5w6j - Revision history

OCA at 14:14, 13 March 2024

OCA — Wed, 13 Mar 2024 14:14:11 GMT

←Older revision		Revision as of 14:14, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='5w6j' size='340' side='right'caption='[[5w6j]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='5w6j' size='340' side='right'caption='[[5w6j]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w6j]] is a 20 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W6J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W6J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w6j]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W6J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.78Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>glgC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~358~~ "~~Achromobacter radiobacter~~" ~~(Beijerinck and van Delden 1902) Bergey et al. 1934])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Glucose-1-phosphate_adenylyltransferase Glucose-1-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.27 2.7.7.27] </~~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=5w6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w6j OCA], [https://pdbe.org/5w6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w6j RCSB], [https://www.ebi.ac.uk/pdbsum/5w6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w6j 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=5w6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w6j OCA], [~~http~~://pdbe.org/5w6j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w6j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w6j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w6j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GLGC_RHIRD GLGC_RHIRD]] Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans.	+	[https://www.uniprot.org/uniprot/GLGC_RHIRD GLGC_RHIRD] Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The pathways for biosynthesis of glycogen in bacteria and starch in plants are evolutionarily and biochemically related. They are regulated primarily by ADP-glucose pyrophosphorylase, which evolved to satisfy metabolic requirements of a particular organism. Despite the importance of these two pathways, little is known about the mechanism that controls pyrophosphorylase activity or the location of its allosteric sites. Here, we report pyruvate-bound crystal structures of ADP-glucose pyrophosphorylase from the bacterium Agrobacterium tumefaciens, identifying a previously elusive activator site for the enzyme. We found that the tetrameric enzyme binds two molecules of pyruvate in a planar conformation. Each binding site is located in a crevice between the C-terminal domains of two subunits where they stack via a distinct beta-helix region. Pyruvate interacts with the side chain of Lys-43 and with the peptide backbone of Ser-328 and Gly-329 from both subunits. These structural insights led to the design of two variants with altered regulatory properties. In one variant (K43A), the allosteric effect was absent, whereas in the other (G329D), the introduced Asp mimicked the presence of pyruvate. The latter generated an enzyme that was pre-activated and insensitive to further activation by pyruvate. Our study furnishes a deeper understanding of how glycogen biosynthesis is regulated in bacteria and the mechanism by which transgenic plants increased their starch production. These insights will facilitate rational approaches to enzyme engineering for starch production in crops of agricultural interest and will promote further study of allosteric signal transmission and molecular evolution in this important enzyme family.	+
-		+
-	Structural analysis reveals a pyruvate-binding activator site in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase.,Hill BL, Mascarenhas R, Patel HP, Asencion Diez MD, Wu R, Iglesias AA, Liu D, Ballicora MA J Biol Chem. 2018 Nov 6. pii: RA118.004246. doi: 10.1074/jbc.RA118.004246. PMID:30401744<ref>PMID:30401744</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5w6j" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Glucose-1-phosphate adenylyltransferase~~]]	+	[[Category: Agrobacterium tumefaciens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ballicora~~, M A~~]]	+	[[Category: Ballicora MA]]
-	[[Category: Hill~~, B L~~]]	+	[[Category: Hill BL]]
-	[[Category: Liu, D]]	+	[[Category: Liu D]]
-	[[Category: Mascarenhas~~, R N~~]]	+	[[Category: Mascarenhas RN]]
-	[[Category: Wu, R]]	+	[[Category: Wu R]]
-	~~[[Category: Allosterism]]~~	+
-	~~[[Category: Glycogen biosynthesis]]~~	+
-	~~[[Category: Starch biosynthesis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:09, 27 November 2019

OCA — Wed, 27 Nov 2019 08:09:48 GMT

←Older revision		Revision as of 08:09, 27 November 2019
Line 1:		Line 1:

	==Agrobacterium tumefaciens ADP-glucose pyrophosphorylase==		==Agrobacterium tumefaciens ADP-glucose pyrophosphorylase==
-	<StructureSection load='5w6j' size='340' side='right' caption='[[5w6j]], [[Resolution\|resolution]] 1.78Å' scene=''>	+	<StructureSection load='5w6j' size='340' side='right'caption='[[5w6j]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5w6j]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W6J FirstGlance]. <br>		<table><tr><td colspan='2'>[[5w6j]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W6J FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Glucose-1-phosphate adenylyltransferase]]		[[Category: Glucose-1-phosphate adenylyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Ballicora, M A]]		[[Category: Ballicora, M A]]
	[[Category: Hill, B L]]		[[Category: Hill, B L]]

