5jy9 - Revision history

OCA at 19:14, 20 September 2023

2023-09-20T19:14:57Z

←Older revision		Revision as of 19:14, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jy9' size='340' side='right'caption='[[5jy9]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='5jy9' size='340' side='right'caption='[[5jy9]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jy9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Yere8 Yere8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JY9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jy9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_enterocolitica_subsp._enterocolitica_8081 Yersinia enterocolitica subsp. enterocolitica 8081]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JY9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</scene~~>, ~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <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]] 2.162Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5jxz\|5jxz]], [[5jy4\|5jy4]], [[5jy8\|5jy8]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ybtS, YE2612 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=393305 YERE8])~~</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=5jy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jy9 OCA], [https://pdbe.org/5jy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jy9 RCSB], [https://www.ebi.ac.uk/pdbsum/5jy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jy9 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=5jy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jy9 OCA], [~~http~~://pdbe.org/5jy9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jy9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jy9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jy9 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A1JTF3_YERE8 A1JTF3_YERE8]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Yere8~~]]	+	[[Category: Yersinia enterocolitica subsp. enterocolitica 8081]]
-	[[Category: Lamb~~, A L~~]]	+	[[Category: Lamb AL]]
-	[[Category: Meneely~~, K M]]~~	+	[[Category: Meneely KM]]
-	~~[[Category: Chorismate]]~~	+
-	~~[[Category: Isochorismate]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 16:25, 11 December 2019

2019-12-11T16:25:06Z

←Older revision		Revision as of 16:25, 11 December 2019
Line 1:		Line 1:

	==An iron-bound structure of the salicylate synthase Irp9==		==An iron-bound structure of the salicylate synthase Irp9==
-	<StructureSection load='5jy9' size='340' side='right' caption='[[5jy9]], [[Resolution\|resolution]] 2.16Å' scene=''>	+	<StructureSection load='5jy9' size='340' side='right'caption='[[5jy9]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jy9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Yere8 Yere8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JY9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jy9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Yere8 Yere8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JY9 FirstGlance]. <br>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Yere8]]		[[Category: Yere8]]
	[[Category: Lamb, A L]]		[[Category: Lamb, A L]]

OCA at 12:57, 6 November 2017

2017-11-06T12:57:18Z

←Older revision		Revision as of 12:57, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5jy9' size='340' side='right' caption='[[5jy9]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='5jy9' size='340' side='right' caption='[[5jy9]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jy9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jy9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Yere8 Yere8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JY9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jxz\|5jxz]], [[5jy4\|5jy4]], [[5jy8\|5jy8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jxz\|5jxz]], [[5jy4\|5jy4]], [[5jy8\|5jy8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybtS, YE2612 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=393305 YERE8])</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=5jy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jy9 OCA], [http://pdbe.org/5jy9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jy9 RCSB], [http://www.ebi.ac.uk/pdbsum/5jy9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jy9 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=5jy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jy9 OCA], [http://pdbe.org/5jy9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jy9 RCSB], [http://www.ebi.ac.uk/pdbsum/5jy9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jy9 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Yere8]]
	[[Category: Lamb, A L]]		[[Category: Lamb, A L]]
	[[Category: Meneely, K M]]		[[Category: Meneely, K M]]

OCA at 15:18, 26 July 2016

2016-07-26T15:18:03Z

←Older revision		Revision as of 15:18, 26 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jy9 is ~~ON HOLD until Paper~~ Publication	+	==An iron-bound structure of the salicylate synthase Irp9==
		+	<StructureSection load='5jy9' size='340' side='right' caption='[[5jy9]], [[Resolution\|resolution]] 2.16Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jy9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JY9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jxz\|5jxz]], [[5jy4\|5jy4]], [[5jy8\|5jy8]]</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=5jy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jy9 OCA], [http://pdbe.org/5jy9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jy9 RCSB], [http://www.ebi.ac.uk/pdbsum/5jy9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jy9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The shikimate pathway of bacteria, fungi, and plants generates chorismate, which is drawn into biosynthetic pathways that form aromatic amino acids and other important metabolites, including folates, menaquinone, and siderophores. Many of the pathways initiated at this branch point transform chorismate using an MST enzyme. The MST enzymes (menaquinone, siderophore, and tryptophan biosynthetic enzymes) are structurally homologous and magnesium-dependent, and all perform similar chemical permutations to chorismate by nucleophilic addition (hydroxyl or amine) at the 2-position of the ring, inducing displacement of the 4-hydroxyl. The isomerase enzymes release isochorismate or aminodeoxychorismate as the product, while the synthase enzymes also have lyase activity that displaces pyruvate to form either salicylate or anthranilate. This has led to the hypothesis that the isomerase and lyase activities performed by the MST enzymes are functionally conserved. Here we have developed tailored pre-steady-state approaches to establish the kinetic mechanisms of the isochorismate and salicylate synthase enzymes of siderophore biosynthesis. Our data are centered on the role of magnesium ions, which inhibit the isochorismate synthase enzymes but not the salicylate synthase enzymes. Prior structural data have suggested that binding of the metal ion occludes access or egress of substrates. Our kinetic data indicate that for the production of isochorismate, a high magnesium ion concentration suppresses the rate of release of product, accounting for the observed inhibition and establishing the basis of the ordered-addition kinetic mechanism. Moreover, we show that isochorismate is channeled through the synthase reaction as an intermediate that is retained in the active site by the magnesium ion. Indeed, the lyase-active enzyme has 3 orders of magnitude higher affinity for the isochorismate complex relative to the chorismate complex. Apparent negative-feedback inhibition by ferrous ions is documented at nanomolar concentrations, which is a potentially physiologically relevant mode of regulation for siderophore biosynthesis in vivo.

-	~~Authors~~: Meneely, ~~K.M.~~, ~~Lamb~~, A.L.	+	An Open and Shut Case: The Interaction of Magnesium with MST Enzymes.,Meneely KM, Sundlov JA, Gulick AM, Moran GR, Lamb AL J Am Chem Soc. 2016 Jul 19. PMID:27373320<ref>PMID:27373320</ref>

-	~~Description: An iron-bound structure~~ of the ~~salicylate synthase Irp9~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Lamb, A.L]]	+	<div class="pdbe-citations 5jy9" style="background-color:#fffaf0;"></div>
-	[[Category: Meneely, K.M]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lamb, A L]]
		+	[[Category: Meneely, K M]]
		+	[[Category: Chorismate]]
		+	[[Category: Isochorismate]]
		+	[[Category: Isomerase]]

OCA at 13:15, 20 June 2016

2016-06-20T13:15:03Z

←Older revision		Revision as of 13:15, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jy9 is ON HOLD	+	The entry 5jy9 is ON HOLD until Paper Publication

	Authors: Meneely, K.M., Lamb, A.L.		Authors: Meneely, K.M., Lamb, A.L.

OCA: Protected "5jy9" [edit=sysop:move=sysop]

2016-06-01T14:02:43Z

Protected "5jy9" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:02, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jy9 is ON HOLD Authors: Meneely, K.M., Lamb, A.L. Description: An iron-bound structure of the salicylate synthase Irp9 [[Category: Unreleased Stru...

2016-06-01T14:02:42Z

New page: '''Unreleased structure''' The entry 5jy9 is ON HOLD Authors: Meneely, K.M., Lamb, A.L. Description: An iron-bound structure of the salicylate synthase Irp9 [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 5jy9 is ON HOLD

Authors: Meneely, K.M., Lamb, A.L.

Description: An iron-bound structure of the salicylate synthase Irp9
[[Category: Unreleased Structures]]
[[Category: Lamb, A.L]]
[[Category: Meneely, K.M]]