1ps6 - Revision history

OCA at 08:10, 14 February 2024

OCA — Wed, 14 Feb 2024 08:10:29 GMT

←Older revision		Revision as of 08:10, 14 February 2024
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	<StructureSection load='1ps6' size='340' side='right'caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='1ps6' size='340' side='right'caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=4TP:4~~-~~HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</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]] 2.25Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1ps7\|1ps7]], [[1ptm\|1ptm]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4TP:4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</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"~~>PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [https://pdbe.org/1ps6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ps6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ps6 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/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </~~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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [~~http~~://pdbe.org/1ps6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ps6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ps6 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PDXA_ECOLI PDXA_ECOLI]] Catalyzes the NAD(P)-dependent oxidation of 4-(phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP).[REFERENCE:5]<ref>PMID:15026039</ref>	+	[https://www.uniprot.org/uniprot/PDXA_ECOLI PDXA_ECOLI] Catalyzes the NAD(P)-dependent oxidation of 4-(phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP).[REFERENCE:5]<ref>PMID:15026039</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ps6 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ps6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Pyridoxal 5'-phosphate is an essential cofactor for many enzymes responsible for the metabolic conversions of amino acids. Two pathways for its de novo synthesis are known. The pathway utilized by Escherichia coli consists of six enzymatic steps catalyzed by six different enzymes. The fourth step is catalyzed by 4-hydroxythreonine-4-phosphate dehydrogenase (PdxA, E.C. 1.1.1.262), which converts 4-hydroxy-l-threonine phosphate (HTP) to 3-amino-2-oxopropyl phosphate. This divalent metal ion-dependent enzyme has a strict requirement for the phosphate ester form of the substrate HTP, but can utilize either NADP+ or NAD+ as redox cofactor. We report the crystal structure of E. coli PdxA and its complex with HTP and Zn2+. The protein forms tightly bound dimers. Each monomer has an alpha/beta/alpha-fold and can be divided into two subdomains. The active site is located at the dimer interface, within a cleft between the two subdomains and involves residues from both monomers. A Zn2+ ion is bound within each active site, coordinated by three conserved histidine residues from both monomers. In addition two conserved amino acids, Asp247 and Asp267, play a role in maintaining integrity of the active site. The substrate is anchored to the enzyme by the interactions of its phospho group and by coordination of the amino and hydroxyl groups by the Zn2+ ion. PdxA is structurally similar to, but limited in sequence similarity with isocitrate dehydrogenase and isopropylmalate dehydrogenase. These structural similarities and the comparison with a NADP-bound isocitrate dehydrogenase suggest that the cofactor binding mode of PdxA is very similar to that of the other two enzymes and that PdxA catalyzes a stepwise oxidative decarboxylation of the substrate HTP.
-
-	Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway.,Sivaraman J, Li Y, Banks J, Cane DE, Matte A, Cygler M J Biol Chem. 2003 Oct 31;278(44):43682-90. Epub 2003 Aug 1. PMID:12896974<ref>PMID:12896974</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ps6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Banks, J]]	+	[[Category: Banks J]]
-	[[Category: Cane~~, D E~~]]	+	[[Category: Cane DE]]
-	[[Category: Cygler, M]]	+	[[Category: Cygler M]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	[[Category: Matte, A]]	+	[[Category: Matte A]]
-	[[Category: Sivaraman, J]]	+	[[Category: Sivaraman J]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pdxa]]~~	+
-	~~[[Category: Plp]]~~	+
-	~~[[Category: Pyridoxal 5'-phosphate biosynthesis~~]]	+

OCA at 07:34, 9 December 2020

OCA — Wed, 09 Dec 2020 07:34:58 GMT

←Older revision		Revision as of 07:34, 9 December 2020
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	==Crystal structure of E.coli PdxA==		==Crystal structure of E.coli PdxA==
-	<StructureSection load='1ps6' size='340' side='right' caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='1ps6' size='340' side='right'caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4TP:4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</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" id="ligandDat"><scene name='pdbligand=4TP:4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</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">[[1ps7\|1ps7]], [[1ptm\|1ptm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ps7\|1ps7]], [[1ptm\|1ptm]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://pdbe.org/1ps6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ps6 ProSAT]</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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://pdbe.org/1ps6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ps6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ps/1ps6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ps/1ps6_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]		[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Banks, J]]		[[Category: Banks, J]]
	[[Category: Cane, D E]]		[[Category: Cane, D E]]