OCA at 07:35, 21 February 2019

OCA — Thu, 21 Feb 2019 07:35:54 GMT

←Older revision		Revision as of 07:35, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='5w6j' size='340' side='right' caption='[[5w6j]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='5w6j' size='340' side='right' caption='[[5w6j]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w6j]] is a 20 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W6J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w6j]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W6J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glgC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose-1-phosphate_adenylyltransferase Glucose-1-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.27 2.7.7.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose-1-phosphate_adenylyltransferase Glucose-1-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.27 2.7.7.27] </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=5w6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w6j OCA], [http://pdbe.org/5w6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w6j RCSB], [http://www.ebi.ac.uk/pdbsum/5w6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w6j 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=5w6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w6j OCA], [http://pdbe.org/5w6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w6j RCSB], [http://www.ebi.ac.uk/pdbsum/5w6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w6j ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GLGC_RHIRD GLGC_RHIRD]] Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans.		[[http://www.uniprot.org/uniprot/GLGC_RHIRD GLGC_RHIRD]] Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The pathways for biosynthesis of glycogen in bacteria and starch in plants are evolutionarily and biochemically related. They are regulated primarily by ADP-glucose pyrophosphorylase, which evolved to satisfy metabolic requirements of a particular organism. Despite the importance of these two pathways, little is known about the mechanism that controls pyrophosphorylase activity or the location of its allosteric sites. Here, we report pyruvate-bound crystal structures of ADP-glucose pyrophosphorylase from the bacterium Agrobacterium tumefaciens, identifying a previously elusive activator site for the enzyme. We found that the tetrameric enzyme binds two molecules of pyruvate in a planar conformation. Each binding site is located in a crevice between the C-terminal domains of two subunits where they stack via a distinct beta-helix region. Pyruvate interacts with the side chain of Lys-43 and with the peptide backbone of Ser-328 and Gly-329 from both subunits. These structural insights led to the design of two variants with altered regulatory properties. In one variant (K43A), the allosteric effect was absent, whereas in the other (G329D), the introduced Asp mimicked the presence of pyruvate. The latter generated an enzyme that was pre-activated and insensitive to further activation by pyruvate. Our study furnishes a deeper understanding of how glycogen biosynthesis is regulated in bacteria and the mechanism by which transgenic plants increased their starch production. These insights will facilitate rational approaches to enzyme engineering for starch production in crops of agricultural interest and will promote further study of allosteric signal transmission and molecular evolution in this important enzyme family.
		+
		+	Structural analysis reveals a pyruvate-binding activator site in the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase.,Hill BL, Mascarenhas R, Patel HP, Asencion Diez MD, Wu R, Iglesias AA, Liu D, Ballicora MA J Biol Chem. 2018 Nov 6. pii: RA118.004246. doi: 10.1074/jbc.RA118.004246. PMID:30401744<ref>PMID:30401744</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5w6j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:02, 14 November 2018

OCA — Wed, 14 Nov 2018 08:02:53 GMT

←Older revision		Revision as of 08:02, 14 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5w6j is ~~ON HOLD until Paper Publication~~	+	==Agrobacterium tumefaciens ADP-glucose pyrophosphorylase==
-		+	<StructureSection load='5w6j' size='340' side='right' caption='[[5w6j]], [[Resolution\|resolution]] 1.78Å' scene=''>
-	~~Authors~~: ~~Mascarenhas~~, R.N., ~~Hill, B~~.L., Wu, R., ~~Ballicora, M~~.A., ~~Liu, D~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5w6j]] is a 20 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W6J FirstGlance]. <br>
-	~~Description~~: ~~Agrobacterium tumefaciens~~ ADP-glucose ~~pyrophosphorylase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose-1-phosphate_adenylyltransferase Glucose-1-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.27 2.7.7.27] </span></td></tr>
-	[[Category: ~~Mascarenhas~~, ~~R.N~~]]	+	<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=5w6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w6j OCA], [http://pdbe.org/5w6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w6j RCSB], [http://www.ebi.ac.uk/pdbsum/5w6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w6j ProSAT]</span></td></tr>
-	[[Category: ~~Ballicora~~, ~~M.A~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLGC_RHIRD GLGC_RHIRD]] Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glucose-1-phosphate adenylyltransferase]]
		+	[[Category: Ballicora, M A]]
		+	[[Category: Hill, B L]]
	[[Category: Liu, D]]		[[Category: Liu, D]]
		+	[[Category: Mascarenhas, R N]]
	[[Category: Wu, R]]		[[Category: Wu, R]]
-	[[Category: ~~Hill, B.L~~]]	+	[[Category: Allosterism]]
		+	[[Category: Glycogen biosynthesis]]
		+	[[Category: Starch biosynthesis]]
		+	[[Category: Transferase]]

OCA at 03:48, 30 May 2018

OCA — Wed, 30 May 2018 03:48:11 GMT

←Older revision		Revision as of 03:48, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5w6j is ON HOLD	+	The entry 5w6j is ON HOLD until Paper Publication

	Authors: Mascarenhas, R.N., Hill, B.L., Wu, R., Ballicora, M.A., Liu, D.		Authors: Mascarenhas, R.N., Hill, B.L., Wu, R., Ballicora, M.A., Liu, D.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Mascarenhas, R.N]]		[[Category: Mascarenhas, R.N]]
		+	[[Category: Ballicora, M.A]]
	[[Category: Liu, D]]		[[Category: Liu, D]]
	[[Category: Wu, R]]		[[Category: Wu, R]]
	[[Category: Hill, B.L]]		[[Category: Hill, B.L]]
-	[[Category: Ballicora, M.A]]

OCA: Protected "5w6j" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 14:29:53 GMT

Protected "5w6j" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:29, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5w6j is ON HOLD Authors: Mascarenhas, R.N., Hill, B.L., Wu, R., Ballicora, M.A., Liu, D. Description: Agrobacterium tumefaciens ADP-glucose pyropho...

OCA — Wed, 27 Sep 2017 14:29:52 GMT

New page: '''Unreleased structure''' The entry 5w6j is ON HOLD Authors: Mascarenhas, R.N., Hill, B.L., Wu, R., Ballicora, M.A., Liu, D. Description: Agrobacterium tumefaciens ADP-glucose pyropho...

New page

'''Unreleased structure'''

The entry 5w6j is ON HOLD

Authors: Mascarenhas, R.N., Hill, B.L., Wu, R., Ballicora, M.A., Liu, D.

Description: Agrobacterium tumefaciens ADP-glucose pyrophosphorylase
[[Category: Unreleased Structures]]
[[Category: Mascarenhas, R.N]]
[[Category: Liu, D]]
[[Category: Wu, R]]
[[Category: Hill, B.L]]
[[Category: Ballicora, M.A]]