1l6r - Revision history

OCA at 07:30, 14 February 2024

OCA — Wed, 14 Feb 2024 07:30:17 GMT

←Older revision		Revision as of 07:30, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1l6r' size='340' side='right'caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='1l6r' size='340' side='right'caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L6R FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 1.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1kyt\|1kyt]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">TA0175 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])~~</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [https://pdbe.org/1l6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [https://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l6r ProSAT], [https://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [https://pdbe.org/1l6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [https://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l6r ProSAT], [https://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PGP_THEAC PGP_THEAC]] Catalyzes the dephosphorylation of 2-phosphoglycolate. Also has significant, but less efficient, pyrophosphatase activity, since it is able to catalyze the release of phosphate from inorganic pyrophosphate (PPi).<ref>PMID:14555659</ref>	+	[https://www.uniprot.org/uniprot/PGP_THEAC PGP_THEAC] Catalyzes the dephosphorylation of 2-phosphoglycolate. Also has significant, but less efficient, pyrophosphatase activity, since it is able to catalyze the release of phosphate from inorganic pyrophosphate (PPi).<ref>PMID:14555659</ref>
	== 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=1l6r 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=1l6r ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The protein TA0175 has a large number of sequence homologues, most of which are annotated as unknown and a few as belonging to the haloacid dehalogenase superfamily, but has no known biological function. Using a combination of amino acid sequence analysis, three-dimensional crystal structure information, and kinetic analysis, we have characterized TA0175 as phosphoglycolate phosphatase from Thermoplasma acidophilum. The crystal structure of TA0175 revealed two distinct domains, a larger core domain and a smaller cap domain. The large domain is composed of a centrally located five-stranded parallel beta-sheet with strand order S10, S9, S8, S1, S2 and a small beta-hairpin, strands S3 and S4. This central sheet is flanked by a set of three alpha-helices on one side and two helices on the other. The smaller domain is composed of an open faced beta-sandwich represented by three antiparallel beta-strands, S5, S6, and S7, flanked by two oppositely oriented alpha-helices, H3 and H4. The topology of the large domain is conserved; however, structural variation is observed in the smaller domain among the different functional classes of the haloacid dehalogenase superfamily. Enzymatic assays on TA0175 revealed that this enzyme catalyzed the dephosphorylation of phosphoglycolate in vitro with similar kinetic properties seen for eukaryotic phosphoglycolate phosphatase. Activation by divalent cations, especially Mg2+, and competitive inhibition behavior with Cl- ions are similar between TA0175 and phosphoglycolate phosphatase. The experimental evidence presented for TA0175 is indicative of phosphoglycolate phosphatase.
-
-	Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum.,Kim Y, Yakunin AF, Kuznetsova E, Xu X, Pennycooke M, Gu J, Cheung F, Proudfoot M, Arrowsmith CH, Joachimiak A, Edwards AM, Christendat D J Biol Chem. 2004 Jan 2;279(1):517-26. Epub 2003 Oct 10. PMID:14555659<ref>PMID:14555659</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1l6r" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cheung, F]]	+	[[Category: Thermoplasma acidophilum]]
-	[[Category: Christendat, D]]	+	[[Category: Cheung F]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Christendat D]]
-	[[Category: Gu, J]]	+	[[Category: Edwards AM]]
-	[[Category: Joachimiak, A]]	+	[[Category: Gu J]]
-	[[Category: Kim, Y]]	+	[[Category: Joachimiak A]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Kim Y]]
-	[[Category: Pennycooke, M]]	+	[[Category: Pennycooke M]]
-	[[Category: Xu, X]]	+	[[Category: Xu X]]
-	~~[[Category: Hypothetical protein]]~~	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Putative hydrolase]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 14:47, 27 October 2021

