3uw1 - Revision history

OCA at 10:29, 1 March 2024

2024-03-01T10:29:01Z

←Older revision		Revision as of 10:29, 1 March 2024
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	<StructureSection load='3uw1' size='340' side='right'caption='[[3uw1]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='3uw1' size='340' side='right'caption='[[3uw1]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Burta Burta~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_thailandensis_E264 Burkholderia thailandensis E264]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UW1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=R5P:RIBOSE~~-~~5-PHOSPHATE'>R5P</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]] 1.71Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3u7j\|3u7j]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>BTH_I2516, rpiA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=271848 BURTA])</td></tr>~~	+
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Ribose~~-5-~~phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6]~~ </~~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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [https://pdbe.org/3uw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [https://www.ebi.ac.uk/pdbsum/3uw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uw1 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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [https://pdbe.org/3uw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [https://www.ebi.ac.uk/pdbsum/3uw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uw1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q2SVL4_BURTA Q2SVL4_BURTA]] Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate (By similarity).[HAMAP-Rule:MF_00170][SAAS:SAAS004788_004_005536]	+	[https://www.uniprot.org/uniprot/Q2SVL4_BURTA Q2SVL4_BURTA] Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate (By similarity).[HAMAP-Rule:MF_00170][SAAS:SAAS004788_004_005536]
-	~~<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 3uw1" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Ribose-5-phosphate isomerase 3D structures\|Ribose-5-phosphate isomerase 3D structures]]		*[[Ribose-5-phosphate isomerase 3D structures\|Ribose-5-phosphate isomerase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burta~~]]	+	[[Category: Burkholderia thailandensis E264]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ribose-5-phosphate isomerase]]
-	[[Category: Structural genomic]]
-	[[Category: Isomerase]]
-	[[Category: Ribose isomerase]]
-	[[Category: Ribose-5-phosphate]]
-	[[Category: Ssgcid]]

OCA at 08:11, 20 July 2022

2022-07-20T08:11:37Z

←Older revision		Revision as of 08:11, 20 July 2022
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	==Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate==		==Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate==
-	<StructureSection load='3uw1' size='340' side='right' caption='[[3uw1]], [[Resolution\|resolution]] 1.71Å' scene=''>	+	<StructureSection load='3uw1' size='340' side='right'caption='[[3uw1]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uw1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Burta Burta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3UW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burta Burta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UW1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u7j\|3u7j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3u7j\|3u7j]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2516, rpiA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 BURTA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2516, rpiA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 BURTA])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [~~http~~://pdbe.org/3uw1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3uw1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3uw1 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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [https://pdbe.org/3uw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [https://www.ebi.ac.uk/pdbsum/3uw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uw1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/Q2SVL4_BURTA Q2SVL4_BURTA]] Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate (By similarity).[HAMAP-Rule:MF_00170][SAAS:SAAS004788_004_005536]	+	[[https://www.uniprot.org/uniprot/Q2SVL4_BURTA Q2SVL4_BURTA]] Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate (By similarity).[HAMAP-Rule:MF_00170][SAAS:SAAS004788_004_005536]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3uw1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3uw1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribose-5-phosphate isomerase 3D structures\|Ribose-5-phosphate isomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Burta]]		[[Category: Burta]]
		+	[[Category: Large Structures]]
	[[Category: Ribose-5-phosphate isomerase]]		[[Category: Ribose-5-phosphate isomerase]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 10:09, 8 November 2017

2017-11-08T10:09:41Z

←Older revision		Revision as of 10:09, 8 November 2017
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3uw1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3uw1" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ribose-5-phosphate isomerase\|Ribose-5-phosphate isomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:02, 5 August 2016

2016-08-05T22:02:17Z

←Older revision		Revision as of 22:02, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate==		==Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate==
	<StructureSection load='3uw1' size='340' side='right' caption='[[3uw1]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='3uw1' size='340' side='right' caption='[[3uw1]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_thailandensis_e264 Burkholderia thailandensis e264~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burta Burta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UW1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u7j\|3u7j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u7j\|3u7j]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2516, rpiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 ~~Burkholderia thailandensis E264~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2516, rpiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 BURTA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [http://www.ebi.ac.uk/pdbsum/3uw1 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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [http://pdbe.org/3uw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [http://www.ebi.ac.uk/pdbsum/3uw1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3uw1 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 3uw1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burkholderia thailandensis e264~~]]	+	[[Category: Burta]]
	[[Category: Ribose-5-phosphate isomerase]]		[[Category: Ribose-5-phosphate isomerase]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 22:17, 25 December 2014

2014-12-25T22:17:00Z

←Older revision		Revision as of 22:17, 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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [http://www.ebi.ac.uk/pdbsum/3uw1 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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [http://www.ebi.ac.uk/pdbsum/3uw1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q2SVL4_BURTA Q2SVL4_BURTA]] Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate (By similarity).[HAMAP-Rule:MF_00170][SAAS:SAAS004788_004_005536]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:28, 21 December 2014

