4dfe - Revision history

OCA at 02:46, 21 November 2024

2024-11-21T02:46:58Z

← Older revision		Revision as of 02:46, 21 November 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q13VL5_PARXL Q13VL5_PARXL] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.[HAMAP-Rule:MF_01815]		[https://www.uniprot.org/uniprot/Q13VL5_PARXL Q13VL5_PARXL] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.[HAMAP-Rule:MF_01815]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			BACKGROUND: The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. METHODOLOGY/PRINCIPAL FINDINGS: We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. CONCLUSIONS/SIGNIFICANCE: This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.

			Combining functional and structural genomics to sample the essential Burkholderia structome.,Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D 3rd, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC PLoS One. 2013;8(1):e53851. doi: 10.1371/journal.pone.0053851. Epub 2013 Jan 31. PMID:23382856<ref>PMID:23382856</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 4dfe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Acyl carrier protein synthase 3D structures\|Acyl carrier protein synthase 3D structures]]		*[[Acyl carrier protein synthase 3D structures\|Acyl carrier protein synthase 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Paraburkholderia xenovorans LB400]]		[[Category: Paraburkholderia xenovorans LB400]]

OCA at 14:34, 14 March 2024

2024-03-14T14:34:16Z

← Older revision		Revision as of 14:34, 14 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q13VL5_PARXL Q13VL5_PARXL] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.[HAMAP-Rule:MF_01815]		[https://www.uniprot.org/uniprot/Q13VL5_PARXL Q13VL5_PARXL] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.[HAMAP-Rule:MF_01815]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	BACKGROUND: The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. METHODOLOGY/PRINCIPAL FINDINGS: We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. CONCLUSIONS/SIGNIFICANCE: This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.

	Combining functional and structural genomics to sample the essential Burkholderia structome.,Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D 3rd, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC PLoS One. 2013;8(1):e53851. doi: 10.1371/journal.pone.0053851. Epub 2013 Jan 31. PMID:23382856<ref>PMID:23382856</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4dfe" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Acyl carrier protein synthase 3D structures\|Acyl carrier protein synthase 3D structures]]		*[[Acyl carrier protein synthase 3D structures\|Acyl carrier protein synthase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Paraburkholderia xenovorans LB400]]		[[Category: Paraburkholderia xenovorans LB400]]

OCA at 08:20, 6 December 2023

2023-12-06T08:20:41Z

← Older revision		Revision as of 08:20, 6 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dfe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dfe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DFE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <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]] 2.35Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [https://pdbe.org/4dfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [https://www.ebi.ac.uk/pdbsum/4dfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dfe 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=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [https://pdbe.org/4dfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [https://www.ebi.ac.uk/pdbsum/4dfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dfe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/Q13VL5_PARXL Q13VL5_PARXL]] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.[HAMAP-Rule:MF_01815]		[https://www.uniprot.org/uniprot/Q13VL5_PARXL Q13VL5_PARXL] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.[HAMAP-Rule:MF_01815]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 08:16, 21 September 2022

2022-09-21T08:16:25Z

← Older revision		Revision as of 08:16, 21 September 2022
Line 1:		Line 1:

	==Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans==		==Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans==
	<StructureSection load='4dfe' size='340' side='right' caption='[[4dfe]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='4dfe' size='340' side='right'caption='[[4dfe]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dfe]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Burxl Burxl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dfe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DFE 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=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene><~~/td></tr>~~		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [https://pdbe.org/4dfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [https://www.ebi.ac.uk/pdbsum/4dfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dfe ProSAT]</span></td></tr>
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">fabH~~, ~~Bxeno_A3336, Bxe_A1072 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 BURXL])</td></tr>~~
	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-ketoacyl-[acyl-carrier-protein]_synthase_III Beta-ketoacyl-[acyl-carrier-protein] synthase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.180 2.3.1.180] </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=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [~~http~~://pdbe.org/4dfe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dfe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dfe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/~~Q13VL5_BURXL Q13VL5_BURXL~~]] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids ~~(By similarity)~~.[HAMAP-Rule:MF_01815]		[[https://www.uniprot.org/uniprot/Q13VL5_PARXL Q13VL5_PARXL]] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.[HAMAP-Rule:MF_01815]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 20:

	==See Also==		==See Also==
	*[[Acyl carrier protein synthase\|Acyl carrier protein synthase]]		*[[Acyl carrier protein synthase 3D structures\|Acyl carrier protein synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Burxl~~]]		[[Category: Large Structures]]
	[[Category: ~~Structural genomic]]~~		[[Category: Paraburkholderia xenovorans LB400]]
	~~[[Category: Ssgcid]]~~
	~~[[Category: Transferase~~]]

OCA at 06:00, 5 August 2016

2016-08-05T06:00:59Z

← Older revision		Revision as of 06:00, 5 August 2016
Line 1:		Line 1:

	==Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans==		==Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans==
	<StructureSection load='4dfe' size='340' side='right' caption='[[4dfe]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='4dfe' size='340' side='right' caption='[[4dfe]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dfe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_xenovorans_lb400 Burkholderia xenovorans lb400~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dfe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DFE 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fabH, Bxeno_A3336, Bxe_A1072 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 ~~Burkholderia xenovorans LB400~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fabH, Bxeno_A3336, Bxe_A1072 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 BURXL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-ketoacyl-[acyl-carrier-protein]_synthase_III Beta-ketoacyl-[acyl-carrier-protein] synthase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.180 2.3.1.180] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-ketoacyl-[acyl-carrier-protein]_synthase_III Beta-ketoacyl-[acyl-carrier-protein] synthase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.180 2.3.1.180] </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=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [http://www.ebi.ac.uk/pdbsum/4dfe 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=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [http://pdbe.org/4dfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [http://www.ebi.ac.uk/pdbsum/4dfe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dfe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4dfe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Burkholderia xenovorans lb400~~]]		[[Category: Burxl]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 16:21, 25 December 2014