OCA — Wed, 27 Oct 2021 14:47:10 GMT

←Older revision		Revision as of 14:47, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1l6r' size='340' side='right'caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='1l6r' size='340' side='right'caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1L6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L6R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kyt\|1kyt]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kyt\|1kyt]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [~~http~~://pdbe.org/1l6r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1l6r ProSAT], [~~http~~://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [https://pdbe.org/1l6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [https://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l6r ProSAT], [https://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PGP_THEAC PGP_THEAC]] Catalyzes the dephosphorylation of 2-phosphoglycolate. Also has significant, but less efficient, pyrophosphatase activity, since it is able to catalyze the release of phosphate from inorganic pyrophosphate (PPi).<ref>PMID:14555659</ref>	+	[[https://www.uniprot.org/uniprot/PGP_THEAC PGP_THEAC]] Catalyzes the dephosphorylation of 2-phosphoglycolate. Also has significant, but less efficient, pyrophosphatase activity, since it is able to catalyze the release of phosphate from inorganic pyrophosphate (PPi).<ref>PMID:14555659</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:55, 25 November 2020

OCA — Wed, 25 Nov 2020 07:55:38 GMT

←Older revision		Revision as of 07:55, 25 November 2020
Line 1:		Line 1:

	==Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)==		==Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)==
-	<StructureSection load='1l6r' size='340' side='right' caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='1l6r' size='340' side='right'caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1L6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1L6R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyt\|1kyt]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kyt\|1kyt]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://pdbe.org/1l6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l6r ProSAT], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://pdbe.org/1l6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l6r ProSAT], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l6/1l6r_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l6/1l6r_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>
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Cheung, F]]		[[Category: Cheung, F]]
	[[Category: Christendat, D]]		[[Category: Christendat, D]]

OCA at 15:36, 12 October 2017

OCA — Thu, 12 Oct 2017 15:36:28 GMT

←Older revision		Revision as of 15:36, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)==		==Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)==
	<StructureSection load='1l6r' size='340' side='right' caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='1l6r' size='340' side='right' caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyt\|1kyt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyt\|1kyt]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://pdbe.org/1l6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://pdbe.org/1l6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l6r ProSAT], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 01:29, 10 February 2016

OCA — Wed, 10 Feb 2016 01:29:29 GMT

←Older revision		Revision as of 01:29, 10 February 2016
Line 18:		Line 18:
	<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=1l6r ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:01, 11 September 2015

OCA — Fri, 11 Sep 2015 04:01:25 GMT

←Older revision		Revision as of 04:01, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1l6r' size='340' side='right' caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='1l6r' size='340' side='right' caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermoplasma_acidophilum Thermoplasma acidophilum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L6R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyt\|1kyt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyt\|1kyt]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma ~~acidophilum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://pdbe.org/1l6r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1l6r" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Thermoplasma acidophilum]]
	[[Category: Cheung, F]]		[[Category: Cheung, F]]
	[[Category: Christendat, D]]		[[Category: Christendat, D]]

OCA at 10:51, 25 December 2014

OCA — Thu, 25 Dec 2014 10:51:20 GMT

←Older revision		Revision as of 10:51, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L6R FirstGlance]. <br>		<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L6R FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyt\|1kyt]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyt\|1kyt]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PGP_THEAC PGP_THEAC]] Catalyzes the dephosphorylation of 2-phosphoglycolate. Also has significant, but less efficient, pyrophosphatase activity, since it is able to catalyze the release of phosphate from inorganic pyrophosphate (PPi).<ref>PMID:14555659</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Thermoplasma acidophilum]]		[[Category: Thermoplasma acidophilum]]
-	[[Category: Cheung, F.]]	+	[[Category: Cheung, F]]
-	[[Category: Christendat, D.]]	+	[[Category: Christendat, D]]
-	[[Category: Edwards, A M.]]	+	[[Category: Edwards, A M]]
-	[[Category: Gu, J.]]	+	[[Category: Gu, J]]
-	[[Category: Joachimiak, A.]]	+	[[Category: Joachimiak, A]]
-	[[Category: Kim, Y.]]	+	[[Category: Kim, Y]]
-	[[Category: ~~MCSG, Midwest Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Pennycooke, M.]]	+	[[Category: Pennycooke, M]]
-	[[Category: Xu, X.]]	+	[[Category: Xu, X]]
	[[Category: Hypothetical protein]]		[[Category: Hypothetical protein]]
	[[Category: Mcsg]]		[[Category: Mcsg]]
-	[[Category: ~~Midwest center for structural genomic]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
-	~~[[Category: Psi~~]]	+
	[[Category: Putative hydrolase]]		[[Category: Putative hydrolase]]
-	[[Category: Structural genomic]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 18:02, 28 September 2014