OCA at 12:17, 12 October 2017

OCA — Thu, 12 Oct 2017 12:17:58 GMT

←Older revision		Revision as of 12:17, 12 October 2017
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		+
	==Crystal structure of E.coli PdxA==		==Crystal structure of E.coli PdxA==
	<StructureSection load='1ps6' size='340' side='right' caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='1ps6' size='340' side='right' caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://pdbe.org/1ps6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum]</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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://pdbe.org/1ps6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ps6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:24, 8 February 2016

OCA — Mon, 08 Feb 2016 19:24:01 GMT

←Older revision		Revision as of 19:24, 8 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ps6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:39, 10 September 2015

OCA — Thu, 10 Sep 2015 14:39:18 GMT

←Older revision		Revision as of 14:39, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ps6' size='340' side='right' caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='1ps6' size='340' side='right' caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4TP:4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</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=4TP:4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</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">[[1ps7\|1ps7]], [[1ptm\|1ptm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ps7\|1ps7]], [[1ptm\|1ptm]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum]</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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://pdbe.org/1ps6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1ps6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]		[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]
-	[[Category: Escherichia coli]]
	[[Category: Banks, J]]		[[Category: Banks, J]]
	[[Category: Cane, D E]]		[[Category: Cane, D E]]

OCA at 01:37, 25 December 2014

OCA — Thu, 25 Dec 2014 01:37:20 GMT

←Older revision		Revision as of 01:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4TP:4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4TP:4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ps7\|1ps7]], [[1ptm\|1ptm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ps7\|1ps7]], [[1ptm\|1ptm]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum]</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=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDXA_ECOLI PDXA_ECOLI]] Catalyzes the NAD(P)-dependent oxidation of 4-(phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP).[REFERENCE:5]<ref>PMID:15026039</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]		[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Banks, J.]]	+	[[Category: Banks, J]]
-	[[Category: Cane, D E.]]	+	[[Category: Cane, D E]]
-	[[Category: Cygler, M.]]	+	[[Category: Cygler, M]]
-	[[Category: Li, Y.]]	+	[[Category: Li, Y]]
-	[[Category: Matte, A.]]	+	[[Category: Matte, A]]
-	[[Category: Sivaraman, J.]]	+	[[Category: Sivaraman, J]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Pdxa]]		[[Category: Pdxa]]
	[[Category: Plp]]		[[Category: Plp]]
	[[Category: Pyridoxal 5'-phosphate biosynthesis]]		[[Category: Pyridoxal 5'-phosphate biosynthesis]]

OCA at 23:09, 28 September 2014

OCA — Sun, 28 Sep 2014 23:09:35 GMT

←Older revision		Revision as of 23:09, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ps6.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of E.coli PdxA==
		+	<StructureSection load='1ps6' size='340' side='right' caption='[[1ps6]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ps6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PS6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4TP:4-HYDROXY-L-THREONINE-5-MONOPHOSPHATE'>4TP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ps7\|1ps7]], [[1ptm\|1ptm]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDXA or B0052 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxythreonine-4-phosphate_dehydrogenase 4-hydroxythreonine-4-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.262 1.1.1.262] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ps6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ps6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ps6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ps6 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ps/1ps6_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyridoxal 5'-phosphate is an essential cofactor for many enzymes responsible for the metabolic conversions of amino acids. Two pathways for its de novo synthesis are known. The pathway utilized by Escherichia coli consists of six enzymatic steps catalyzed by six different enzymes. The fourth step is catalyzed by 4-hydroxythreonine-4-phosphate dehydrogenase (PdxA, E.C. 1.1.1.262), which converts 4-hydroxy-l-threonine phosphate (HTP) to 3-amino-2-oxopropyl phosphate. This divalent metal ion-dependent enzyme has a strict requirement for the phosphate ester form of the substrate HTP, but can utilize either NADP+ or NAD+ as redox cofactor. We report the crystal structure of E. coli PdxA and its complex with HTP and Zn2+. The protein forms tightly bound dimers. Each monomer has an alpha/beta/alpha-fold and can be divided into two subdomains. The active site is located at the dimer interface, within a cleft between the two subdomains and involves residues from both monomers. A Zn2+ ion is bound within each active site, coordinated by three conserved histidine residues from both monomers. In addition two conserved amino acids, Asp247 and Asp267, play a role in maintaining integrity of the active site. The substrate is anchored to the enzyme by the interactions of its phospho group and by coordination of the amino and hydroxyl groups by the Zn2+ ion. PdxA is structurally similar to, but limited in sequence similarity with isocitrate dehydrogenase and isopropylmalate dehydrogenase. These structural similarities and the comparison with a NADP-bound isocitrate dehydrogenase suggest that the cofactor binding mode of PdxA is very similar to that of the other two enzymes and that PdxA catalyzes a stepwise oxidative decarboxylation of the substrate HTP.

