5e4n - Revision history

OCA at 06:12, 5 July 2023

OCA — Wed, 05 Jul 2023 06:12:46 GMT

←Older revision		Revision as of 06:12, 5 July 2023
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	<StructureSection load='5e4n' size='340' side='right'caption='[[5e4n]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5e4n' size='340' side='right'caption='[[5e4n]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e4n]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E4N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5E4N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e4n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E4N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTY:D-TYROSINE'>DTY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.05Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nv8\|3nv8]], [[5e40\|5e40]], [[2ypp\|2ypp]], [[5e2l\|5e2l]], [[3kgf\|3kgf]], [[2ypq\|2ypq]], [[3nud\|3nud]], [[3nue\|3nue]], [[3rzi\|3rzi]], [[2ypo\|2ypo]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTY:D-TYROSINE'>DTY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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">aroG_1, ERS024751_03564, ERS094182_00944, ERS124362_02783 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=5e4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e4n OCA], [https://pdbe.org/5e4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e4n RCSB], [https://www.ebi.ac.uk/pdbsum/5e4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e4n 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/3-deoxy-7-phosphoheptulonate_synthase 3-deoxy-7-phosphoheptulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.54 2.5.1.54] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5e4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e4n OCA], [~~http~~://pdbe.org/5e4n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e4n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e4n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e4n ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AROG_MYCTU AROG_MYCTU] Catalyzes an aldol-like condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) to generate 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) and inorganic phosphate.<ref>PMID:16288916</ref>
	<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: 3-deoxy-7-phosphoheptulonate synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Jiao, W~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Parker, E J~~]]	+	[[Category: Jiao W]]
-	[[Category: ~~Reichau, S~~]]	+	[[Category: Parker EJ]]
-	[[Category: ~~3-deoxy-d-arabino-heptulosonate 7-phosphate synthase]]~~	+	[[Category: Reichau S]]
-	~~[[Category: Allosteric regulation]]~~	+
-	~~[[Category: Amino acid]]~~	+
-	~~[[Category: Shikimate pathway]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:44, 22 April 2020

OCA — Wed, 22 Apr 2020 06:44:00 GMT

←Older revision		Revision as of 06:44, 22 April 2020
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	==3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the tyrosine and phenylalanine binding sites==		==3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the tyrosine and phenylalanine binding sites==
-	<StructureSection load='5e4n' size='340' side='right' caption='[[5e4n]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5e4n' size='340' side='right'caption='[[5e4n]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e4n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E4N OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E4N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E4N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5E4N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTY:D-TYROSINE'>DTY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTY:D-TYROSINE'>DTY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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">[[3nv8\|3nv8]], [[5e40\|5e40]], [[2ypp\|2ypp]], [[5e2l\|5e2l]], [[3kgf\|3kgf]], [[2ypq\|2ypq]], [[3nud\|3nud]], [[3nue\|3nue]], [[3rzi\|3rzi]], [[2ypo\|2ypo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nv8\|3nv8]], [[5e40\|5e40]], [[2ypp\|2ypp]], [[5e2l\|5e2l]], [[3kgf\|3kgf]], [[2ypq\|2ypq]], [[3nud\|3nud]], [[3nue\|3nue]], [[3rzi\|3rzi]], [[2ypo\|2ypo]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroG_1, ERS024751_03564, ERS094182_00944, ERS124362_02783 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-7-phosphoheptulonate_synthase 3-deoxy-7-phosphoheptulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.54 2.5.1.54] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-7-phosphoheptulonate_synthase 3-deoxy-7-phosphoheptulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.54 2.5.1.54] </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=5e4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e4n OCA], [http://pdbe.org/5e4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e4n RCSB], [http://www.ebi.ac.uk/pdbsum/5e4n PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5e4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e4n OCA], [http://pdbe.org/5e4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e4n RCSB], [http://www.ebi.ac.uk/pdbsum/5e4n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e4n ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5e4n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5e4n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DAHP synthase 3D structures\|DAHP synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: 3-deoxy-7-phosphoheptulonate synthase]]		[[Category: 3-deoxy-7-phosphoheptulonate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Jiao, W]]		[[Category: Jiao, W]]
	[[Category: Parker, E J]]		[[Category: Parker, E J]]

