2r8x - Revision history

OCA at 09:20, 21 February 2024

OCA — Wed, 21 Feb 2024 09:20:53 GMT

←Older revision		Revision as of 09:20, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2r8x' size='340' side='right'caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2r8x' size='340' side='right'caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8X FirstGlance]. <br>
-	</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></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]] 2.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[2r8e\|2r8e]]~~, [[~~2r8y~~\|~~2r8y]], [[2r8z\|2r8z~~]]~~</div>~~</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></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>yrbI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </~~span~~></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [https://pdbe.org/2r8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [https://www.ebi.ac.uk/pdbsum/2r8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8x ProSAT]</span></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [https://pdbe.org/2r8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [https://www.ebi.ac.uk/pdbsum/2r8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KDSC_ECOL6 KDSC_ECOL6]] Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.	+	[https://www.uniprot.org/uniprot/KDSC_ECOL6 KDSC_ECOL6] Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=2r8x ConSurf].		</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=2r8x ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The phosphatase KdsC cleaves 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of inorganic phosphate and Kdo. Kdo is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. Because lipopolysaccharide is an important determinant of bacterial resistance and toxicity, KdsC is a potential target for novel antibacterial agents. KdsC belongs to the broad haloacid dehalogenase superfamily. In haloacid dehalogenase superfamily enzymes, substrate specificity and catalytic efficiency are generally dictated by a fold feature called the cap domain. It is therefore not clear why KdsC, which lacks a cap domain, is catalytically efficient and highly specific to 3-deoxy-D-manno-octulosonate 8-phosphate. Here, we present a set of seven structures of tetrameric Escherichia coli KdsC (ranging from 1.4 to 3.06 A in resolution) that model different intermediate states in its catalytic mechanism. A crystal structure of product-bound E. coli KdsC shows how the interface between adjacent monomers defines the active site pocket. Kdo is engaged in a network of polar and nonpolar interactions with residues at this interface, which explains substrate specificity. Furthermore, this structural and kinetic analysis strongly suggests that the binding of the flexible C-terminal region (tail) to the active site makes KdsC catalytically efficient by facilitating product release.
-
-	The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase.,Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW, Tsodikov OV J Biol Chem. 2009 Oct 30;284(44):30594-603. Epub 2009 Sep 2. PMID:19726684<ref>PMID:19726684</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2r8x" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: 3-deoxy-manno-octulosonate-8-phosphatase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aggarwal, P]]	+	[[Category: Aggarwal P]]
-	[[Category: Biswas, T]]	+	[[Category: Biswas T]]
-	[[Category: Rubin~~, J R~~]]	+	[[Category: Rubin JR]]
-	[[Category: Stuckey~~, J A~~]]	+	[[Category: Stuckey JA]]
-	[[Category: Tsodikov~~, O V~~]]	+	[[Category: Tsodikov OV]]
-	[[Category: Woodard~~, R W]]~~	+	[[Category: Woodard RW]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phosphatase kdo8-p]]~~	+
-	~~[[Category: Yrbi~~]]	+

OCA at 04:18, 2 July 2021

OCA — Fri, 02 Jul 2021 04:18:22 GMT

←Older revision		Revision as of 04:18, 2 July 2021
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	==Crystal structure of YrbI phosphatase from Escherichia coli==		==Crystal structure of YrbI phosphatase from Escherichia coli==
-	<StructureSection load='2r8x' size='340' side='right' caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='2r8x' size='340' side='right'caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2R8X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</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></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r8e\|2r8e]], [[2r8y\|2r8y]], [[2r8z\|2r8z]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2r8e\|2r8e]], [[2r8y\|2r8y]], [[2r8z\|2r8z]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [~~http~~://pdbe.org/2r8x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2r8x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8x ProSAT]</span></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [https://pdbe.org/2r8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [https://www.ebi.ac.uk/pdbsum/2r8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KDSC_ECOL6 KDSC_ECOL6]] Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.	+	[[https://www.uniprot.org/uniprot/KDSC_ECOL6 KDSC_ECOL6]] Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]		[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]
		+	[[Category: Large Structures]]
	[[Category: Aggarwal, P]]		[[Category: Aggarwal, P]]
	[[Category: Biswas, T]]		[[Category: Biswas, T]]