-	~~{{STRUCTURE_1ps6\| PDB=1ps6 \| SCENE= }}~~	+	Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway.,Sivaraman J, Li Y, Banks J, Cane DE, Matte A, Cygler M J Biol Chem. 2003 Oct 31;278(44):43682-90. Epub 2003 Aug 1. PMID:12896974<ref>PMID:12896974</ref>

-	~~===Crystal structure~~ of E.~~coli PdxA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12896974}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1ps6]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012896974<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]		[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "1ps6" [edit=sysop:move=sysop]

OCA — Wed, 19 Dec 2012 11:44:57 GMT

Protected "1ps6" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:44, 19 December 2012

OCA at 11:44, 19 December 2012

OCA — Wed, 19 Dec 2012 11:44:54 GMT

←Older revision		Revision as of 11:44, 19 December 2012
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-	{{Seed}}
	[[Image:1ps6.png\|left\|200px]]		[[Image:1ps6.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ps6", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1ps6\| PDB=1ps6 \| SCENE= }}		{{STRUCTURE_1ps6\| PDB=1ps6 \| SCENE= }}

	===Crystal structure of E.coli PdxA===		===Crystal structure of E.coli PdxA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12896974}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12896974 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12896974}}		{{ABSTRACT_PUBMED_12896974}}

	==About this Structure==		==About this Structure==
-	~~1PS6~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA].	+	[[1ps6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12896974~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012896974</ref><references group="xtra"/>
	[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]		[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 32:		Line 20:
	[[Category: Matte, A.]]		[[Category: Matte, A.]]
	[[Category: Sivaraman, J.]]		[[Category: Sivaraman, J.]]
-	[[Category: ~~Crystal structure~~]]	+	[[Category: Oxidoreductase]]
	[[Category: Pdxa]]		[[Category: Pdxa]]
	[[Category: Plp]]		[[Category: Plp]]
	[[Category: Pyridoxal 5'-phosphate biosynthesis]]		[[Category: Pyridoxal 5'-phosphate biosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:17:05 2009''

OCA at 00:17, 17 February 2009

OCA — Tue, 17 Feb 2009 00:17:06 GMT

←Older revision		Revision as of 00:17, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1PS6 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA].	+	1PS6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PS6 OCA].

	==Reference==		==Reference==
-	Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway., Sivaraman J, Li Y, Banks J, Cane DE, Matte A, Cygler M, J Biol Chem. 2003 Oct 31;278(44):43682-90. Epub 2003 Aug 1. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12896974 12896974]~~	+	<ref group="xtra">PMID:12896974</ref><references group="xtra"/>
	[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]		[[Category: 4-hydroxythreonine-4-phosphate dehydrogenase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Banks, J.]]		[[Category: Banks, J.]]
	[[Category: Cane, D E.]]		[[Category: Cane, D E.]]
Line 38:		Line 37:
	[[Category: Pyridoxal 5'-phosphate biosynthesis]]		[[Category: Pyridoxal 5'-phosphate biosynthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 06~~:06:~~47 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:17:05 2009''