2pa4 - Revision history

OCA at 09:08, 21 February 2024

2024-02-21T09:08:53Z

←Older revision		Revision as of 09:08, 21 February 2024
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	<StructureSection load='2pa4' size='340' side='right'caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2pa4' size='340' side='right'caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Corgl Corgl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>galU1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~196627 CORGL])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/UTP~~--~~glucose~~-~~1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [https://pdbe.org/2pa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [https://www.ebi.ac.uk/pdbsum/2pa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pa4 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=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [https://pdbe.org/2pa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [https://www.ebi.ac.uk/pdbsum/2pa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pa4 ProSAT]</span></td></tr>
	</table>		</table>
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	</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=2pa4 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=2pa4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Glucose-1-phosphate uridylyltransferase, or UGPase, catalyzes the production of UDP-glucose from glucose-1-phosphate and UTP. Because of the biological role of UDP-glucose in glycogen synthesis and in the formation of glycolipids, glycoproteins, and proteoglycans, the enzyme is widespread in nature. Recently this laboratory reported the three-dimensional structure of UGPase from Escherichia coli. While the initial X-ray analysis revealed the overall fold of the enzyme, details concerning its active site geometry were limited because crystals of the protein complexed with either substrates or products could never be obtained. In an effort to more fully investigate the active site geometry of the enzyme, UGPase from Corynebacterium glutamicum was subsequently cloned and purified. Here we report the X-ray structure of UGPase crystallized in the presence of both magnesium and UDP-glucose. Residues involved in anchoring the ligand to the active site include the polypeptide chain backbone atoms of Ala 20, Gly 21, Gly 117, Gly 180, and Ala 214, and the side chains of Glu 36, Gln 112, Asp 143, Glu 201, and Lys 202. Two magnesium ions are observed coordinated to the UDP-glucose. An alpha- and a beta-phosphoryl oxygen, three waters, and the side chain of Asp 142 ligate the first magnesium, whereas the second ion is coordinated by an alpha-phosphoryl oxygen and five waters. The position of the first magnesium is conserved in both the glucose-1-phosphate thymidylyltransferases and the cytidylyltransferases. The structure presented here provides further support for the role of the conserved magnesium ion in the catalytic mechanisms of the sugar-1-phosphate nucleotidylyltransferases.
-
-	Active site geometry of glucose-1-phosphate uridylyltransferase.,Thoden JB, Holden HM Protein Sci. 2007 Jul;16(7):1379-88. Epub 2007 Jun 13. PMID:17567737<ref>PMID:17567737</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2pa4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Corgl~~]]	+	[[Category: Corynebacterium glutamicum ATCC 13032]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UTP--glucose-1-phosphate uridylyltransferase]]~~	+	[[Category: Holden HM]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Thoden JB]]
-	[[Category: Thoden~~, J B]]~~	+
-	~~[[Category: Metabolism]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Phosphorylase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 15:19, 17 June 2021

2021-06-17T15:19:38Z

←Older revision		Revision as of 15:19, 17 June 2021
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	==Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose==		==Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose==
-	<StructureSection load='2pa4' size='340' side='right' caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2pa4' size='340' side='right'caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Corgl Corgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Corgl Corgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [~~http~~://pdbe.org/2pa4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pa4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pa4 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=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [https://pdbe.org/2pa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [https://www.ebi.ac.uk/pdbsum/2pa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pa4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Corgl]]		[[Category: Corgl]]
		+	[[Category: Large Structures]]
	[[Category: UTP--glucose-1-phosphate uridylyltransferase]]		[[Category: UTP--glucose-1-phosphate uridylyltransferase]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

OCA at 08:41, 29 August 2018

2018-08-29T08:41:12Z

←Older revision		Revision as of 08:41, 29 August 2018
Line 1:		Line 1:
		+
	==Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose==		==Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose==
	<StructureSection load='2pa4' size='340' side='right' caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2pa4' size='340' side='right' caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [http://pdbe.org/2pa4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [http://www.ebi.ac.uk/pdbsum/2pa4 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=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [http://pdbe.org/2pa4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [http://www.ebi.ac.uk/pdbsum/2pa4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pa4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pa/2pa4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pa/2pa4_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>
	</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=2pa4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:18, 11 September 2015

