5v0s - Revision history

OCA at 06:58, 7 April 2021

OCA — Wed, 07 Apr 2021 06:58:18 GMT

←Older revision		Revision as of 06:58, 7 April 2021
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	==Crystal structure of the ACT domain of prephenate dehydrogenase tyrA from Bacillus anthracis==		==Crystal structure of the ACT domain of prephenate dehydrogenase tyrA from Bacillus anthracis==
-	<StructureSection load='5v0s' size='340' side='right' caption='[[5v0s]], [[Resolution\|resolution]] 2.01Å' scene=''>	+	<StructureSection load='5v0s' size='340' side='right'caption='[[5v0s]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v0s]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V0S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V0S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v0s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V0S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5usc\|5usc]], [[5uyy\|5uyy]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5usc\|5usc]], [[5uyy\|5uyy]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tyrA, GBAA_2954, BASH2_02940 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tyrA, GBAA_2954, BASH2_02940 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Prephenate_dehydrogenase Prephenate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.12 1.3.1.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Prephenate_dehydrogenase Prephenate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.12 1.3.1.12] </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=5v0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v0s OCA], [~~http~~://pdbe.org/5v0s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v0s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v0s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v0s ProSAT]</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=5v0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v0s OCA], [https://pdbe.org/5v0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v0s RCSB], [https://www.ebi.ac.uk/pdbsum/5v0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v0s ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tyrosine biosynthesis via the shikimate pathway is absent in humans and other animals, making it an attractive target for next-generation antibiotics, which is increasingly important due to the looming proliferation of multidrug-resistant pathogens. Tyrosine biosynthesis is also of commercial importance for the environmentally friendly production of numerous compounds, such as pharmaceuticals, opioids, aromatic polymers, and petrochemical aromatics. Prephenate dehydrogenase (PDH) catalyzes the penultimate step of tyrosine biosynthesis in bacteria: the oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate. The majority of PDHs are competitively inhibited by tyrosine and consist of a nucleotide-binding domain and a dimerization domain. Certain PDHs, including several from pathogens on the World Health Organization priority list of antibiotic-resistant bacteria, possess an additional ACT domain. However, biochemical and structural knowledge was lacking for these enzymes. In this study, we successfully established a recombinant protein expression system for PDH from Bacillus anthracis (BaPDH), the causative agent of anthrax, and determined the structure of a BaPDH ternary complex with NAD(+) and tyrosine, a binary complex with tyrosine, and a structure of an isolated ACT domain dimer. We also conducted detailed kinetic and biophysical analyses of the enzyme. We show that BaPDH is allosterically regulated by tyrosine binding to the ACT domains, resulting in an asymmetric conformation of the BaDPH dimer that sterically prevents prephenate binding to either active site. The presented mode of allosteric inhibition is unique compared to both the competitive inhibition established for other PDHs and to the allosteric mechanisms for other ACT-containing enzymes. This study provides new structural and mechanistic insights that advance our understanding of tyrosine biosynthesis in bacteria. ENZYMES: Prephenate dehydrogenase from Bacillus anthracis (PDH): EC database ID: 1.3.1.12. DATABASES: Coordinates and structure factors have been deposited in the Protein Data Bank (PDB) with accession numbers PDB ID: 6U60 (BaPDH complex with NAD(+) and tyrosine), PDB ID: 5UYY (BaPDH complex with tyrosine), and PDB ID: 5V0S (BaPDH isolated ACT domain dimer). The diffraction images are available at http://proteindiffraction.org with DOIs: https://doi.org/10.18430/M35USC, https://doi.org/10.18430/M35UYY, and https://doi.org/10.18430/M35V0S.
		+
		+	Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.,Shabalin IG, Gritsunov A, Hou J, Slawek J, Miks CD, Cooper DR, Minor W, Christendat D FEBS J. 2020 Jun;287(11):2235-2255. doi: 10.1111/febs.15150. Epub 2019 Dec 26. PMID:31750992<ref>PMID:31750992</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5v0s" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Prephenate dehydrogenase]]		[[Category: Prephenate dehydrogenase]]
	[[Category: Anderson, W F]]		[[Category: Anderson, W F]]

OCA at 19:50, 15 November 2017

OCA — Wed, 15 Nov 2017 19:50:52 GMT

←Older revision		Revision as of 19:50, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5v0s' size='340' side='right' caption='[[5v0s]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='5v0s' size='340' side='right' caption='[[5v0s]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v0s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V0S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V0S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v0s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V0S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V0S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5usc\|5usc]], [[5uyy\|5uyy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5usc\|5usc]], [[5uyy\|5uyy]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tyrA, GBAA_2954, BASH2_02940 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prephenate_dehydrogenase Prephenate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.12 1.3.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prephenate_dehydrogenase Prephenate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.12 1.3.1.12] </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=5v0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v0s OCA], [http://pdbe.org/5v0s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v0s RCSB], [http://www.ebi.ac.uk/pdbsum/5v0s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v0s 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=5v0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v0s OCA], [http://pdbe.org/5v0s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v0s RCSB], [http://www.ebi.ac.uk/pdbsum/5v0s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v0s ProSAT]</span></td></tr>

OCA: Protected "5v0s" [edit=sysop:move=sysop]

OCA — Sat, 11 Mar 2017 19:21:29 GMT

Protected "5v0s" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:21, 11 March 2017

OCA: New page: ==Crystal structure of the ACT domain of prephenate dehydrogenase tyrA from Bacillus anthracis== == Structural highlights ==
<table><tr><td colspan='2'>[[5v0s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V0S OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V0S FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl">[[Non-Standard_Residue|NonStd Res:]]</td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[5usc|5usc]], [[5uyy|5uyy]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Prephenate_dehydrogenase Prephenate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.12 1.3.1.12] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5v0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v0s OCA], [http://pdbe.org/5v0s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v0s RCSB], [http://www.ebi.ac.uk/pdbsum/5v0s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v0s ProSAT]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Prephenate dehydrogenase]]
[[Category: Anderson, W F]]
[[Category: Structural genomic]]
[[Category: Christendat, D]]
[[Category: Cymborowski, M T]]
[[Category: Gritsunov, A]]
[[Category: Hou, J]]
[[Category: Kwon, K]]
[[Category: Minor, W]]
[[Category: Otwinowski, Z]]
[[Category: Shabalin, I G]]
[[Category: Bacillus anthracis]]
[[Category: Csgid]]
[[Category: Oxidoreductase]]
[[Category: Tyra]]