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5kbi" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:44, 27 September 2023

2023-09-27T10:44:28Z

←Older revision		Revision as of 10:44, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5kbi' size='340' side='right'caption='[[5kbi]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5kbi' size='340' side='right'caption='[[5kbi]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kbi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Acica Acica~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KBI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kbi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_calcoaceticus Acinetobacter calcoaceticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KBI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5kbe\|5kbe]], [[5kbg\|5kbg]], [[5kbh\|5kbh]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">mopR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=471 ACICA])~~</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=5kbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kbi OCA], [https://pdbe.org/5kbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kbi RCSB], [https://www.ebi.ac.uk/pdbsum/5kbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kbi ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5kbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kbi OCA], [~~http~~://pdbe.org/5kbi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kbi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kbi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kbi ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MOPR_ACIGI MOPR_ACIGI] Involved in the regulation of the phenol degradation pathway. Activates phenol hydroxylase expression in the presence of phenol.<ref>PMID:9023219</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acica~~]]	+	[[Category: Acinetobacter calcoaceticus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Anand, R]]	+	[[Category: Anand R]]
-	[[Category: Panjikar, S]]	+	[[Category: Panjikar S]]
-	[[Category: Ray, S]]	+	[[Category: Ray S]]
-	~~[[Category: Aromatic sensor]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 09:32, 1 July 2020

2020-07-01T09:32:01Z

←Older revision		Revision as of 09:32, 1 July 2020
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH CATACHOL==		==CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH CATACHOL==
-	<StructureSection load='5kbi' size='340' side='right' caption='[[5kbi]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5kbi' size='340' side='right'caption='[[5kbi]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kbi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KBI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kbi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acica Acica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KBI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KBI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kbe\|5kbe]], [[5kbg\|5kbg]], [[5kbh\|5kbh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kbe\|5kbe]], [[5kbg\|5kbg]], [[5kbh\|5kbh]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5kbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kbi OCA], [http://pdbe.org/5kbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kbi RCSB], [http://www.ebi.ac.uk/pdbsum/5kbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kbi ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mopR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=471 ACICA])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5kbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kbi OCA], [http://pdbe.org/5kbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kbi RCSB], [http://www.ebi.ac.uk/pdbsum/5kbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kbi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Acica]]
		+	[[Category: Large Structures]]
	[[Category: Anand, R]]		[[Category: Anand, R]]
	[[Category: Panjikar, S]]		[[Category: Panjikar, S]]

OCA at 11:49, 14 July 2016

2016-07-14T11:49:49Z

←Older revision		Revision as of 11:49, 14 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kbi is ~~ON HOLD until Paper~~ Publication	+	==CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH CATACHOL==
		+	<StructureSection load='5kbi' size='340' side='right' caption='[[5kbi]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kbi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KBI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kbe\|5kbe]], [[5kbg\|5kbg]], [[5kbh\|5kbh]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5kbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kbi OCA], [http://pdbe.org/5kbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kbi RCSB], [http://www.ebi.ac.uk/pdbsum/5kbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kbi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phenol and its derivatives are common pollutants that are present in industrial discharge and are major xenobiotics that lead to water pollution. To monitor as well as improve water quality, attempts have been made in the past to engineer bacterial in vivo biosensors. However, due to the paucity of structural information, there is insufficiency in gauging the factors that lead to high sensitivity and selectivity, thereby impeding development. Here, we present the crystal structure of the sensor domain of MopR (MopRAB) from Acinetobacter calcoaceticus in complex with phenol and its derivatives to a maximum resolution of 2.5 A. The structure reveals that the N-terminal residues 21-47 possess a unique fold, which are involved in stabilization of the biological dimer, and the central ligand binding domain belongs to the "nitric oxide signaling and golgi transport" fold, commonly present in eukaryotic proteins that bind long-chain fatty acids. In addition, MopRAB nests a zinc atom within a novel zinc binding motif, crucial for maintaining structural integrity. We propose that this motif is crucial for orchestrated motions associated with the formation of the effector binding pocket. Our studies reveal that residues W134 and H106 play an important role in ligand binding and are the key selectivity determinants. Furthermore, comparative analysis of MopR with XylR and DmpR sensor domains enabled the design of a MopR binding pocket that is competent in binding DmpR-specific ligands. Collectively, these findings pave way towards development of specific/broad based biosensors, which can act as useful tools for detection of this class of pollutants.

-	~~Authors: Ray~~, S., ~~Anand~~, R., ~~Panjikar~~, S.	+	Structural Basis of Selective Aromatic Pollutant Sensing by the Effector Binding Domain of MopR, an NtrC Family Transcriptional Regulator.,Ray S, Gunzburg MJ, Wilce M, Panjikar S, Anand R ACS Chem Biol. 2016 Jun 30. PMID:27362503<ref>PMID:27362503</ref>

-	~~Description: CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH CATACHOL~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5kbi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Anand, R]]		[[Category: Anand, R]]
-	[[Category: Ray, S]]
	[[Category: Panjikar, S]]		[[Category: Panjikar, S]]
		+	[[Category: Ray, S]]
		+	[[Category: Aromatic sensor]]
		+	[[Category: Transcription]]

OCA at 00:12, 13 July 2016

2016-07-13T00:12:33Z

←Older revision		Revision as of 00:12, 13 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kbi is ON HOLD	+	The entry 5kbi is ON HOLD until Paper Publication

	Authors: Ray, S., Anand, R., Panjikar, S.		Authors: Ray, S., Anand, R., Panjikar, S.

OCA: Protected "5kbi" [edit=sysop:move=sysop]

2016-06-20T13:40:44Z

Protected "5kbi" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:40, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kbi is ON HOLD Authors: Ray, S., Anand, R., Panjikar, S. Description: CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH CATA...

2016-06-20T13:40:42Z

New page: '''Unreleased structure''' The entry 5kbi is ON HOLD Authors: Ray, S., Anand, R., Panjikar, S. Description: CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH CATA...

New page

'''Unreleased structure'''

The entry 5kbi is ON HOLD

Authors: Ray, S., Anand, R., Panjikar, S.

Description: CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH CATACHOL
[[Category: Unreleased Structures]]
[[Category: Anand, R]]
[[Category: Ray, S]]
[[Category: Panjikar, S]]