5vjf - Revision history

OCA at 13:49, 4 October 2023

OCA — Wed, 04 Oct 2023 13:49:56 GMT

←Older revision		Revision as of 13:49, 4 October 2023
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	<StructureSection load='5vjf' size='340' side='right'caption='[[5vjf]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5vjf' size='340' side='right'caption='[[5vjf]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vjf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Campylobacter_pylori Campylobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vjf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VJF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.85Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vje\|5vje]], [[5vjd\|5vjd]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fba, HP_0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=5vjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjf OCA], [https://pdbe.org/5vjf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vjf RCSB], [https://www.ebi.ac.uk/pdbsum/5vjf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjf ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase Fructose-bisphosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.13 4.1.2.13] </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=5vjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjf OCA], [~~http~~://pdbe.org/5vjf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vjf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vjf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ALF_HELPY ALF_HELPY]] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity).	+	[https://www.uniprot.org/uniprot/ALF_HELPY ALF_HELPY] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Campylobacter~~ pylori]]	+	[[Category: Helicobacter pylori 26695]]
-	~~[[Category: Fructose-bisphosphate aldolase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Coincon, M]]	+	[[Category: Coincon M]]
-	[[Category: Sygusch, J]]	+	[[Category: Sygusch J]]
-	~~[[Category: Glycolysis]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Metalloenzyme~~]]	+

OCA at 08:26, 8 January 2020

OCA — Wed, 08 Jan 2020 08:26:23 GMT

←Older revision		Revision as of 08:26, 8 January 2020
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	==Class II fructose-1,6-bisphosphate aldolase of Helicobacter pylori with DHAP==		==Class II fructose-1,6-bisphosphate aldolase of Helicobacter pylori with DHAP==
-	<StructureSection load='5vjf' size='340' side='right' caption='[[5vjf]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5vjf' size='340' side='right'caption='[[5vjf]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJF FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJF FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5vjf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vjf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aldolase 3D structures\|Aldolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Campylobacter pylori]]		[[Category: Campylobacter pylori]]
	[[Category: Fructose-bisphosphate aldolase]]		[[Category: Fructose-bisphosphate aldolase]]
		+	[[Category: Large Structures]]
	[[Category: Coincon, M]]		[[Category: Coincon, M]]
	[[Category: Sygusch, J]]		[[Category: Sygusch, J]]

OCA at 05:48, 30 May 2018

OCA — Wed, 30 May 2018 05:48:43 GMT

←Older revision		Revision as of 05:48, 30 May 2018
Line 3:		Line 3:
	<StructureSection load='5vjf' size='340' side='right' caption='[[5vjf]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5vjf' size='340' side='right' caption='[[5vjf]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vjf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vjf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vje\|5vje]], [[5vjd\|5vjd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vje\|5vje]], [[5vjd\|5vjd]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fba, HP_0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase Fructose-bisphosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.13 4.1.2.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase Fructose-bisphosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.13 4.1.2.13] </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=5vjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjf OCA], [http://pdbe.org/5vjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjf RCSB], [http://www.ebi.ac.uk/pdbsum/5vjf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjf 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=5vjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjf OCA], [http://pdbe.org/5vjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjf RCSB], [http://www.ebi.ac.uk/pdbsum/5vjf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjf ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter pylori]]
	[[Category: Fructose-bisphosphate aldolase]]		[[Category: Fructose-bisphosphate aldolase]]
	[[Category: Coincon, M]]		[[Category: Coincon, M]]

OCA at 13:45, 11 April 2018

OCA — Wed, 11 Apr 2018 13:45:29 GMT

←Older revision		Revision as of 13:45, 11 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vjf is ~~ON HOLD until Paper~~ Publication	+	==Class II fructose-1,6-bisphosphate aldolase of Helicobacter pylori with DHAP==
		+	<StructureSection load='5vjf' size='340' side='right' caption='[[5vjf]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vjf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vje\|5vje]], [[5vjd\|5vjd]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase Fructose-bisphosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.13 4.1.2.13] </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=5vjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjf OCA], [http://pdbe.org/5vjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjf RCSB], [http://www.ebi.ac.uk/pdbsum/5vjf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALF_HELPY ALF_HELPY]] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystal structures of two bacterial metal (Zn) dependent D-fructose 1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 A resolution. The ligand complexes cryotrapped in native or mutant H. pylori aldolase crystals enabled a novel mechanistic description of FBP C3-C4 bond cleavage. The reaction mechanism uses active site remodelling during the catalytic cycle implicating relocation of the Zn cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes, triggered upon P1-phosphate binding, which liberates the Zn chelating His180, allowing it to act as a general base for the proton abstraction at the FBP C4-hydroxyl group. A second zinc chelating His83 hydrogen bonds the substrate C4- hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu142 is essential for protonation of the enediolate form, prior to product release. A D-tagatose 1,6-bisphosphate enzymatic complex reveals how His180 mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and D-glyceraldehyde-3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp82 and Asp255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops beta5-alpha7 and beta6-alpha8 (containing catalytic residues Glu142 and His180, respectively) drive active site remodelling enabling the relocation of the metal cofactor.

-	~~Authors~~:	+	Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.,Jacques B, Coincon M, Sygusch J J Biol Chem. 2018 Mar 28. pii: RA117.001098. doi: 10.1074/jbc.RA117.001098. PMID:29593097<ref>PMID:29593097</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vjf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fructose-bisphosphate aldolase]]
		+	[[Category: Coincon, M]]
		+	[[Category: Sygusch, J]]
		+	[[Category: Glycolysis]]
		+	[[Category: Lyase]]
		+	[[Category: Metalloenzyme]]

OCA at 11:22, 4 May 2017

OCA — Thu, 04 May 2017 11:22:28 GMT

←Older revision		Revision as of 11:22, 4 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Thu, 27 Apr 2017 12:21:32 GMT

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

←Older revision

Revision as of 12:21, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vjf is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 27 Apr 2017 12:21:31 GMT

New page: '''Unreleased structure''' The entry 5vjf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vjf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]