OCA at 11:33, 5 September 2018

OCA — Wed, 05 Sep 2018 11:33:30 GMT

←Older revision		Revision as of 11:33, 5 September 2018
Line 1:		Line 1:
		+
	==Crystal structure of YrbI phosphatase from Escherichia coli==		==Crystal structure of YrbI phosphatase from Escherichia coli==
	<StructureSection load='2r8x' size='340' side='right' caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2r8x' size='340' side='right' caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [http://pdbe.org/2r8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [http://www.ebi.ac.uk/pdbsum/2r8x PDBsum]</span></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [http://pdbe.org/2r8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [http://www.ebi.ac.uk/pdbsum/2r8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r8/2r8x_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r8/2r8x_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 00:42, 10 February 2016

OCA — Wed, 10 Feb 2016 00:42:37 GMT

←Older revision		Revision as of 00:42, 10 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=2r8x ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:39, 11 September 2015

OCA — Fri, 11 Sep 2015 03:39:40 GMT

←Older revision		Revision as of 03:39, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2r8x' size='340' side='right' caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2r8x' size='340' side='right' caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r8e\|2r8e]], [[2r8y\|2r8y]], [[2r8z\|2r8z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r8e\|2r8e]], [[2r8y\|2r8y]], [[2r8z\|2r8z]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [http://www.ebi.ac.uk/pdbsum/2r8x PDBsum]</span></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [http://pdbe.org/2r8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [http://www.ebi.ac.uk/pdbsum/2r8x PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2r8x" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]		[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]
-	[[Category: Escherichia coli]]
	[[Category: Aggarwal, P]]		[[Category: Aggarwal, P]]
	[[Category: Biswas, T]]		[[Category: Biswas, T]]

OCA at 10:35, 25 December 2014

OCA — Thu, 25 Dec 2014 10:35:54 GMT

←Older revision		Revision as of 10:35, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8X FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8X FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r8e\|2r8e]], [[2r8y\|2r8y]], [[2r8z\|2r8z]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r8e\|2r8e]], [[2r8y\|2r8y]], [[2r8z\|2r8z]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [http://www.ebi.ac.uk/pdbsum/2r8x PDBsum]</span></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=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [http://www.ebi.ac.uk/pdbsum/2r8x PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KDSC_ECOL6 KDSC_ECOL6]] Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]		[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Aggarwal, P.]]	+	[[Category: Aggarwal, P]]
-	[[Category: Biswas, T.]]	+	[[Category: Biswas, T]]
-	[[Category: Rubin, J R.]]	+	[[Category: Rubin, J R]]
-	[[Category: Stuckey, J A.]]	+	[[Category: Stuckey, J A]]
-	[[Category: Tsodikov, O V.]]	+	[[Category: Tsodikov, O V]]
-	[[Category: Woodard, R W.]]	+	[[Category: Woodard, R W]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Phosphatase kdo8-p]]		[[Category: Phosphatase kdo8-p]]
	[[Category: Yrbi]]		[[Category: Yrbi]]

