2ddw - Revision history

OCA at 08:25, 25 October 2023

OCA — Wed, 25 Oct 2023 08:25:49 GMT

←Older revision		Revision as of 08:25, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2ddw' size='340' side='right'caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2ddw' size='340' side='right'caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ddw]] is a 2 chain structure with sequence from [https://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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ddw]] 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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PXL:3~~-~~HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</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]] 3.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2ddm\|2ddm]], [[2ddo\|2ddo]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PdxK ([https://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~~'>~~[https://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35]~~ </~~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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [https://pdbe.org/2ddw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [https://www.ebi.ac.uk/pdbsum/2ddw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddw 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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [https://pdbe.org/2ddw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [https://www.ebi.ac.uk/pdbsum/2ddw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PDXK_ECOLI PDXK_ECOLI]] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates.	+	[https://www.uniprot.org/uniprot/PDXK_ECOLI PDXK_ECOLI] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pyridoxal kinase]]~~	+	[[Category: Claude JB]]
-	[[Category: Claude~~, J B~~]]	+	[[Category: Hunt S]]
-	[[Category: Hunt, S]]	+	[[Category: Musayev FN]]
-	[[Category: Musayev~~, F N~~]]	+	[[Category: Safo MK]]
-	[[Category: Safo~~, M K]]~~	+	[[Category: Schirch V]]
-	~~[[Category: Salvo, M L.di~~]]	+	[[Category: Di Salvo ML]]
-	[[Category: Schirch, V]]	+
-	[[Category: ~~Phosphorylation]]~~	+
-	~~[[Category: Pyridoxal 5'-phosphate]]~~	+
-	~~[[Category: Ribokinase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Vitamin b6~~]]	+

OCA at 12:00, 3 February 2021

OCA — Wed, 03 Feb 2021 12:00:51 GMT

←Older revision		Revision as of 12:00, 3 February 2021
Line 1:		Line 1:

	==Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution==		==Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution==
-	<StructureSection load='2ddw' size='340' side='right' caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='2ddw' size='340' side='right'caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ddw]] 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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ddw]] is a 2 chain structure with sequence from [https://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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddm\|2ddm]], [[2ddo\|2ddo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ddm\|2ddm]], [[2ddo\|2ddo]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PdxK ([~~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">PdxK ([https://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/Pyridoxal_kinase Pyridoxal kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [~~http~~://pdbe.org/2ddw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ddw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddw 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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [https://pdbe.org/2ddw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [https://www.ebi.ac.uk/pdbsum/2ddw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PDXK_ECOLI PDXK_ECOLI]] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates.	+	[[https://www.uniprot.org/uniprot/PDXK_ECOLI PDXK_ECOLI]] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2ddw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2ddw_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>
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2ddw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2ddw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pyridoxal kinase\|Pyridoxal kinase]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Pyridoxal kinase]]		[[Category: Pyridoxal kinase]]
	[[Category: Claude, J B]]		[[Category: Claude, J B]]

OCA at 16:27, 12 October 2017

OCA — Thu, 12 Oct 2017 16:27:46 GMT

←Older revision		Revision as of 16:27, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution==		==Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution==
	<StructureSection load='2ddw' size='340' side='right' caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2ddw' size='340' side='right' caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PdxK ([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">PdxK ([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/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [http://pdbe.org/2ddw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [http://www.ebi.ac.uk/pdbsum/2ddw 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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [http://pdbe.org/2ddw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [http://www.ebi.ac.uk/pdbsum/2ddw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=2ddw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2ddw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2ddw" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Pyridoxal kinase\|Pyridoxal kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:19, 11 September 2015

OCA — Fri, 11 Sep 2015 13:19:17 GMT

←Older revision		Revision as of 13:19, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2ddw' size='340' side='right' caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2ddw' size='340' side='right' caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ddw]] 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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ddw]] 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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddm\|2ddm]], [[2ddo\|2ddo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddm\|2ddm]], [[2ddo\|2ddo]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PdxK ([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">PdxK ([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/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [http://www.ebi.ac.uk/pdbsum/2ddw 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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [http://pdbe.org/2ddw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [http://www.ebi.ac.uk/pdbsum/2ddw PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2ddw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Pyridoxal kinase]]		[[Category: Pyridoxal kinase]]
	[[Category: Claude, J B]]		[[Category: Claude, J B]]

OCA at 16:58, 25 December 2014

OCA — Thu, 25 Dec 2014 16:58:34 GMT

←Older revision		Revision as of 16:58, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ddw]] 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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDW FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ddw]] 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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddm\|2ddm]], [[2ddo\|2ddo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddm\|2ddm]], [[2ddo\|2ddo]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PdxK ([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">PdxK ([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/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [http://www.ebi.ac.uk/pdbsum/2ddw 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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [http://www.ebi.ac.uk/pdbsum/2ddw PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDXK_ECOLI PDXK_ECOLI]] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Pyridoxal kinase]]		[[Category: Pyridoxal kinase]]
-	[[Category: Claude, J B.]]	+	[[Category: Claude, J B]]
-	[[Category: Hunt, S.]]	+	[[Category: Hunt, S]]
-	[[Category: Musayev, F N.]]	+	[[Category: Musayev, F N]]
-	[[Category: Safo, M K.]]	+	[[Category: Safo, M K]]
-	[[Category: Salvo, M L.di.]]	+	[[Category: Salvo, M L.di]]
-	[[Category: Schirch, V.]]	+	[[Category: Schirch, V]]
	[[Category: Phosphorylation]]		[[Category: Phosphorylation]]
	[[Category: Pyridoxal 5'-phosphate]]		[[Category: Pyridoxal 5'-phosphate]]
-	[[Category: Pyridoxal kinase]]
	[[Category: Ribokinase]]		[[Category: Ribokinase]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Vitamin b6]]		[[Category: Vitamin b6]]