2015-09-11T09:18:37Z

←Older revision		Revision as of 09:18, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2pa4' size='340' side='right' caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2pa4' size='340' side='right' caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Corynebacterium_glutamicum_atcc_13032 Corynebacterium glutamicum atcc 13032~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Corgl Corgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 ~~Corynebacterium glutamicum ATCC 13032~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [http://www.ebi.ac.uk/pdbsum/2pa4 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=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [http://pdbe.org/2pa4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [http://www.ebi.ac.uk/pdbsum/2pa4 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2pa4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Corynebacterium glutamicum atcc 13032~~]]	+	[[Category: Corgl]]
	[[Category: UTP--glucose-1-phosphate uridylyltransferase]]		[[Category: UTP--glucose-1-phosphate uridylyltransferase]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

OCA at 16:48, 19 January 2015

2015-01-19T16:48:06Z

←Older revision		Revision as of 16:48, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum_atcc_13032 Corynebacterium glutamicum atcc 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum_atcc_13032 Corynebacterium glutamicum atcc 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 Corynebacterium glutamicum ATCC 13032])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 Corynebacterium glutamicum ATCC 13032])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></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=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [http://www.ebi.ac.uk/pdbsum/2pa4 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=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [http://www.ebi.ac.uk/pdbsum/2pa4 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:
	[[Category: Corynebacterium glutamicum atcc 13032]]		[[Category: Corynebacterium glutamicum atcc 13032]]
	[[Category: UTP--glucose-1-phosphate uridylyltransferase]]		[[Category: UTP--glucose-1-phosphate uridylyltransferase]]
-	[[Category: Holden, H M.]]	+	[[Category: Holden, H M]]
-	[[Category: Thoden, J B.]]	+	[[Category: Thoden, J B]]
	[[Category: Metabolism]]		[[Category: Metabolism]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 04:17, 3 October 2014

2014-10-03T04:17:52Z

←Older revision		Revision as of 04:17, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2pa4\| PDB=2pa4 \| SCENE= }}~~	+	==Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose==
-	===Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose===	+	<StructureSection load='2pa4' size='340' side='right' caption='[[2pa4]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_17567737}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum_atcc_13032 Corynebacterium glutamicum atcc 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">galU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 Corynebacterium glutamicum ATCC 13032])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></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=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [http://www.ebi.ac.uk/pdbsum/2pa4 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/pa/2pa4_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 ==
		+	Glucose-1-phosphate uridylyltransferase, or UGPase, catalyzes the production of UDP-glucose from glucose-1-phosphate and UTP. Because of the biological role of UDP-glucose in glycogen synthesis and in the formation of glycolipids, glycoproteins, and proteoglycans, the enzyme is widespread in nature. Recently this laboratory reported the three-dimensional structure of UGPase from Escherichia coli. While the initial X-ray analysis revealed the overall fold of the enzyme, details concerning its active site geometry were limited because crystals of the protein complexed with either substrates or products could never be obtained. In an effort to more fully investigate the active site geometry of the enzyme, UGPase from Corynebacterium glutamicum was subsequently cloned and purified. Here we report the X-ray structure of UGPase crystallized in the presence of both magnesium and UDP-glucose. Residues involved in anchoring the ligand to the active site include the polypeptide chain backbone atoms of Ala 20, Gly 21, Gly 117, Gly 180, and Ala 214, and the side chains of Glu 36, Gln 112, Asp 143, Glu 201, and Lys 202. Two magnesium ions are observed coordinated to the UDP-glucose. An alpha- and a beta-phosphoryl oxygen, three waters, and the side chain of Asp 142 ligate the first magnesium, whereas the second ion is coordinated by an alpha-phosphoryl oxygen and five waters. The position of the first magnesium is conserved in both the glucose-1-phosphate thymidylyltransferases and the cytidylyltransferases. The structure presented here provides further support for the role of the conserved magnesium ion in the catalytic mechanisms of the sugar-1-phosphate nucleotidylyltransferases.

