3qyr - Revision history

OCA at 12:03, 14 March 2024

OCA — Thu, 14 Mar 2024 12:03:21 GMT

←Older revision		Revision as of 12:03, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3qyr' size='340' side='right'caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='3qyr' size='340' side='right'caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qyr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_paratuberculosis"_(bergey_et_al~~.~~_1923)_krasil'nikov_1941 "bacillus~~ paratuberculosis~~" (bergey et al. 1923) krasil'nikov 1941~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qyr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_avium_subsp._paratuberculosis Mycobacterium avium subsp. paratuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</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]] 2.45Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>echA16, MAP_2904 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1770~~ "~~Bacillus paratuberculosis~~" ~~(Bergey et al. 1923) Krasil'nikov 1941])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Enoyl-CoA_hydratase Enoyl-CoA hydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.17 4.2.1.17]~~ </~~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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [https://pdbe.org/3qyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [https://www.ebi.ac.uk/pdbsum/3qyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyr 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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [https://pdbe.org/3qyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [https://www.ebi.ac.uk/pdbsum/3qyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyr ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q73VV7_MYCPA Q73VV7_MYCPA]
-	High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Calpha RMSD <1 A, >85% side chain identity, and >/=80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.	+
-		+
-	Increasing the structural coverage of tuberculosis drug targets.,Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D 3rd, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ Tuberculosis (Edinb). 2014 Dec 19. pii: ~~S1472-9792(14)20565-8. doi:, 10.1016~~/~~j.tube.2014.12.003. PMID:25613812<ref>PMID:25613812<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3qyr" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Enoyl-CoA hydratase 3D structures\|Enoyl-CoA hydratase 3D structures]]		*[[Enoyl-CoA hydratase 3D structures\|Enoyl-CoA hydratase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Enoyl-CoA hydratase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Structural genomic]]~~	+	[[Category: Mycobacterium avium subsp. paratuberculosis]]
-	~~[[Category: Emerald biostructure]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Niaid]]~~	+
-	~~[[Category: Nih]]~~	+
-	~~[[Category: Sbri]]~~	+
-	~~[[Category: Ssgcid]]~~	+
-	~~[[Category: Uw~~]]	+

OCA at 05:41, 15 June 2022

OCA — Wed, 15 Jun 2022 05:41:49 GMT

←Older revision		Revision as of 05:41, 15 June 2022
Line 1:		Line 1:

	==Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10==		==Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10==
-	<StructureSection load='3qyr' size='340' side='right' caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='3qyr' size='340' side='right'caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qyr]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_paratuberculosis"_(bergey_et_al._1923)_krasil'nikov_1941 "bacillus paratuberculosis" (bergey et al. 1923) krasil'nikov 1941]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qyr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_paratuberculosis"_(bergey_et_al._1923)_krasil'nikov_1941 "bacillus paratuberculosis" (bergey et al. 1923) krasil'nikov 1941]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">echA16, MAP_2904 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1770 "Bacillus paratuberculosis" (Bergey et al. 1923) Krasil'nikov 1941])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">echA16, MAP_2904 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1770 "Bacillus paratuberculosis" (Bergey et al. 1923) Krasil'nikov 1941])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Enoyl-CoA_hydratase Enoyl-CoA hydratase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.17 4.2.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Enoyl-CoA_hydratase Enoyl-CoA hydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.17 4.2.1.17] </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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [~~http~~://pdbe.org/3qyr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qyr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyr 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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [https://pdbe.org/3qyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [https://www.ebi.ac.uk/pdbsum/3qyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 3qyr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3qyr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Enoyl-CoA hydratase 3D structures\|Enoyl-CoA hydratase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Enoyl-CoA hydratase]]		[[Category: Enoyl-CoA hydratase]]
		+	[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Emerald biostructure]]		[[Category: Emerald biostructure]]

OCA at 18:40, 1 February 2017

OCA — Wed, 01 Feb 2017 18:40:38 GMT

←Older revision		Revision as of 18:40, 1 February 2017
Line 1:		Line 1:
		+
	==Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10==		==Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10==
	<StructureSection load='3qyr' size='340' side='right' caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='3qyr' size='340' side='right' caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">echA16, MAP_2904 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1770 "Bacillus paratuberculosis" (Bergey et al. 1923) Krasil'nikov 1941])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">echA16, MAP_2904 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1770 "Bacillus paratuberculosis" (Bergey et al. 1923) Krasil'nikov 1941])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Enoyl-CoA_hydratase Enoyl-CoA hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.17 4.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Enoyl-CoA_hydratase Enoyl-CoA hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.17 4.2.1.17] </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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [http://www.ebi.ac.uk/pdbsum/3qyr 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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [http://pdbe.org/3qyr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [http://www.ebi.ac.uk/pdbsum/3qyr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3qyr" style="background-color:#fffaf0;"></div>
-	==~~See Also==~~	+
-	*[[Enoyl-CoA hydratase\|Enoyl-~~CoA hydratase]]~~	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:45, 22 April 2015

