3v9p - Revision history

OCA at 14:22, 14 March 2024

OCA — Thu, 14 Mar 2024 14:22:00 GMT

←Older revision		Revision as of 14:22, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3v9p' size='340' side='right'caption='[[3v9p]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3v9p' size='340' side='right'caption='[[3v9p]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v9p]] is a 2 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=3V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v9p]] is a 2 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=3V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V9P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.9Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2154, tmk, YP_442675.1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 BURTA])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [https://pdbe.org/3v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [https://www.ebi.ac.uk/pdbsum/3v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v9p 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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [https://pdbe.org/3v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [https://www.ebi.ac.uk/pdbsum/3v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v9p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KTHY_BURTA KTHY_BURTA]] Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity).	+	[https://www.uniprot.org/uniprot/KTHY_BURTA KTHY_BURTA] Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity).
-	~~<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 3v9p" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Thymidylate kinase 3D structures\|Thymidylate kinase 3D structures]]		*[[Thymidylate kinase 3D structures\|Thymidylate kinase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burta~~]]	+	[[Category: Burkholderia thailandensis E264]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: DTMP kinase]]
-	[[Category: Structural genomic]]
-	[[Category: Burkholderia thailandensis]]
-	[[Category: Ssgcid]]
-	[[Category: Thymidylate kinase]]
-	[[Category: Transferase]]

OCA at 08:43, 20 July 2022

OCA — Wed, 20 Jul 2022 08:43:44 GMT

←Older revision		Revision as of 08:43, 20 July 2022
Line 1:		Line 1:

	==Crystal structure of Thymidylate kinase from Burkholderia thailandensis==		==Crystal structure of Thymidylate kinase from Burkholderia thailandensis==
-	<StructureSection load='3v9p' size='340' side='right' caption='[[3v9p]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3v9p' size='340' side='right'caption='[[3v9p]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v9p]] is a 2 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=3V9P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v9p]] is a 2 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=3V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V9P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2154, tmk, YP_442675.1 ([~~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_I2154, tmk, YP_442675.1 ([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/dTMP_kinase dTMP kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [~~http~~://pdbe.org/3v9p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3v9p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3v9p 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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [https://pdbe.org/3v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [https://www.ebi.ac.uk/pdbsum/3v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v9p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KTHY_BURTA KTHY_BURTA]] Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity).	+	[[https://www.uniprot.org/uniprot/KTHY_BURTA KTHY_BURTA]] Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Thymidylate kinase\|Thymidylate kinase]]	+	*[[Thymidylate kinase 3D structures\|Thymidylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Burta]]		[[Category: Burta]]
		+	[[Category: Large Structures]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 07:11, 5 August 2016

OCA — Fri, 05 Aug 2016 07:11:51 GMT

←Older revision		Revision as of 07:11, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Thymidylate kinase from Burkholderia thailandensis==		==Crystal structure of Thymidylate kinase from Burkholderia thailandensis==
	<StructureSection load='3v9p' size='340' side='right' caption='[[3v9p]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3v9p' size='340' side='right' caption='[[3v9p]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v9p]] is a 2 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=3V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v9p]] is a 2 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=3V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V9P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2154, tmk, YP_442675.1 ([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_I2154, tmk, YP_442675.1 ([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/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [http://www.ebi.ac.uk/pdbsum/3v9p 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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [http://pdbe.org/3v9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [http://www.ebi.ac.uk/pdbsum/3v9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3v9p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3v9p" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burkholderia thailandensis e264~~]]	+	[[Category: Burta]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 16:46, 25 December 2014

OCA — Thu, 25 Dec 2014 16:46:44 GMT

←Older revision		Revision as of 16:46, 25 December 2014
Line 8:		Line 8:
	<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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [http://www.ebi.ac.uk/pdbsum/3v9p 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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [http://www.ebi.ac.uk/pdbsum/3v9p PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KTHY_BURTA KTHY_BURTA]] Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:02, 21 December 2014

