2oga - Revision history

OCA at 00:18, 28 December 2023

2023-12-28T00:18:25Z

←Older revision		Revision as of 00:18, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='2oga' size='340' side='right'caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2oga' size='340' side='right'caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OGA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OGA 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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</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='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='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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [https://pdbe.org/2oga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [https://www.ebi.ac.uk/pdbsum/2oga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oga 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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [https://pdbe.org/2oga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [https://www.ebi.ac.uk/pdbsum/2oga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oga 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 33:		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: ~~Antibiotic]]~~	+	[[Category: Holden HM]]
-	~~[[Category: Deoxysugar]]~~	+
-	~~[[Category: Desosamine]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Plp-dependent enzyme]]~~	+
-	~~[[Category: Transaminase~~]]	+

OCA at 12:55, 9 June 2021

2021-06-09T12:55:46Z

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

	==X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate==		==X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate==
-	<StructureSection load='2oga' size='340' side='right' caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='2oga' size='340' side='right'caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OGA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OGA 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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</scene></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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [~~http~~://pdbe.org/2oga PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2oga PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2oga 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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [https://pdbe.org/2oga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [https://www.ebi.ac.uk/pdbsum/2oga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oga 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 34:		Line 34:
	</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 06:46, 22 August 2018

2018-08-22T06:46:37Z

←Older revision		Revision as of 06:46, 22 August 2018
Line 1:		Line 1:
		+
	==X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate==		==X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate==
	<StructureSection load='2oga' size='340' side='right' caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2oga' size='340' side='right' caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 5:		Line 6:
	</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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</scene></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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [http://pdbe.org/2oga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [http://www.ebi.ac.uk/pdbsum/2oga 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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [http://pdbe.org/2oga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [http://www.ebi.ac.uk/pdbsum/2oga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oga ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/2oga_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/2oga_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 10:39, 9 February 2016

2016-02-09T10:39:22Z

←Older revision		Revision as of 10:39, 9 February 2016
Line 17:		Line 17:
	<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=2oga ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:28, 10 September 2015

2015-09-10T21:28:06Z

←Older revision		Revision as of 21:28, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2oga' size='340' side='right' caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2oga' size='340' side='right' caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGA 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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</scene></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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [http://www.ebi.ac.uk/pdbsum/2oga 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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [http://pdbe.org/2oga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [http://www.ebi.ac.uk/pdbsum/2oga 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 25:		Line 27:
	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 2oga" 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 17:17, 19 January 2015

2015-01-19T17:17:58Z

←Older revision		Revision as of 17:17, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGA 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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</scene></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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [http://www.ebi.ac.uk/pdbsum/2oga 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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [http://www.ebi.ac.uk/pdbsum/2oga 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 30:		Line 30:
	</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: Antibiotic]]		[[Category: Antibiotic]]
	[[Category: Deoxysugar]]		[[Category: Deoxysugar]]

OCA at 19:50, 30 September 2014

2014-09-30T19:50:18Z

←Older revision		Revision as of 19:50, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2oga.~~png~~\|~~left~~\|200px]]	+	==X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate==
		+	<StructureSection load='2oga' size='340' side='right' caption='[[2oga]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2oga]] 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=2OGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OGA 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>, <scene name='pdbligand=PGU:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC+ACID'>PGU</scene><br>
		+	<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=2oga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oga OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oga RCSB], [http://www.ebi.ac.uk/pdbsum/2oga 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/2oga_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_2oga\| PDB=2oga \| 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 crystal structure~~ of S. ~~venezuelae DesV in complex with ketimine intermediate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17456741}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2oga]] 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=2OGA 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 "2oga" [edit=sysop:move=sysop]

2013-01-07T14:49:32Z

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

←Older revision

Revision as of 14:49, 7 January 2013

OCA at 14:49, 7 January 2013

2013-01-07T14:49:30Z

←Older revision		Revision as of 14:49, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2oga.png\|left\|200px]]		[[Image:2oga.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2oga", 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_2oga\| PDB=2oga \| SCENE= }}		{{STRUCTURE_2oga\| PDB=2oga \| SCENE= }}

	===X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate===		===X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate===

-
-	<!--
-	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==
-	~~2OGA~~ 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=2OGA OCA].	+	[[2oga]] 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=2OGA 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 30:		Line 18:
	[[Category: Deoxysugar]]		[[Category: Deoxysugar]]
	[[Category: Desosamine]]		[[Category: Desosamine]]
		+	[[Category: Hydrolase]]
	[[Category: Plp-dependent enzyme]]		[[Category: Plp-dependent enzyme]]
	[[Category: Transaminase]]		[[Category: Transaminase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:12:32 2009''

OCA at 07:12, 17 February 2009

2009-02-17T07:12:33Z

←Older revision		Revision as of 07:12, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2OGA 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=2OGA OCA].	+	2OGA 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=2OGA 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 12~~:44:~~21 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:12:32 2009''