2oge - Revision history

OCA at 00:18, 28 December 2023

OCA — Thu, 28 Dec 2023 00:18:26 GMT

←Older revision		Revision as of 00:18, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='2oge' size='340' side='right'caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2oge' size='340' side='right'caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~As_4.1526 As 4.1526~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OGE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OGE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.05Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[2oga\|2oga]]~~</~~div~~>~~</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 AS 4.1526])~~</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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [https://pdbe.org/2oge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [https://www.ebi.ac.uk/pdbsum/2oge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oge 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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [https://pdbe.org/2oge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [https://www.ebi.ac.uk/pdbsum/2oge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oge ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DESV_STRVZ DESV_STRVZ]] Involved in the biosynthesis of dTDP-alpha-D-desosamine, a sugar found in several bacterial macrolide antibiotics. Catalyzes the reversible transfer of the amino group from L-glutamate to the C-3 position of dTDP-3-keto-4,6-deoxyglucose to yield dTDP-3-amino-3,4,6-trideoxyglucose.<ref>PMID:17456741</ref>	+	[https://www.uniprot.org/uniprot/DESV_STRVZ DESV_STRVZ] Involved in the biosynthesis of dTDP-alpha-D-desosamine, a sugar found in several bacterial macrolide antibiotics. Catalyzes the reversible transfer of the amino group from L-glutamate to the C-3 position of dTDP-3-keto-4,6-deoxyglucose to yield dTDP-3-amino-3,4,6-trideoxyglucose.<ref>PMID:17456741</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: As 4 1526]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Burgie, E S~~]]	+	[[Category: Streptomyces venezuelae]]
-	[[Category: ~~Holden, H M~~]]	+	[[Category: Burgie ES]]
-	[[Category: ~~Deoxysugar]]~~	+	[[Category: Holden HM]]
-	~~[[Category: Desosamine]]~~	+
-	~~[[Category: Macrolide antibiotic]]~~	+
-	~~[[Category: Plp-dependent enzyme]]~~	+
-	~~[[Category: Transaminase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 12:55, 9 June 2021

OCA — Wed, 09 Jun 2021 12:55:50 GMT

←Older revision		Revision as of 12:55, 9 June 2021
Line 1:		Line 1:

	==x-ray structure of S. venezuelae DesV in its internal aldimine form==		==x-ray structure of S. venezuelae DesV in its internal aldimine form==
-	<StructureSection load='2oge' size='340' side='right' caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='2oge' size='340' side='right'caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/As_4.1526 As 4.1526]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OGE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/As_4.1526 As 4.1526]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OGE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2oga\|2oga]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 AS 4.1526])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 AS 4.1526])</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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [~~http~~://pdbe.org/2oge PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2oge PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2oge 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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [https://pdbe.org/2oge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [https://www.ebi.ac.uk/pdbsum/2oge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oge ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DESV_STRVZ DESV_STRVZ]] Involved in the biosynthesis of dTDP-alpha-D-desosamine, a sugar found in several bacterial macrolide antibiotics. Catalyzes the reversible transfer of the amino group from L-glutamate to the C-3 position of dTDP-3-keto-4,6-deoxyglucose to yield dTDP-3-amino-3,4,6-trideoxyglucose.<ref>PMID:17456741</ref>	+	[[https://www.uniprot.org/uniprot/DESV_STRVZ DESV_STRVZ]] Involved in the biosynthesis of dTDP-alpha-D-desosamine, a sugar found in several bacterial macrolide antibiotics. Catalyzes the reversible transfer of the amino group from L-glutamate to the C-3 position of dTDP-3-keto-4,6-deoxyglucose to yield dTDP-3-amino-3,4,6-trideoxyglucose.<ref>PMID:17456741</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: As 4 1526]]		[[Category: As 4 1526]]
		+	[[Category: Large Structures]]
	[[Category: Burgie, E S]]		[[Category: Burgie, E S]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

OCA at 07:23, 22 August 2018

OCA — Wed, 22 Aug 2018 07:23:41 GMT

←Older revision		Revision as of 07:23, 22 August 2018
Line 1:		Line 1:
		+
	==x-ray structure of S. venezuelae DesV in its internal aldimine form==		==x-ray structure of S. venezuelae DesV in its internal aldimine form==
	<StructureSection load='2oge' size='340' side='right' caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2oge' size='340' side='right' caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 AS 4.1526])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 AS 4.1526])</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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [http://pdbe.org/2oge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [http://www.ebi.ac.uk/pdbsum/2oge 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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [http://pdbe.org/2oge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [http://www.ebi.ac.uk/pdbsum/2oge PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oge ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/2oge_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/2oge_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 18:58, 8 February 2016

OCA — Mon, 08 Feb 2016 18:58:14 GMT

←Older revision		Revision as of 18:58, 8 February 2016
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1526 As 4.1526]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1526 As 4.1526]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-~~LYSINE(~~3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-~~YLMETHANE)~~'>LLP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 AS 4.1526])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 AS 4.1526])</td></tr>
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2oge ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:28, 10 September 2015

OCA — Thu, 10 Sep 2015 14:28:21 GMT

←Older revision		Revision as of 14:28, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2oge' size='340' side='right' caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2oge' size='340' side='right' caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_venezuelae Streptomyces venezuelae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1526 As 4.1526]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 ~~Streptomyces venezuelae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 AS 4.1526])</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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [http://www.ebi.ac.uk/pdbsum/2oge 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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [http://pdbe.org/2oge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [http://www.ebi.ac.uk/pdbsum/2oge PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DESV_STRVZ DESV_STRVZ]] Involved in the biosynthesis of dTDP-alpha-D-desosamine, a sugar found in several bacterial macrolide antibiotics. Catalyzes the reversible transfer of the amino group from L-glutamate to the C-3 position of dTDP-3-keto-4,6-deoxyglucose to yield dTDP-3-amino-3,4,6-trideoxyglucose.<ref>PMID:17456741</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 29:
	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 2oge" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptomyces venezuelae~~]]	+	[[Category: As 4 1526]]
	[[Category: Burgie, E S]]		[[Category: Burgie, E S]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