OCA — Wed, 22 Apr 2015 06:45:15 GMT

←Older revision		Revision as of 06:45, 22 April 2015
Line 2:		Line 2:
	<StructureSection load='3qyr' size='340' side='right' caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='3qyr' size='340' side='right' caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qyr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_avium_subsp._paratuberculosis Mycobacterium avium subsp~~. paratuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qyr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_paratuberculosis"_(bergey_et_al._1923)_krasil'nikov_1941 "bacillus paratuberculosis" (bergey et al. 1923) krasil'nikov 1941]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">echA16, MAP_2904 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1770 ~~Mycobacterium avium subsp.~~ paratuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">echA16, MAP_2904 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1770 "Bacillus paratuberculosis" (Bergey et al. 1923) Krasil'nikov 1941])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Enoyl-CoA_hydratase Enoyl-CoA hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.17 4.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Enoyl-CoA_hydratase Enoyl-CoA hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.17 4.2.1.17] </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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [http://www.ebi.ac.uk/pdbsum/3qyr 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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [http://www.ebi.ac.uk/pdbsum/3qyr PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Calpha RMSD <1 A, >85% side chain identity, and >/=80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
		+
		+	Increasing the structural coverage of tuberculosis drug targets.,Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D 3rd, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ Tuberculosis (Edinb). 2014 Dec 19. pii: S1472-9792(14)20565-8. doi:, 10.1016/j.tube.2014.12.003. PMID:25613812<ref>PMID:25613812</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+
		+	==See Also==
		+	*[[Enoyl-CoA hydratase\|Enoyl-CoA hydratase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Enoyl-CoA hydratase]]		[[Category: Enoyl-CoA hydratase]]
-	[[Category: Mycobacterium avium subsp. paratuberculosis]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Emerald biostructure]]		[[Category: Emerald biostructure]]

OCA at 10:18, 19 December 2014

OCA — Fri, 19 Dec 2014 10:18:10 GMT

←Older revision		Revision as of 10:18, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3qyr\| PDB=3qyr \| SCENE= }}~~	+	==Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10==
-	===Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10===	+	<StructureSection load='3qyr' size='340' side='right' caption='[[3qyr]], [[Resolution\|resolution]] 2.45Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[3qyr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_avium_subsp._paratuberculosis Mycobacterium avium subsp. paratuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYR FirstGlance]. <br>
-	[[3qyr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_avium_subsp._paratuberculosis Mycobacterium avium subsp. paratuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">echA16, MAP_2904 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1770 Mycobacterium avium subsp. paratuberculosis])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Enoyl-CoA_hydratase Enoyl-CoA hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.17 4.2.1.17] </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=3qyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyr RCSB], [http://www.ebi.ac.uk/pdbsum/3qyr PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Enoyl-CoA hydratase]]		[[Category: Enoyl-CoA hydratase]]
	[[Category: Mycobacterium avium subsp. paratuberculosis]]		[[Category: Mycobacterium avium subsp. paratuberculosis]]
-	[[Category: ~~SSGCID, Seattle~~ Structural ~~Genomics Center for Infectious Disease.~~]]	+	[[Category: Structural genomic]]
	[[Category: Emerald biostructure]]		[[Category: Emerald biostructure]]
	[[Category: Lyase]]		[[Category: Lyase]]
Line 12:		Line 18:
	[[Category: Nih]]		[[Category: Nih]]
	[[Category: Sbri]]		[[Category: Sbri]]
-	[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
-	[[Category: Structural genomic]]
	[[Category: Uw]]		[[Category: Uw]]

OCA at 07:52, 16 May 2013

OCA — Thu, 16 May 2013 07:52:33 GMT

←Older revision		Revision as of 07:52, 16 May 2013
Line 1:		Line 1:
-	[[Image:3qyr.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3qyr", 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_3qyr\| PDB=3qyr \| SCENE= }}		{{STRUCTURE_3qyr\| PDB=3qyr \| SCENE= }}
-
	===Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10===		===Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10===
-

	==About this Structure==		==About this Structure==
Line 17:		Line 7:
	[[Category: Mycobacterium avium subsp. paratuberculosis]]		[[Category: Mycobacterium avium subsp. paratuberculosis]]
	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]		[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
		+	[[Category: Emerald biostructure]]
		+	[[Category: Lyase]]
		+	[[Category: Niaid]]
		+	[[Category: Nih]]
		+	[[Category: Sbri]]
		+	[[Category: Seattle structural genomics center for infectious disease]]
		+	[[Category: Ssgcid]]
		+	[[Category: Structural genomic]]
		+	[[Category: Uw]]

OCA at 08:38, 16 March 2011

OCA — Wed, 16 Mar 2011 08:38:04 GMT

←Older revision		Revision as of 08:38, 16 March 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3qyr.jpg\|left\|200px]]

-	The ~~entry 3qyr~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qyr", 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_3qyr\| PDB=3qyr \| SCENE= }}

-	~~Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	===Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10===

-	~~Description: Crystal~~ structure ~~of enoyl-coA hydratase EchA16_2~~ Mycobacterium paratuberculosis ~~ATCC BAA~~-~~968~~ / K-10	+
		+	==About this Structure==
		+	[[3qyr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_avium_subsp._paratuberculosis Mycobacterium avium subsp. paratuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYR OCA].
		+	[[Category: Enoyl-CoA hydratase]]
		+	[[Category: Mycobacterium avium subsp. paratuberculosis]]
		+	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]

OCA: Protected "3qyr" [edit=sysop:move=sysop]

OCA — Wed, 09 Mar 2011 06:11:30 GMT

Protected "3qyr" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:11, 9 March 2011

OCA: New page: '''Unreleased structure''' The entry 3qyr is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of enoyl-coA hydratase E...

OCA — Wed, 09 Mar 2011 06:11:29 GMT

New page: '''Unreleased structure''' The entry 3qyr is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of enoyl-coA hydratase E...

New page

'''Unreleased structure'''

The entry 3qyr is ON HOLD

Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Description: Crystal structure of enoyl-coA hydratase EchA16_2 Mycobacterium paratuberculosis ATCC BAA-968 / K-10