OCA at 15:33, 1 June 2016

OCA — Wed, 01 Jun 2016 15:33:32 GMT

←Older revision		Revision as of 15:33, 1 June 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5e4n is ~~ON HOLD until Paper~~ Publication	+	==3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the tyrosine and phenylalanine binding sites==
		+	<StructureSection load='5e4n' size='340' side='right' caption='[[5e4n]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5e4n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E4N FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DTY:D-TYROSINE'>DTY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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">[[3nv8\|3nv8]], [[5e40\|5e40]], [[2ypp\|2ypp]], [[5e2l\|5e2l]], [[3kgf\|3kgf]], [[2ypq\|2ypq]], [[3nud\|3nud]], [[3nue\|3nue]], [[3rzi\|3rzi]], [[2ypo\|2ypo]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-7-phosphoheptulonate_synthase 3-deoxy-7-phosphoheptulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.54 2.5.1.54] </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=5e4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e4n OCA], [http://pdbe.org/5e4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e4n RCSB], [http://www.ebi.ac.uk/pdbsum/5e4n PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chirality plays a major role in recognition and interaction of biologically important molecules. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first enzyme of the shikimate pathway, which is responsible for the synthesis of aromatic amino acids in bacteria and plants, and a potential target for the development of antibiotics and herbicides. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) displays an unprecedented complexity of allosteric regulation, with three interdependent allosteric binding sites and a ternary allosteric response to combinations of the aromatic amino acids l-Trp, l-Phe and l-Tyr. In order to further investigate the intricacies of this system and identify key residues in the allosteric network of MtuDAH7PS, we studied the interaction of MtuDAH7PS with aromatic amino acids that bear the non-natural d-configuration, and showed that the d-amino acids do not elicit an allosteric response. We investigated the binding mode of d-amino acids using X-ray crystallography, site directed mutagenesis and isothermal titration calorimetry. Key differences in the binding mode were identified: in the Phe site, a hydrogen bond between the amino group of the allosteric ligands to the side chain of Asn175 is not established due to the inverted configuration of the ligands. In the Trp site, d-Trp forms no interaction with the main chain carbonyl group of Thr240 and less favourable interactions with Asn237 when compared to the l-Trp binding mode. Investigation of the MtuDAH7PSN175A variant further supports the hypothesis that the lack of key interactions in the binding mode of the aromatic d-amino acids are responsible for the absence of an allosteric response, which gives further insight into which residues of MtuDAH7PS play a key role in the transduction of the allosteric signal.

-	~~Authors~~:	+	Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using -Amino Acids.,Reichau S, Blackmore NJ, Jiao W, Parker EJ PLoS One. 2016 Apr 29;11(4):e0152723. doi: 10.1371/journal.pone.0152723., eCollection 2016. PMID:27128682<ref>PMID:27128682</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5e4n" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 3-deoxy-7-phosphoheptulonate synthase]]
		+	[[Category: Jiao, W]]
		+	[[Category: Parker, E J]]
		+	[[Category: Reichau, S]]
		+	[[Category: 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase]]
		+	[[Category: Allosteric regulation]]
		+	[[Category: Amino acid]]
		+	[[Category: Shikimate pathway]]
		+	[[Category: Transferase]]

OCA at 12:12, 15 May 2016

OCA — Sun, 15 May 2016 12:12:53 GMT

←Older revision		Revision as of 12:12, 15 May 2016
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	The entry 5e4n is ON HOLD until Paper Publication		The entry 5e4n is ON HOLD until Paper Publication

-	Authors: ~~Reichau, S., Jiao, W., Parker, E.J.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Reichau, S]]
-	[[Category: Jiao, W]]
-	[[Category: Parker, E.J]]

OCA: Protected "5e4n" [edit=sysop:move=sysop]

OCA — Fri, 16 Oct 2015 02:59:32 GMT

Protected "5e4n" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:59, 16 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e4n is ON HOLD until Paper Publication Authors: Reichau, S., Jiao, W., Parker, E.J. Description: Category: Unreleased Structures [[Category: ...

OCA — Fri, 16 Oct 2015 02:59:31 GMT

New page: '''Unreleased structure''' The entry 5e4n is ON HOLD until Paper Publication Authors: Reichau, S., Jiao, W., Parker, E.J. Description: Category: Unreleased Structures [[Category: ...

New page

'''Unreleased structure'''

The entry 5e4n is ON HOLD until Paper Publication

Authors: Reichau, S., Jiao, W., Parker, E.J.

Description:
[[Category: Unreleased Structures]]
[[Category: Reichau, S]]
[[Category: Jiao, W]]
[[Category: Parker, E.J]]