OCA — Sun, 28 Sep 2014 18:02:25 GMT

←Older revision		Revision as of 18:02, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1l6r.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)==
		+	<StructureSection load='1l6r' size='340' side='right' caption='[[1l6r]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L6R FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyt\|1kyt]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TA0175 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</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=1l6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l6r RCSB], [http://www.ebi.ac.uk/pdbsum/1l6r PDBsum], [http://www.topsan.org/Proteins/MCSG/1l6r TOPSAN]</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/l6/1l6r_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 protein TA0175 has a large number of sequence homologues, most of which are annotated as unknown and a few as belonging to the haloacid dehalogenase superfamily, but has no known biological function. Using a combination of amino acid sequence analysis, three-dimensional crystal structure information, and kinetic analysis, we have characterized TA0175 as phosphoglycolate phosphatase from Thermoplasma acidophilum. The crystal structure of TA0175 revealed two distinct domains, a larger core domain and a smaller cap domain. The large domain is composed of a centrally located five-stranded parallel beta-sheet with strand order S10, S9, S8, S1, S2 and a small beta-hairpin, strands S3 and S4. This central sheet is flanked by a set of three alpha-helices on one side and two helices on the other. The smaller domain is composed of an open faced beta-sandwich represented by three antiparallel beta-strands, S5, S6, and S7, flanked by two oppositely oriented alpha-helices, H3 and H4. The topology of the large domain is conserved; however, structural variation is observed in the smaller domain among the different functional classes of the haloacid dehalogenase superfamily. Enzymatic assays on TA0175 revealed that this enzyme catalyzed the dephosphorylation of phosphoglycolate in vitro with similar kinetic properties seen for eukaryotic phosphoglycolate phosphatase. Activation by divalent cations, especially Mg2+, and competitive inhibition behavior with Cl- ions are similar between TA0175 and phosphoglycolate phosphatase. The experimental evidence presented for TA0175 is indicative of phosphoglycolate phosphatase.

-	~~{{STRUCTURE_1l6r\| PDB=1l6r \| SCENE= }}~~	+	Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum.,Kim Y, Yakunin AF, Kuznetsova E, Xu X, Pennycooke M, Gu J, Cheung F, Proudfoot M, Arrowsmith CH, Joachimiak A, Edwards AM, Christendat D J Biol Chem. 2004 Jan 2;279(1):517-26. Epub 2003 Oct 10. PMID:14555659<ref>PMID:14555659</ref>

-	~~===Crystal Structure~~ of ~~Thermoplasma acidophilum 0175 (APC0014)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14555659}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1l6r]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:014555659<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermoplasma acidophilum]]		[[Category: Thermoplasma acidophilum]]
	[[Category: Cheung, F.]]		[[Category: Cheung, F.]]

OCA: Protected "1l6r" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 20:56:51 GMT

Protected "1l6r" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:56, 5 December 2012

OCA at 20:56, 5 December 2012

OCA — Wed, 05 Dec 2012 20:56:48 GMT

←Older revision		Revision as of 20:56, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1l6r.png\|left\|200px]]		[[Image:1l6r.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1l6r", 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_1l6r\| PDB=1l6r \| SCENE= }}		{{STRUCTURE_1l6r\| PDB=1l6r \| SCENE= }}

	===Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)===		===Crystal Structure of Thermoplasma acidophilum 0175 (APC0014)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14555659}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14555659 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14555659}}		{{ABSTRACT_PUBMED_14555659}}

	==About this Structure==		==About this Structure==
-	~~1L6R~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA].	+	[[1l6r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L6R OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14555659~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014555659</ref><references group="xtra"/>
	[[Category: Thermoplasma acidophilum]]		[[Category: Thermoplasma acidophilum]]
	[[Category: Cheung, F.]]		[[Category: Cheung, F.]]
Line 41:		Line 29:
	[[Category: Putative hydrolase]]		[[Category: Putative hydrolase]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-		+	[[Category: Unknown function]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 14:19:32 2009''~~	+