OCA at 03:00, 30 September 2014

OCA — Tue, 30 Sep 2014 03:00:14 GMT

←Older revision		Revision as of 03:00, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2ddw.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution==
		+	<StructureSection load='2ddw' size='340' side='right' caption='[[2ddw]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ddw]] 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=2DDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DDW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ddm\|2ddm]], [[2ddo\|2ddo]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PdxK ([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/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [http://www.ebi.ac.uk/pdbsum/2ddw 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/dd/2ddw_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 ==
		+	The pdxK and pdxY genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the pdxY and pdxK genes, respectively. We now report the crystal structure of E. coli pyridoxal kinase 1 (ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-A resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4' substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4' of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.

-	~~{{STRUCTURE_2ddw\| PDB=2ddw \| SCENE= }}~~	+	Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.,Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V J Bacteriol. 2006 Jun;188(12):4542-52. PMID:16740960<ref>PMID:16740960</ref>

-	~~===Crystal Structure~~ of ~~Pyridoxal Kinase from~~ the ~~Escherichia coli PdxK gene complexed with pyridoxal at 3~~.~~2 A resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_16740960}}~~	+	==See Also==
-		+	*[[Pyridoxal kinase\|Pyridoxal kinase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2ddw~~]] 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=2DDW OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:016740960<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Pyridoxal kinase]]		[[Category: Pyridoxal kinase]]

OCA: Protected "2ddw" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 12:10:16 GMT

Protected "2ddw" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:10, 6 January 2013

OCA at 12:10, 6 January 2013

OCA — Sun, 06 Jan 2013 12:10:14 GMT

←Older revision		Revision as of 12:10, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2ddw.png\|left\|200px]]		[[Image:2ddw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2ddw", 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_2ddw\| PDB=2ddw \| SCENE= }}		{{STRUCTURE_2ddw\| PDB=2ddw \| SCENE= }}

	===Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution===		===Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16740960}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16740960 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16740960}}		{{ABSTRACT_PUBMED_16740960}}

	==About this Structure==		==About this Structure==
-	~~2DDW~~ 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=2DDW OCA].	+	[[2ddw]] 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=2DDW OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16740960~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016740960</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Pyridoxal kinase]]		[[Category: Pyridoxal kinase]]
Line 36:		Line 24:
	[[Category: Pyridoxal kinase]]		[[Category: Pyridoxal kinase]]
	[[Category: Ribokinase]]		[[Category: Ribokinase]]
		+	[[Category: Transferase]]
	[[Category: Vitamin b6]]		[[Category: Vitamin b6]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:33:22 2009''

OCA at 20:33, 17 February 2009

OCA — Tue, 17 Feb 2009 20:33:27 GMT

←Older revision		Revision as of 20:33, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2DDW 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=2DDW OCA].	+	2DDW 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=2DDW OCA].

	==Reference==		==Reference==
-	Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases., Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V, J Bacteriol. 2006 Jun;188(12):4542-52. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16740960 16740960]~~	+	<ref group="xtra">PMID:16740960</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Pyridoxal kinase]]		[[Category: Pyridoxal kinase]]
-	[[Category: Single protein]]
	[[Category: Claude, J B.]]		[[Category: Claude, J B.]]
	[[Category: Hunt, S.]]		[[Category: Hunt, S.]]
Line 39:		Line 38:
	[[Category: Vitamin b6]]		[[Category: Vitamin b6]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 06~~:43:~~15 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:33:22 2009''

OCA at 03:43, 29 July 2008

OCA — Tue, 29 Jul 2008 03:43:17 GMT

←Older revision		Revision as of 03:43, 29 July 2008
Line 1:		Line 1:
-	[[Image:2ddw.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2ddw.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2ddw\| PDB=2ddw \| SCENE= }}		{{STRUCTURE_2ddw\| PDB=2ddw \| SCENE= }}

-	~~'''~~Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution~~'''~~	+	===Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution===


-	~~==Overview==~~	+	<!--
-	The ~~pdxK and pdxY genes have been found to code for pyridoxal kinases~~, ~~enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published~~, ~~including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of~~ the ~~pdxY and pdxK genes, respectively. We now report~~ the ~~crystal structure of E. coli pyridoxal kinase 1~~ (~~ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2~~. ~~The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2~~.1-, 2.6-, and 3.2-A resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4' substituent on the substrate. This is the ~~result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site~~. ~~Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C~~-4' of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16740960}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16740960 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16740960}}

	==About this Structure==		==About this Structure==
Line 34:		Line 38:
	[[Category: Ribokinase]]		[[Category: Ribokinase]]
	[[Category: Vitamin b6]]		[[Category: Vitamin b6]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 00~~:14:34 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:43:15 2008''