3dr4 - Revision history

OCA at 12:51, 30 August 2023

OCA — Wed, 30 Aug 2023 12:51:48 GMT

←Older revision		Revision as of 12:51, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3dr4' size='340' side='right'caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3dr4' size='340' side='right'caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Cauvc Cauvc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bn1\|3bn1]], [[3dr7\|3dr7]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">per ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUVC])~~</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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [https://pdbe.org/3dr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [https://pdbe.org/3dr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~O85354_CAUCE O85354_CAUCE]~~] Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.<ref>PMID:11390676</ref> <ref>PMID:18247575</ref> <ref>PMID:18795799</ref>	+	[https://www.uniprot.org/uniprot/GDPPS_CAUVC GDPPS_CAUVC] Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.<ref>PMID:11390676</ref> <ref>PMID:18247575</ref> <ref>PMID:18795799</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cauvc~~]]	+	[[Category: Caulobacter vibrioides]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carney~~, A E~~]]	+	[[Category: Carney AE]]
-	[[Category: Cook~~, P D~~]]	+	[[Category: Cook PD]]
-	[[Category: Holden~~, H M]]~~	+	[[Category: Holden HM]]
-	~~[[Category: Aspartate aminotransferase]]~~	+
-	~~[[Category: Deoxysugar]]~~	+
-	~~[[Category: O-antigen]]~~	+
-	~~[[Category: Perosamine]]~~	+
-	~~[[Category: Pyridoxal phosphate]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:38, 28 July 2021

OCA — Wed, 28 Jul 2021 10:38:01 GMT

←Older revision		Revision as of 10:38, 28 July 2021
Line 1:		Line 1:

	==GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand==		==GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand==
-	<StructureSection load='3dr4' size='340' side='right' caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3dr4' size='340' side='right'caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Caulobacter_crescentus Caulobacter crescentus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bn1\|3bn1]], [[3dr7\|3dr7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bn1\|3bn1]], [[3dr7\|3dr7]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">per ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~155892 Caulobacter crescentus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">per ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUVC])</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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [~~http~~://pdbe.org/3dr4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [https://pdbe.org/3dr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/O85354_CAUCE O85354_CAUCE]] Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.<ref>PMID:11390676</ref> <ref>PMID:18247575</ref> <ref>PMID:18795799</ref>	+	[[https://www.uniprot.org/uniprot/O85354_CAUCE O85354_CAUCE]] Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.<ref>PMID:11390676</ref> <ref>PMID:18247575</ref> <ref>PMID:18795799</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caulobacter crescentus~~]]	+	[[Category: Cauvc]]
		+	[[Category: Large Structures]]
	[[Category: Carney, A E]]		[[Category: Carney, A E]]
	[[Category: Cook, P D]]		[[Category: Cook, P D]]

OCA at 09:50, 14 November 2018

OCA — Wed, 14 Nov 2018 09:50:34 GMT

←Older revision		Revision as of 09:50, 14 November 2018
Line 3:		Line 3:
	<StructureSection load='3dr4' size='340' side='right' caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3dr4' size='340' side='right' caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Caulobacter_vibrioides~~ Caulobacter ~~vibrioides~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_crescentus Caulobacter crescentus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bn1\|3bn1]], [[3dr7\|3dr7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bn1\|3bn1]], [[3dr7\|3dr7]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">per ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155892 Caulobacter ~~vibrioides~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">per ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155892 Caulobacter crescentus])</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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [http://pdbe.org/3dr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 ProSAT]</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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [http://pdbe.org/3dr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 ProSAT]</span></td></tr>
	</table>		</table>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/3dr4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/3dr4_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>
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Caulobacter ~~vibrioides~~]]	+	[[Category: Caulobacter crescentus]]
	[[Category: Carney, A E]]		[[Category: Carney, A E]]
	[[Category: Cook, P D]]		[[Category: Cook, P D]]

OCA at 14:47, 11 August 2016

OCA — Thu, 11 Aug 2016 14:47:34 GMT

←Older revision		Revision as of 14:47, 11 August 2016
Line 1:		Line 1:
		+
	==GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand==		==GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand==
	<StructureSection load='3dr4' size='340' side='right' caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3dr4' size='340' side='right' caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bn1\|3bn1]], [[3dr7\|3dr7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bn1\|3bn1]], [[3dr7\|3dr7]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">per ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155892 Caulobacter vibrioides])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">per ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155892 Caulobacter vibrioides])</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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dr4 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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [http://pdbe.org/3dr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/O85354_CAUCE O85354_CAUCE]] Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.<ref>PMID:11390676</ref> <ref>PMID:18247575</ref> <ref>PMID:18795799</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		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=3dr4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		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 3dr4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:07, 12 November 2014