2014-12-25T16:21:13Z

← Older revision		Revision as of 16:21, 25 December 2014
Line 9:		Line 9:
	<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=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [http://www.ebi.ac.uk/pdbsum/4dfe 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=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [http://www.ebi.ac.uk/pdbsum/4dfe PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q13VL5_BURXL Q13VL5_BURXL]] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids (By similarity).[HAMAP-Rule:MF_01815]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 09:41, 21 December 2014

2014-12-21T09:41:30Z

← Older revision		Revision as of 09:41, 21 December 2014
Line 1:		Line 1:
	~~{{STRUCTURE_4dfe\| PDB=4dfe \| SCENE= }}~~		==Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans==
	===Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans===		<StructureSection load='4dfe' size='340' side='right' caption='[[4dfe]], [[Resolution\|resolution]] 2.35Å' scene=''>
	~~{{ABSTRACT_PUBMED_23382856}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4dfe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans_lb400 Burkholderia xenovorans lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DFE 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>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fabH, Bxeno_A3336, Bxe_A1072 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 Burkholderia xenovorans LB400])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-ketoacyl-[acyl-carrier-protein]_synthase_III Beta-ketoacyl-[acyl-carrier-protein] synthase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.180 2.3.1.180] </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=4dfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dfe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dfe RCSB], [http://www.ebi.ac.uk/pdbsum/4dfe PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			BACKGROUND: The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. METHODOLOGY/PRINCIPAL FINDINGS: We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. CONCLUSIONS/SIGNIFICANCE: This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.

	~~==Function==~~		Combining functional and structural genomics to sample the essential Burkholderia structome.,Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D 3rd, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC PLoS One. 2013;8(1):e53851. doi: 10.1371/journal.pone.0053851. Epub 2013 Jan 31. PMID:23382856<ref>PMID:23382856</ref>
	~~[[http~~:~~//www~~.~~uniprot~~.~~org/uniprot~~/~~Q13VL5_BURXL Q13VL5_BURXL]] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP~~. ~~Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production~~. ~~Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities~~. ~~Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids (By similarity)~~.~~[HAMAP-Rule~~:~~MF_01815]~~

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[4dfe]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Burkholderia_xenovorans_lb400 Burkholderia xenovorans lb400]~~. ~~Full crystallographic information is available from [http:/~~/~~oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA].~~		</div>

	==See Also==		==See Also==
	*[[Acyl carrier protein synthase\|Acyl carrier protein synthase]]		*[[Acyl carrier protein synthase\|Acyl carrier protein synthase]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:023382856</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Burkholderia xenovorans lb400]]		[[Category: Burkholderia xenovorans lb400]]
	[[Category: ~~SSGCID, Seattle~~ Structural ~~Genomics Center for Infectious Disease.]]~~		[[Category: Structural genomic]]
	~~[[Category: Seattle structural genomics center for infectious disease~~]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 05:02, 10 October 2013

2013-10-10T05:02:23Z

← Older revision		Revision as of 05:02, 10 October 2013
Line 1:		Line 1:
	~~[[Image:4dfe.png\|left\|200px]]~~

	{{STRUCTURE_4dfe\| PDB=4dfe \| SCENE= }}		{{STRUCTURE_4dfe\| PDB=4dfe \| SCENE= }}

	===Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans===		===Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans===
			{{ABSTRACT_PUBMED_23382856}}

			==Function==
			[[http://www.uniprot.org/uniprot/Q13VL5_BURXL Q13VL5_BURXL]] Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids (By similarity).[HAMAP-Rule:MF_01815]

	==About this Structure==		==About this Structure==
	[[4dfe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_xenovorans~~ Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA].		[[4dfe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans_lb400 Burkholderia xenovorans lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA].

	==See Also==		==See Also==
	*[[Acyl carrier protein synthase\|Acyl carrier protein synthase]]		*[[Acyl carrier protein synthase\|Acyl carrier protein synthase]]
	~~[[Category~~: ~~Beta-ketoacyl-acyl-carrier-protein synthase III]]~~
	[[Category: Burkholderia xenovorans]]		==Reference==
			<ref group="xtra">PMID:023382856</ref><references group="xtra"/><references/>
			[[Category: Burkholderia xenovorans lb400]]
	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]		[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
	[[Category: Seattle structural genomics center for infectious disease]]		[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 18:50, 20 October 2012

2012-10-20T18:50:28Z

← Older revision		Revision as of 18:50, 20 October 2012
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
	[[4dfe]] is a 4 chain structure ~~of [[Acyl carrier protein synthase]]~~ with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA].		[[4dfe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA].

	==See Also==		==See Also==

OCA at 05:23, 27 July 2012

2012-07-27T05:23:49Z

← Older revision		Revision as of 05:23, 27 July 2012
Line 1:		Line 1:
	[[Image:4dfe.~~jpg~~\|left\|200px]]		[[Image:4dfe.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_4dfe", 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_4dfe\| PDB=4dfe \| SCENE= }}		{{STRUCTURE_4dfe\| PDB=4dfe \| SCENE= }}

Line 13:		Line 7:

	==About this Structure==		==About this Structure==
	[[4dfe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA].		[[4dfe]] is a 4 chain structure of [[Acyl carrier protein synthase]] with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DFE OCA].

			==See Also==
			*[[Acyl carrier protein synthase\|Acyl carrier protein synthase]]
	[[Category: Beta-ketoacyl-acyl-carrier-protein synthase III]]		[[Category: Beta-ketoacyl-acyl-carrier-protein synthase III]]
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]