OCA — Sun, 21 Dec 2014 07:02:07 GMT

←Older revision		Revision as of 07:02, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3v9p\| PDB~~=3v9p \| ~~SCENE~~= }}	+	==Crystal structure of Thymidylate kinase from Burkholderia thailandensis==
-	===~~Crystal~~ structure ~~of Thymidylate kinase~~ from Burkholderia thailandensis===	+	<StructureSection load='3v9p' size='340' side='right' caption='[[3v9p]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23382856}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3v9p]] is a 2 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=3V9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V9P FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTH_I2154, tmk, YP_442675.1 ([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/dTMP_kinase dTMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.9 2.7.4.9] </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=3v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v9p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v9p RCSB], [http://www.ebi.ac.uk/pdbsum/3v9p 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/KTHY_BURTA KTHY_BURTA]] Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis~~ (~~By similarity~~).	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3v9p]] is~~ a ~~2 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=3V9P OCA].~~	+	</div>

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

OCA at 05:11, 10 October 2013

OCA — Thu, 10 Oct 2013 05:11:58 GMT

←Older revision		Revision as of 05:11, 10 October 2013
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-	[[Image:3v9p.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3v9p", 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_3v9p\| PDB=3v9p \| SCENE= }}		{{STRUCTURE_3v9p\| PDB=3v9p \| SCENE= }}
-
	===Crystal structure of Thymidylate kinase from Burkholderia thailandensis===		===Crystal structure of Thymidylate kinase from Burkholderia thailandensis===
		+	{{ABSTRACT_PUBMED_23382856}}

		+	==Function==
		+	[[http://www.uniprot.org/uniprot/KTHY_BURTA KTHY_BURTA]] Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis (By similarity).

	==About this Structure==		==About this Structure==
-	[[3v9p]] is a 2 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=3V9P OCA].	+	[[3v9p]] is a 2 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=3V9P OCA].
-	[[Category: Burkholderia thailandensis]]	+
		+	==See Also==
		+	*[[Thymidylate kinase\|Thymidylate kinase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023382856</ref><references group="xtra"/><references/>
		+	[[Category: Burkholderia thailandensis e264]]
	[[Category: DTMP kinase]]		[[Category: DTMP kinase]]
	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]		[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]

OCA at 07:31, 1 February 2012

OCA — Wed, 01 Feb 2012 07:31:56 GMT

←Older revision		Revision as of 07:31, 1 February 2012
Line 1:		Line 1:
-	[[Image:3v9p.~~jpg~~\|left\|200px]]	+	[[Image:3v9p.png\|left\|200px]]

	<!--		<!--

OCA at 06:48, 25 January 2012

OCA — Wed, 25 Jan 2012 06:48:21 GMT

←Older revision		Revision as of 06:48, 25 January 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3v9p.jpg\|left\|200px]]

-	The ~~entry 3v9p~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3v9p", 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_3v9p\| PDB=3v9p \| SCENE= }}

-	~~Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	===Crystal structure of Thymidylate kinase from Burkholderia thailandensis===

-	~~Description: Crystal~~ structure ~~of Thymidylate kinase~~ from Burkholderia thailandensis	+
		+	==About this Structure==
		+	[[3v9p]] is a 2 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=3V9P OCA].
		+	[[Category: Burkholderia thailandensis]]
		+	[[Category: DTMP kinase]]
		+	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
		+	[[Category: Burkholderia thailandensis]]
		+	[[Category: Seattle structural genomics center for infectious disease]]
		+	[[Category: Ssgcid]]
		+	[[Category: Structural genomic]]
		+	[[Category: Thymidylate kinase]]
		+	[[Category: Transferase]]

OCA: Protected "3v9p" [edit=sysop:move=sysop]

OCA — Wed, 04 Jan 2012 05:47:25 GMT

Protected "3v9p" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:47, 4 January 2012

OCA: New page: '''Unreleased structure''' The entry 3v9p is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of Thymidylate kinase fr...

OCA — Wed, 04 Jan 2012 05:47:24 GMT

New page: '''Unreleased structure''' The entry 3v9p is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of Thymidylate kinase fr...

New page

'''Unreleased structure'''

The entry 3v9p is ON HOLD

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

Description: Crystal structure of Thymidylate kinase from Burkholderia thailandensis