OCA at 19:44, 30 September 2014

OCA — Tue, 30 Sep 2014 19:44:32 GMT

←Older revision		Revision as of 19:44, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2r8x.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of YrbI phosphatase from Escherichia coli==
		+	<StructureSection load='2r8x' size='340' side='right' caption='[[2r8x]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2r8x]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8X FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r8e\|2r8e]], [[2r8y\|2r8y]], [[2r8z\|2r8z]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yrbI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate-8-phosphatase 3-deoxy-manno-octulosonate-8-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.45 3.1.3.45] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8x RCSB], [http://www.ebi.ac.uk/pdbsum/2r8x PDBsum]</span></td></tr>
		+	<table>
		+	== 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/r8/2r8x_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The phosphatase KdsC cleaves 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of inorganic phosphate and Kdo. Kdo is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. Because lipopolysaccharide is an important determinant of bacterial resistance and toxicity, KdsC is a potential target for novel antibacterial agents. KdsC belongs to the broad haloacid dehalogenase superfamily. In haloacid dehalogenase superfamily enzymes, substrate specificity and catalytic efficiency are generally dictated by a fold feature called the cap domain. It is therefore not clear why KdsC, which lacks a cap domain, is catalytically efficient and highly specific to 3-deoxy-D-manno-octulosonate 8-phosphate. Here, we present a set of seven structures of tetrameric Escherichia coli KdsC (ranging from 1.4 to 3.06 A in resolution) that model different intermediate states in its catalytic mechanism. A crystal structure of product-bound E. coli KdsC shows how the interface between adjacent monomers defines the active site pocket. Kdo is engaged in a network of polar and nonpolar interactions with residues at this interface, which explains substrate specificity. Furthermore, this structural and kinetic analysis strongly suggests that the binding of the flexible C-terminal region (tail) to the active site makes KdsC catalytically efficient by facilitating product release.

-	~~{{STRUCTURE_2r8x\| PDB=2r8x \| SCENE= }}~~	+	The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase.,Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW, Tsodikov OV J Biol Chem. 2009 Oct 30;284(44):30594-603. Epub 2009 Sep 2. PMID:19726684<ref>PMID:19726684</ref>

-	~~===Crystal structure~~ of ~~YrbI phosphatase from Escherichia coli===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19726684}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2r8x]] is a 16 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019726684<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]		[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "2r8x" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 22:38:18 GMT

Protected "2r8x" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:38, 7 January 2013

OCA at 22:38, 7 January 2013

OCA — Mon, 07 Jan 2013 22:38:15 GMT

←Older revision		Revision as of 22:38, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2r8x.png\|left\|200px]]		[[Image:2r8x.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2r8x", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2r8x\| PDB=2r8x \| SCENE= }}		{{STRUCTURE_2r8x\| PDB=2r8x \| SCENE= }}

	===Crystal structure of YrbI phosphatase from Escherichia coli===		===Crystal structure of YrbI phosphatase from Escherichia coli===

		+	{{ABSTRACT_PUBMED_19726684}}

	==About this Structure==		==About this Structure==
-	~~2R8X~~ is a 16 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA].	+	[[2r8x]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:019726684</ref><references group="xtra"/>
	[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]		[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 26:		Line 23:
	[[Category: Phosphatase kdo8-p]]		[[Category: Phosphatase kdo8-p]]
	[[Category: Yrbi]]		[[Category: Yrbi]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 4 20:31:40 2009''

OCA at 18:22, 4 November 2009

OCA — Wed, 04 Nov 2009 18:22:52 GMT

←Older revision		Revision as of 18:22, 4 November 2009
Line 12:		Line 12:
	===Crystal structure of YrbI phosphatase from Escherichia coli===		===Crystal structure of YrbI phosphatase from Escherichia coli===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19726684}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19726684 is the PubMed ID number.
-	-->
-	{{ABSTRACT_PUBMED_19726684}}

	==About this Structure==		==About this Structure==
	2R8X is a 16 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA].		2R8X is a 16 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8X OCA].
-
-	==Reference==
-	<ref group="xtra">PMID:19726684</ref><references group="xtra"/>
	[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]		[[Category: 3-deoxy-manno-octulosonate-8-phosphatase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 36:		Line 27:
	[[Category: Yrbi]]		[[Category: Yrbi]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 4 12:05:42 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 4 20:31:40 2009''