4nap - Revision history

OCA at 08:18, 11 January 2023

OCA — Wed, 11 Jan 2023 08:18:03 GMT

←Older revision		Revision as of 08:18, 11 January 2023
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	==Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan==		==Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan==
-	<StructureSection load='4nap' size='340' side='right' caption='[[4nap]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4nap' size='340' side='right'caption='[[4nap]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nap]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Desdg Desdg~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NAP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NAP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nap]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oleidesulfovibrio_alaskensis_G20 Oleidesulfovibrio alaskensis G20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NAP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTR:D-TRYPTOPHAN'>DTR</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTR:D-TRYPTOPHAN'>DTR</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4nap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nap OCA], [https://pdbe.org/4nap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nap RCSB], [https://www.ebi.ac.uk/pdbsum/4nap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nap ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dde_0634 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207559 DESDG])~~</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=4nap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nap OCA], [~~http~~://pdbe.org/4nap PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nap RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nap PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nap ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DCTP2_OLEA2 DCTP2_OLEA2] Solute-binding protein that binds indole-3-pyruvate and indole-3-acetate (in vitro). Can also bind D-tryptophan (in vitro), but that is probably not a physiological ligand (PubMed:25540822). Probably part of a tripartite ATP-independent periplasmic (TRAP) transport system that mediates solute transport into the cytoplasm.<ref>PMID:25540822</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desdg~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Almo, S C~~]]	+	[[Category: Oleidesulfovibrio alaskensis G20]]
-	[[Category: ~~Attonito, J D~~]]	+	[[Category: Al Obaidi NF]]
-	[[Category: ~~Chowdhury, S~~]]	+	[[Category: Almo SC]]
-	[[Category: ~~EFI, Enzyme Function Initiative~~]]	+	[[Category: Attonito JD]]
-	[[Category: ~~Evans, B~~]]	+	[[Category: Chowdhury S]]
-	[[Category: ~~Gerlt, J A~~]]	+	[[Category: Evans B]]
-	[[Category: ~~Glenn, A Scott~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Hillerich, B]]	+	[[Category: Hillerich B]]
-	[[Category: Imker~~, H J~~]]	+	[[Category: Imker HJ]]
-	[[Category: Love, J]]	+	[[Category: Love J]]
-	[[Category: Morisco~~, L L~~]]	+	[[Category: Morisco LL]]
-	[[Category: ~~Obaidi, N F.Al~~]]	+	[[Category: Scott Glenn A]]
-	[[Category: Seidel~~, R D~~]]	+	[[Category: Seidel RD]]
-	[[Category: Sojitra, S]]	+	[[Category: Sojitra S]]
-	[[Category: Stead, M]]	+	[[Category: Stead M]]
-	[[Category: Vetting~~, M W~~]]	+	[[Category: Vetting MW]]
-	[[Category: Wasserman~~, S R]]~~	+	[[Category: Wasserman SR]]
-	~~[[Category: Efi]]~~	+
-	~~[[Category: Enzyme function initiative]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Trap periplasmic solute binding family~~]]	+

OCA at 07:29, 23 December 2016

OCA — Fri, 23 Dec 2016 07:29:59 GMT

←Older revision		Revision as of 07:29, 23 December 2016
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		+
	==Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan==		==Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan==
	<StructureSection load='4nap' size='340' side='right' caption='[[4nap]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4nap' size='340' side='right' caption='[[4nap]], [[Resolution\|resolution]] 2.30Å' scene=''>
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	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dde_0634 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207559 DESDG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dde_0634 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207559 DESDG])</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=4nap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nap RCSB], [http://www.ebi.ac.uk/pdbsum/4nap 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=4nap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nap OCA], [http://pdbe.org/4nap PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nap RCSB], [http://www.ebi.ac.uk/pdbsum/4nap PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nap ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4nap" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:20, 25 February 2015

OCA — Wed, 25 Feb 2015 08:20:27 GMT

←Older revision		Revision as of 08:20, 25 February 2015
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	<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=4nap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nap RCSB], [http://www.ebi.ac.uk/pdbsum/4nap 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=4nap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nap RCSB], [http://www.ebi.ac.uk/pdbsum/4nap PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.
		+
		+	Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.,Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16. PMID:25540822<ref>PMID:25540822</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:49, 5 January 2015

OCA — Mon, 05 Jan 2015 08:49:12 GMT

←Older revision		Revision as of 08:49, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4nap\| PDB=4nap \| SCENE= }}~~	+	==Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan==
-	===Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan===	+	<StructureSection load='4nap' size='340' side='right' caption='[[4nap]], [[Resolution\|resolution]] 2.30Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[4nap]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Desdg Desdg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NAP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NAP FirstGlance]. <br>
-	[[4nap]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NAP OCA].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTR:D-TRYPTOPHAN'>DTR</scene></td></tr>
-	[[Category: Almo, S C.]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[Category: Attonito, J D.]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dde_0634 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207559 DESDG])</td></tr>
-	[[Category: Chowdhury, S.]]	+	<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=4nap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nap RCSB], [http://www.ebi.ac.uk/pdbsum/4nap PDBsum]</span></td></tr>
-	[[Category: EFI, Enzyme Function Initiative.]]	+	</table>
-	[[Category: Evans, B.]]	+	__TOC__
-	[[Category: Gerlt, J A.]]	+	</StructureSection>
-	[[Category: Glenn, A Scott.]]	+	[[Category: Desdg]]
-	[[Category: Hillerich, B.]]	+	[[Category: Almo, S C]]
-	[[Category: Imker, H J.]]	+	[[Category: Attonito, J D]]
-	[[Category: Love, J.]]	+	[[Category: Chowdhury, S]]
-	[[Category: Morisco, L L.]]	+	[[Category: EFI, Enzyme Function Initiative]]
-	[[Category: Obaidi, N F.Al.]]	+	[[Category: Evans, B]]
-	[[Category: Seidel, R D.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Sojitra, S.]]	+	[[Category: Glenn, A Scott]]
-	[[Category: Stead, M.]]	+	[[Category: Hillerich, B]]
-	[[Category: Vetting, M W.]]	+	[[Category: Imker, H J]]
-	[[Category: Wasserman, S R.]]	+	[[Category: Love, J]]
		+	[[Category: Morisco, L L]]
		+	[[Category: Obaidi, N F.Al]]
		+	[[Category: Seidel, R D]]
		+	[[Category: Sojitra, S]]
		+	[[Category: Stead, M]]
		+	[[Category: Vetting, M W]]
		+	[[Category: Wasserman, S R]]
	[[Category: Efi]]		[[Category: Efi]]
	[[Category: Enzyme function initiative]]		[[Category: Enzyme function initiative]]

OCA at 08:33, 13 November 2013

OCA — Wed, 13 Nov 2013 08:33:38 GMT

←Older revision		Revision as of 08:33, 13 November 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4nap\| PDB=4nap \| SCENE= }}
		+	===Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan===

-	~~The entry~~ 4nap is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4nap]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NAP OCA].
-	~~Authors~~: ~~Vetting, M~~.W.~~, Al Obaidi, N~~.F.~~, Morisco, L.L., Wasserman~~, S.~~R., Sojitra, S., Stead, M.,~~ Attonito, J.D.~~, Scott Glenn, A.,~~ Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., ~~Imker, H~~.J., ~~Gerlt, J.A~~.~~, Almo~~, S.~~C.,~~ Enzyme ~~Function Initiative (EFI)~~	+	[[Category: Almo, S C.]]
-		+	[[Category: Attonito, J D.]]
-	~~Description~~: ~~CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634), TARGET EFI-510102, WITH BOUND D-TRYPTOPHAN~~	+	[[Category: Chowdhury, S.]]
		+	[[Category: EFI, Enzyme Function Initiative.]]
		+	[[Category: Evans, B.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Glenn, A Scott.]]
		+	[[Category: Hillerich, B.]]
		+	[[Category: Imker, H J.]]
		+	[[Category: Love, J.]]
		+	[[Category: Morisco, L L.]]
		+	[[Category: Obaidi, N F.Al.]]
		+	[[Category: Seidel, R D.]]
		+	[[Category: Sojitra, S.]]
		+	[[Category: Stead, M.]]
		+	[[Category: Vetting, M W.]]
		+	[[Category: Wasserman, S R.]]
		+	[[Category: Efi]]
		+	[[Category: Enzyme function initiative]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transport protein]]
		+	[[Category: Trap periplasmic solute binding family]]

OCA: Protected "4nap" [edit=sysop:move=sysop]

OCA — Wed, 06 Nov 2013 07:06:27 GMT

Protected "4nap" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:06, 6 November 2013

OCA: New page: '''Unreleased structure''' The entry 4nap is ON HOLD Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Ch...

OCA — Wed, 06 Nov 2013 07:06:27 GMT

New page: '''Unreleased structure''' The entry 4nap is ON HOLD Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Ch...

New page

'''Unreleased structure'''

The entry 4nap is ON HOLD

Authors: Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Description: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634), TARGET EFI-510102, WITH BOUND D-TRYPTOPHAN