-	~~==About this Structure==~~	+	Active site geometry of glucose-1-phosphate uridylyltransferase.,Thoden JB, Holden HM Protein Sci. 2007 Jul;16(7):1379-88. Epub 2007 Jun 13. PMID:17567737<ref>PMID:17567737</ref>
-	~~[[2pa4]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Corynebacterium_glutamicum_atcc_13032 Corynebacterium glutamicum atcc 13032]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2PA4 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:017567737</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Corynebacterium glutamicum atcc 13032]]		[[Category: Corynebacterium glutamicum atcc 13032]]
	[[Category: UTP--glucose-1-phosphate uridylyltransferase]]		[[Category: UTP--glucose-1-phosphate uridylyltransferase]]

OCA at 06:43, 8 May 2013

2013-05-08T06:43:35Z

←Older revision		Revision as of 06:43, 8 May 2013
Line 1:		Line 1:
-	[[Image:2pa4.png\|left\|200px]]
-
	{{STRUCTURE_2pa4\| PDB=2pa4 \| SCENE= }}		{{STRUCTURE_2pa4\| PDB=2pa4 \| SCENE= }}
-
	===Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose===		===Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose===
-
	{{ABSTRACT_PUBMED_17567737}}		{{ABSTRACT_PUBMED_17567737}}

Line 11:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:017567737</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017567737</ref><references group="xtra"/><references/>
	[[Category: Corynebacterium glutamicum atcc 13032]]		[[Category: Corynebacterium glutamicum atcc 13032]]
	[[Category: UTP--glucose-1-phosphate uridylyltransferase]]		[[Category: UTP--glucose-1-phosphate uridylyltransferase]]

OCA: Protected "2pa4" [edit=sysop:move=sysop]

2013-01-07T14:28:42Z

Protected "2pa4" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:28, 7 January 2013

OCA at 14:28, 7 January 2013

2013-01-07T14:28:40Z

←Older revision		Revision as of 14:28, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2pa4.png\|left\|200px]]		[[Image:2pa4.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2pa4", 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_2pa4\| PDB=2pa4 \| SCENE= }}		{{STRUCTURE_2pa4\| PDB=2pa4 \| SCENE= }}

	===Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose===		===Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17567737}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17567737 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17567737}}		{{ABSTRACT_PUBMED_17567737}}

	==About this Structure==		==About this Structure==
-	~~2PA4~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Corynebacterium_glutamicum~~ Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA].	+	[[2pa4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum_atcc_13032 Corynebacterium glutamicum atcc 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17567737~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017567737</ref><references group="xtra"/>
-	[[Category: Corynebacterium glutamicum]]	+	[[Category: Corynebacterium glutamicum atcc 13032]]
	[[Category: UTP--glucose-1-phosphate uridylyltransferase]]		[[Category: UTP--glucose-1-phosphate uridylyltransferase]]
	[[Category: Holden, H M.]]		[[Category: Holden, H M.]]
Line 31:		Line 19:
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 18:37:16 2009''~~	+

OCA at 16:37, 17 February 2009

2009-02-17T16:37:18Z

←Older revision		Revision as of 16:37, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2PA4 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA].	+	2PA4 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA].

	==Reference==		==Reference==
-	~~Active site geometry of glucose-1-phosphate uridylyltransferase., Thoden JB, Holden HM, Protein Sci. 2007 Jul;16(7):1379-88. Epub 2007 Jun 13.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17567737 17567737]~~	+	<ref group="xtra">PMID:17567737</ref><references group="xtra"/>
	[[Category: Corynebacterium glutamicum]]		[[Category: Corynebacterium glutamicum]]
-	[[Category: Single protein]]
	[[Category: UTP--glucose-1-phosphate uridylyltransferase]]		[[Category: UTP--glucose-1-phosphate uridylyltransferase]]
	[[Category: Holden, H M.]]		[[Category: Holden, H M.]]
Line 33:		Line 32:
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:37:~~04 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:37:16 2009''