OCA at 15:52, 19 January 2015

OCA — Mon, 19 Jan 2015 15:52:00 GMT

←Older revision		Revision as of 15:52, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 Streptomyces venezuelae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 Streptomyces venezuelae])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [http://www.ebi.ac.uk/pdbsum/2oge 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=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [http://www.ebi.ac.uk/pdbsum/2oge PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Streptomyces venezuelae]]		[[Category: Streptomyces venezuelae]]
-	[[Category: Burgie, E S.]]	+	[[Category: Burgie, E S]]
-	[[Category: Holden, H M.]]	+	[[Category: Holden, H M]]
	[[Category: Deoxysugar]]		[[Category: Deoxysugar]]
	[[Category: Desosamine]]		[[Category: Desosamine]]

OCA at 18:59, 30 September 2014

OCA — Tue, 30 Sep 2014 18:59:25 GMT

←Older revision		Revision as of 18:59, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2oge.~~png~~\|~~left~~\|200px]]	+	==x-ray structure of S. venezuelae DesV in its internal aldimine form==
		+	<StructureSection load='2oge' size='340' side='right' caption='[[2oge]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2oge]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGE FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2oga\|2oga]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">desV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54571 Streptomyces venezuelae])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oge OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oge RCSB], [http://www.ebi.ac.uk/pdbsum/2oge PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/2oge_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found in certain macrolide antibiotics such as the commonly prescribed erythromycin. Six enzymes are required for its biosynthesis in Streptomyces venezuelae. The focus of this article is DesV, which catalyzes the PLP-dependent replacement of a 3-keto group with an amino functionality in the fifth step of the pathway. For this study the three-dimensional structures of both the internal aldimine and the ketimine intermediate with glutamate were determined to 2.05 A resolution. DesV is a homodimer with each subunit containing 12 alpha-helical regions and 12 beta-strands that together form three layers of sheet. The structure of the internal aldimine demonstrates that the PLP-cofactor is held in place by residues contributed from both subunits (Asp 164 and Gln 167 from Subunit I and Tyr 221 and Asn 235 from Subunit II). When the ketimine intermediate is present in the active site, the loop defined by Gln 225 to Ser 228 from Subunit II closes down upon the active site. The structure of DesV is similar to another sugar-modifying enzyme referred to as PseC. This enzyme is involved in the biosynthesis of pseudaminic acid, which is a sialic acid-like nonulosonate found in the flagellin of Helicobacter pylori. In the case of PseC, however, the amino group is transferred to the C-4 rather than the C-3 position. Details concerning the structural analysis of DesV and a comparison of its molecular architecture to that of PseC are presented.

-	~~{{STRUCTURE_2oge\| PDB=2oge \| SCENE= }}~~	+	Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine.,Burgie ES, Thoden JB, Holden HM Protein Sci. 2007 May;16(5):887-96. PMID:17456741<ref>PMID:17456741</ref>

-	~~===x-ray structure~~ of S. ~~venezuelae DesV in its internal aldimine form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17456741}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2oge]] is a 4 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017456741<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Streptomyces venezuelae]]		[[Category: Streptomyces venezuelae]]
	[[Category: Burgie, E S.]]		[[Category: Burgie, E S.]]

OCA: Protected "2oge" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 13:55:15 GMT

Protected "2oge" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:55, 7 January 2013

OCA at 13:55, 7 January 2013

OCA — Mon, 07 Jan 2013 13:55:12 GMT

←Older revision		Revision as of 13:55, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2oge.png\|left\|200px]]		[[Image:2oge.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2oge", 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_2oge\| PDB=2oge \| SCENE= }}		{{STRUCTURE_2oge\| PDB=2oge \| SCENE= }}

	===x-ray structure of S. venezuelae DesV in its internal aldimine form===		===x-ray structure of S. venezuelae DesV in its internal aldimine form===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17456741}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17456741 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17456741}}		{{ABSTRACT_PUBMED_17456741}}

	==About this Structure==		==About this Structure==
-	~~2OGE~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA].	+	[[2oge]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17456741~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017456741</ref><references group="xtra"/>
	[[Category: Streptomyces venezuelae]]		[[Category: Streptomyces venezuelae]]
	[[Category: Burgie, E S.]]		[[Category: Burgie, E S.]]
Line 32:		Line 20:
	[[Category: Plp-dependent enzyme]]		[[Category: Plp-dependent enzyme]]
	[[Category: Transaminase]]		[[Category: Transaminase]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 01:58:00 2009''~~	+

OCA at 23:58, 16 February 2009

OCA — Mon, 16 Feb 2009 23:58:00 GMT

←Older revision		Revision as of 23:58, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2OGE is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA].	+	2OGE is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGE OCA].

	==Reference==		==Reference==
-	Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine., Burgie ES, Thoden JB, Holden HM, Protein Sci. 2007 May;16(5):887-96. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17456741 17456741]~~	+	<ref group="xtra">PMID:17456741</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Streptomyces venezuelae]]		[[Category: Streptomyces venezuelae]]
	[[Category: Burgie, E S.]]		[[Category: Burgie, E S.]]
Line 34:		Line 33:
	[[Category: Transaminase]]		[[Category: Transaminase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 05~~:56:~~02 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 01:58:00 2009''