2014-12-21T07:28:46Z

←Older revision		Revision as of 07:28, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3uw1\| PDB=3uw1 \| SCENE= }}~~	+	==Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate==
-	===Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate===	+	<StructureSection load='3uw1' size='340' side='right' caption='[[3uw1]], [[Resolution\|resolution]] 1.71Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23382856}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3uw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_thailandensis_e264 Burkholderia thailandensis e264]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UW1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3u7j\|3u7j]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2516, rpiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 Burkholderia thailandensis E264])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </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=3uw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uw1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uw1 RCSB], [http://www.ebi.ac.uk/pdbsum/3uw1 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/Q2SVL4_BURTA Q2SVL4_BURTA]] Catalyzes~~ the ~~reversible conversion of ribose~~-~~5-phosphate to ribulose 5-phosphate~~ (~~By similarity~~).~~[HAMAP-Rule~~:~~MF_00170][SAAS~~:~~SAAS004788_004_005536]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3uw1]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Burkholderia_thailandensis_e264 Burkholderia thailandensis e264]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Ribose-5-phosphate isomerase\|Ribose-5-phosphate isomerase]]		*[[Ribose-5-phosphate isomerase\|Ribose-5-phosphate isomerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023382856</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Burkholderia thailandensis e264]]		[[Category: Burkholderia thailandensis e264]]
	[[Category: Ribose-5-phosphate isomerase]]		[[Category: Ribose-5-phosphate isomerase]]
-	[[Category: ~~SSGCID, Seattle~~ Structural ~~Genomics Center for Infectious Disease.~~]]	+	[[Category: Structural genomic]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Ribose isomerase]]		[[Category: Ribose isomerase]]
	[[Category: Ribose-5-phosphate]]		[[Category: Ribose-5-phosphate]]
-	[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]

OCA at 08:34, 30 October 2013

2013-10-30T08:34:20Z

←Older revision		Revision as of 08:34, 30 October 2013
Line 1:		Line 1:
-	[[Image:3uw1.png\|left\|200px]]
-
	{{STRUCTURE_3uw1\| PDB=3uw1 \| SCENE= }}		{{STRUCTURE_3uw1\| PDB=3uw1 \| SCENE= }}
-
	===Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate===		===Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate===
		+	{{ABSTRACT_PUBMED_23382856}}

		+	==Function==
		+	[[http://www.uniprot.org/uniprot/Q2SVL4_BURTA Q2SVL4_BURTA]] Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate (By similarity).[HAMAP-Rule:MF_00170][SAAS:SAAS004788_004_005536]

	==About this Structure==		==About this Structure==
-	[[3uw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_thailandensis~~ Burkholderia thailandensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA].	+	[[3uw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_thailandensis_e264 Burkholderia thailandensis e264]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA].

	==See Also==		==See Also==
	*[[Ribose-5-phosphate isomerase\|Ribose-5-phosphate isomerase]]		*[[Ribose-5-phosphate isomerase\|Ribose-5-phosphate isomerase]]
-	[[Category: Burkholderia thailandensis]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:023382856</ref><references group="xtra"/><references/>
		+	[[Category: Burkholderia thailandensis e264]]
	[[Category: Ribose-5-phosphate isomerase]]		[[Category: Ribose-5-phosphate isomerase]]
	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]		[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]

OCA at 22:17, 20 October 2012

2012-10-20T22:17:59Z

←Older revision		Revision as of 22:17, 20 October 2012
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3uw1]] is a 1 chain structure ~~of [[Ribose-5-phosphate isomerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Burkholderia_thailandensis Burkholderia thailandensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA].	+	[[3uw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_thailandensis Burkholderia thailandensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA].

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

OCA at 15:51, 27 July 2012

2012-07-27T15:51:36Z

←Older revision		Revision as of 15:51, 27 July 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3uw1.png\|left\|200px]]

-	~~The entry~~ 3uw1 ~~is ON HOLD~~	+	{{STRUCTURE_3uw1\| PDB=3uw1 \| SCENE= }}

-	~~Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	===Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate===

-	~~Description: Crystal~~ structure of ~~ribose~~-5-phosphate isomerase a from ~~burkholderia~~ thailandensis ~~with ribose~~-5-phosphate	+
		+	==About this Structure==
		+	[[3uw1]] is a 1 chain structure of [[Ribose-5-phosphate isomerase]] with sequence from [http://en.wikipedia.org/wiki/Burkholderia_thailandensis Burkholderia thailandensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UW1 OCA].
		+
		+	==See Also==
		+	*[[Ribose-5-phosphate isomerase\|Ribose-5-phosphate isomerase]]
		+	[[Category: Burkholderia thailandensis]]
		+	[[Category: Ribose-5-phosphate isomerase]]
		+	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
		+	[[Category: Isomerase]]
		+	[[Category: Ribose isomerase]]
		+	[[Category: Ribose-5-phosphate]]
		+	[[Category: Seattle structural genomics center for infectious disease]]
		+	[[Category: Ssgcid]]

OCA at 11:12, 14 December 2011

2011-12-14T11:12:56Z

←Older revision		Revision as of 11:12, 14 December 2011
Line 5:		Line 5:
	Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)		Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

-	Description: ~~CRYSTAL STRUCTURE OF RIBOSE~~-5-~~PHOSPHATE ISOMERASE A FROM BURKHOLDERIA THAILANDENSIS WITH RIBOSE~~-5-~~PHOSPHATE~~	+	Description: Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate