6nmx - Revision history

OCA at 06:56, 11 October 2023

OCA — Wed, 11 Oct 2023 06:56:23 GMT

←Older revision		Revision as of 06:56, 11 October 2023
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	<StructureSection load='6nmx' size='340' side='right'caption='[[6nmx]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='6nmx' size='340' side='right'caption='[[6nmx]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nmx]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacpn Bacpn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NMX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NMX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nmx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_spizizenii Bacillus spizizenii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NMX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=LJS:(2E,3Z)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-5-phosphonopent-3-enoic+acid'>LJS</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]] 1.971Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[6cgq\|6cgq~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LJS:(2E,3Z)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-5-phosphonopent-3-enoic+acid'>LJS</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>thrC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=96241 BACPN])</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=6nmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nmx OCA], [https://pdbe.org/6nmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nmx RCSB], [https://www.ebi.ac.uk/pdbsum/6nmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nmx 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/Threonine_synthase Threonine synthase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=4.~~2.3~~.1 4.~~2.3~~.1]~~ </~~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=6nmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nmx OCA], [~~http~~://pdbe.org/6nmx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nmx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nmx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nmx ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A8HUA2_BACPN A8HUA2_BACPN]~~] Catalyzes the gamma-elimination of phosphate from L-phosphohomoserine and the beta-addition of water to produce L-threonine.[PIRNR:PIRNR038945]	+	[https://www.uniprot.org/uniprot/A8HUA2_BACSC A8HUA2_BACSC] Catalyzes the gamma-elimination of phosphate from L-phosphohomoserine and the beta-addition of water to produce L-threonine.[ARBA:ARBA00003648][PIRNR:PIRNR038945]
	<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: ~~Bacpn~~]]	+	[[Category: Bacillus spizizenii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Threonine synthase]]~~	+	[[Category: Nair SK]]
-	[[Category: Nair~~, S K~~]]	+	[[Category: Petronikolou N]]
-	[[Category: Petronikolou, N]]	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Thrc~~]]	+

OCA at 09:22, 1 May 2019

OCA — Wed, 01 May 2019 09:22:02 GMT

←Older revision		Revision as of 09:22, 1 May 2019
Line 3:		Line 3:
	<StructureSection load='6nmx' size='340' side='right'caption='[[6nmx]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='6nmx' size='340' side='right'caption='[[6nmx]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nmx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NMX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacpn Bacpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NMX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LJS:(2E,3Z)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-5-phosphonopent-3-enoic+acid'>LJS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LJS:(2E,3Z)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-5-phosphonopent-3-enoic+acid'>LJS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cgq\|6cgq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cgq\|6cgq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thrC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=96241 BACPN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine_synthase Threonine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.1 4.2.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine_synthase Threonine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.1 4.2.3.1] </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=6nmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nmx OCA], [http://pdbe.org/6nmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nmx RCSB], [http://www.ebi.ac.uk/pdbsum/6nmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nmx 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=6nmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nmx OCA], [http://pdbe.org/6nmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nmx RCSB], [http://www.ebi.ac.uk/pdbsum/6nmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nmx ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacpn]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Threonine synthase]]		[[Category: Threonine synthase]]

OCA at 12:22, 13 March 2019

OCA — Wed, 13 Mar 2019 12:22:39 GMT

←Older revision		Revision as of 12:22, 13 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nmx is ~~ON HOLD~~	+	==Threonine synthase from Bacillus subtilis ATCC 6633 with PLP and APPA==
		+	<StructureSection load='6nmx' size='340' side='right'caption='[[6nmx]], [[Resolution\|resolution]] 1.97Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6nmx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NMX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LJS:(2E,3Z)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-5-phosphonopent-3-enoic+acid'>LJS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6cgq\|6cgq]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine_synthase Threonine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.3.1 4.2.3.1] </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=6nmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nmx OCA], [http://pdbe.org/6nmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nmx RCSB], [http://www.ebi.ac.uk/pdbsum/6nmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nmx ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A8HUA2_BACPN A8HUA2_BACPN]] Catalyzes the gamma-elimination of phosphate from L-phosphohomoserine and the beta-addition of water to produce L-threonine.[PIRNR:PIRNR038945]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rhizocticins are phosphono-oligopeptide antibiotics that contain a toxic C-terminal (Z)-L-2-amino-5-phosphono-3-pentenoic acid (APPA) moiety. APPA is an irreversible inhibitor of threonine synthase (ThrC), a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of O-phospho-L-homoserine to L-threonine. ThrCs are essential for the viability of bacteria, plants, and fungi and are a target for antibiotic development, as de novo threonine biosynthetic pathway is not found in humans. Given the ability of APPA to interfere in threonine metabolism, it is unclear how the producing strain B. subtilis ATCC6633 circumvents APPA toxicity. Notably, in addition to the housekeeping APPA-sensitive ThrC (BsThrC), B. subtilis encodes a second threonine synthase (RhiB) encoded within the rhizocticin biosynthetic gene cluster. Kinetic and spectroscopic analyses show that PLP-dependent RhiB is an authentic threonine synthase, converting O-phospho-L-homoserine to threonine with a catalytic efficiency comparable to BsThrC. To understand the structural basis of inhibition, we determined the crystal structure of APPA bound to the housekeeping BsThrC, revealing a covalent complex between the inhibitor and PLP. Structure-based sequence analyses reveal structural determinants within the RhiB active site that contribute to rendering this ThrC homolog resistant to APPA. Together, this work establishes the self-resistance mechanism utilized by B. subtilis ATCC6633 against APPA exemplifying one of many ways by which bacteria can overcome phosphonate toxicity.

-	~~Authors: Petronikolou~~, N., Nair, S.K.	+	Molecular basis of Bacillus subtilis ATCC6633 self-resistance to the phosphono-oligopeptide antibiotic rhizocticin.,Petronikolou N, Ortega MA, Borisova SA, Nair SK, Metcalf WW ACS Chem Biol. 2019 Mar 4. doi: 10.1021/acschembio.9b00030. PMID:30830751<ref>PMID:30830751</ref>

-	~~Description~~: Threonine synthase ~~from Bacillus subtilis ATCC 6633 with PLP and APPA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6nmx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Threonine synthase]]
		+	[[Category: Nair, S K]]
	[[Category: Petronikolou, N]]		[[Category: Petronikolou, N]]
-	[[Category: ~~Nair, S.K~~]]	+	[[Category: Lyase]]
		+	[[Category: Thrc]]

OCA: Protected "6nmx" [edit=sysop:move=sysop]

OCA — Wed, 30 Jan 2019 06:36:46 GMT

Protected "6nmx" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:36, 30 January 2019

OCA: New page: '''Unreleased structure''' The entry 6nmx is ON HOLD Authors: Petronikolou, N., Nair, S.K. Description: Threonine synthase from Bacillus subtilis ATCC 6633 with PLP and APPA [[Category...

OCA — Wed, 30 Jan 2019 06:36:44 GMT

New page: '''Unreleased structure''' The entry 6nmx is ON HOLD Authors: Petronikolou, N., Nair, S.K. Description: Threonine synthase from Bacillus subtilis ATCC 6633 with PLP and APPA [[Category...

New page

'''Unreleased structure'''

The entry 6nmx is ON HOLD

Authors: Petronikolou, N., Nair, S.K.

Description: Threonine synthase from Bacillus subtilis ATCC 6633 with PLP and APPA
[[Category: Unreleased Structures]]
[[Category: Petronikolou, N]]
[[Category: Nair, S.K]]