OCA — Wed, 12 Nov 2014 08:07:40 GMT

←Older revision		Revision as of 08:07, 12 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3dr4.~~png~~\|~~left~~\|200px]]	+	==GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand==
		+	<StructureSection load='3dr4' size='340' side='right' caption='[[3dr4]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bn1\|3bn1]], [[3dr7\|3dr7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">per ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155892 Caulobacter vibrioides])</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=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [http://www.ebi.ac.uk/pdbsum/3dr4 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/dr/3dr4_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 ==
		+	Perosamine (4-amino-4,6-dideoxy- d-mannose), or its N-acetylated form, is one of several dideoxy sugars found in the O-antigens of such infamous Gram-negative bacteria as Vibrio cholerae O1 and Escherichia coli O157:H7. It is added to the bacterial O-antigen via a nucleotide-linked version, namely GDP-perosamine. Three enzymes are required for the biosynthesis of GDP-perosamine starting from mannose 1-phosphate. The focus of this investigation is GDP-perosamine synthase from Caulobacter crescentus, which catalyzes the final step in GDP-perosamine synthesis, the conversion of GDP-4-keto-6-deoxymannose to GDP-perosamine. The enzyme is PLP-dependent and belongs to the aspartate aminotransferase superfamily. It contains the typically conserved active site lysine residue, which forms a Schiff base with the PLP cofactor. Two crystal structures were determined for this investigation: a site-directed mutant protein (K186A) complexed with GDP-perosamine and the wild-type enzyme complexed with an unnatural ligand, GDP-3-deoxyperosamine. These structures, determined to 1.6 and 1.7 A resolution, respectively, revealed the manner in which products, and presumably substrates, are accommodated within the active site pocket of GDP-perosamine synthase. Additional kinetic analyses using both the natural and unnatural substrates revealed that the K m for the unnatural substrate was unperturbed relative to that of the natural substrate, but the k cat was lowered by a factor of approximately 200. Taken together, these studies shed light on why GDP-perosamine synthase functions as an aminotransferase whereas another very similar PLP-dependent enzyme, GDP-4-keto-6-deoxy- d-mannose 3-dehydratase or ColD, catalyzes a dehydration reaction using the same substrate.

-	~~{{STRUCTURE_3dr4\| PDB=3dr4 \| SCENE= }}~~	+	Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase.,Cook PD, Carney AE, Holden HM Biochemistry. 2008 Oct 7;47(40):10685-93. Epub 2008 Sep 17. PMID:18795799<ref>PMID:18795799</ref>

-	~~===GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18795799}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3dr4]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018795799<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
-	[[Category: Carney, A E.]]	+	[[Category: Carney, A E]]
-	[[Category: Cook, P D.]]	+	[[Category: Cook, P D]]
-	[[Category: Holden, H M.]]	+	[[Category: Holden, H M]]
	[[Category: Aspartate aminotransferase]]		[[Category: Aspartate aminotransferase]]
	[[Category: Deoxysugar]]		[[Category: Deoxysugar]]

OCA: Protected "3dr4" [edit=sysop:move=sysop]

OCA — Wed, 09 Jan 2013 08:52:03 GMT

Protected "3dr4" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:52, 9 January 2013

OCA at 08:51, 9 January 2013

OCA — Wed, 09 Jan 2013 08:51:59 GMT

←Older revision		Revision as of 08:51, 9 January 2013
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-	{{Seed}}
	[[Image:3dr4.png\|left\|200px]]		[[Image:3dr4.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dr4", 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_3dr4\| PDB=3dr4 \| SCENE= }}		{{STRUCTURE_3dr4\| PDB=3dr4 \| SCENE= }}

	===GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand===		===GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18795799}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18795799 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18795799}}		{{ABSTRACT_PUBMED_18795799}}

	==About this Structure==		==About this Structure==
-	~~3DR4~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].	+	[[3dr4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18795799~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018795799</ref><references group="xtra"/>
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
	[[Category: Carney, A E.]]		[[Category: Carney, A E.]]
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	[[Category: Perosamine]]		[[Category: Perosamine]]
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 04:20:45 2009''~~	+

OCA at 02:20, 18 February 2009

OCA — Wed, 18 Feb 2009 02:20:47 GMT

←Older revision		Revision as of 02:20, 18 February 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3dr4.~~jpg~~\|left\|200px]]	+	[[Image:3dr4.png\|left\|200px]]

	<!--		<!--
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	==About this Structure==		==About this Structure==
-	3DR4 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].	+	3DR4 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].

	==Reference==		==Reference==
-	~~Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase., Cook PD, Carney AE, Holden HM, Biochemistry. 2008 Oct 7;47(40):10685-93. Epub 2008 Sep 17.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18795799 18795799]~~	+	<ref group="xtra">PMID:18795799</ref><references group="xtra"/>
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
-	[[Category: Single protein]]
	[[Category: Carney, A E.]]		[[Category: Carney, A E.]]
	[[Category: Cook, P D.]]		[[Category: Cook, P D.]]
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	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Oct 15 16~~:03:~~19 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:20:45 2009''

OCA at 14:03, 15 October 2008

OCA — Wed, 15 Oct 2008 14:03:20 GMT

←Older revision		Revision as of 14:03, 15 October 2008
Line 12:		Line 12:
	===GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand===		===GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18795799}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18795799 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18795799}}

	==About this Structure==		==About this Structure==
	3DR4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].		3DR4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].
		+
		+	==Reference==
		+	Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase., Cook PD, Carney AE, Holden HM, Biochemistry. 2008 Oct 7;47(40):10685-93. Epub 2008 Sep 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18795799 18795799]
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
	[[Category: Single protein]]		[[Category: Single protein]]
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	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 15 14:48:00 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 15 16:03:19 2008''

OCA at 12:48, 15 October 2008

OCA — Wed, 15 Oct 2008 12:48:01 GMT

←Older revision		Revision as of 12:48, 15 October 2008
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3dr4.jpg\|left\|200px]]

-	The ~~entry 3dr4~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3dr4", 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_3dr4\| PDB=3dr4 \| SCENE= }}

-	~~Authors: Holden, H.M., Cook, P.D., Carney, A.E.~~	+	===GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand===

-	Description: GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Aug 27 10~~:58:33 2008''	+	==About this Structure==
		+	3DR4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].
		+	[[Category: Caulobacter vibrioides]]
		+	[[Category: Single protein]]
		+	[[Category: Carney, A E.]]
		+	[[Category: Cook, P D.]]
		+	[[Category: Holden, H M.]]
		+	[[Category: Aspartate aminotransferase]]
		+	[[Category: Deoxysugar]]
		+	[[Category: O-antigen]]
		+	[[Category: Perosamine]]
		+	[[Category: Pyridoxal phosphate]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 15 14:48:00 2008''