1szr - Revision history

OCA at 06:22, 23 August 2023

2023-08-23T06:22:37Z

←Older revision		Revision as of 06:22, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1szr' size='340' side='right'caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1szr' size='340' side='right'caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Trybb Trybb~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SZR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SZR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</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]] 2.15Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [https://pdbe.org/1szr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [https://www.ebi.ac.uk/pdbsum/1szr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1szr 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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [https://pdbe.org/1szr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [https://www.ebi.ac.uk/pdbsum/1szr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1szr ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DCOR_TRYBB DCOR_TRYBB]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ornithine decarboxylase]]~~	+	[[Category: Trypanosoma brucei brucei]]
-	~~[[Category: Trybb~~]]	+	[[Category: Baldwin J]]
-	[[Category: Baldwin, J]]	+	[[Category: Goldsmith EJ]]
-	[[Category: Goldsmith~~, E J~~]]	+	[[Category: Jackson LK]]
-	[[Category: Jackson~~, L K~~]]	+	[[Category: Phillips MA]]
-	[[Category: Phillips~~, M A]]~~	+
-	~~[[Category: Beta-alpha-barrel]]~~	+
-	~~[[Category: Carbinolamine]]~~	+
-	~~[[Category: Dimer interface]]~~	+
-	~~[[Category: Gem-diamine]]~~	+
-	~~[[Category: Greek key]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Odc]]~~	+
-	~~[[Category: Pxp]]~~	+
-	~~[[Category: Pyridoxal phosphate~~]]	+

OCA at 07:39, 22 September 2021

2021-09-22T07:39:54Z

←Older revision		Revision as of 07:39, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1szr' size='340' side='right'caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1szr' size='340' side='right'caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SZR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SZR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [~~http~~://pdbe.org/1szr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1szr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1szr 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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [https://pdbe.org/1szr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [https://www.ebi.ac.uk/pdbsum/1szr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1szr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 14:06, 18 December 2019

2019-12-18T14:06:29Z

←Older revision		Revision as of 14:06, 18 December 2019
Line 1:		Line 1:

	==A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate==		==A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate==
-	<StructureSection load='1szr' size='340' side='right' caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='1szr' size='340' side='right'caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SZR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SZR FirstGlance]. <br>
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
	[[Category: Trybb]]		[[Category: Trybb]]

OCA at 07:47, 14 March 2018

2018-03-14T07:47:51Z

←Older revision		Revision as of 07:47, 14 March 2018
Line 1:		Line 1:
		+
	==A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate==		==A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate==
	<StructureSection load='1szr' size='340' side='right' caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1szr' size='340' side='right' caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [http://pdbe.org/1szr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [http://www.ebi.ac.uk/pdbsum/1szr 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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [http://pdbe.org/1szr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [http://www.ebi.ac.uk/pdbsum/1szr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1szr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sz/1szr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sz/1szr_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>

OCA at 15:15, 9 February 2016

2016-02-09T15:15:29Z

←Older revision		Revision as of 15:15, 9 February 2016
Line 16:		Line 16:
	<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=1szr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:29, 10 September 2015

2015-09-10T23:29:19Z

←Older revision		Revision as of 23:29, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1szr' size='340' side='right' caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1szr' size='340' side='right' caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Trypanosoma_brucei_brucei Trypanosoma brucei brucei~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SZR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SZR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [http://www.ebi.ac.uk/pdbsum/1szr 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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [http://pdbe.org/1szr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [http://www.ebi.ac.uk/pdbsum/1szr PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1szr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
-	[[Category: ~~Trypanosoma brucei brucei~~]]	+	[[Category: Trybb]]
	[[Category: Baldwin, J]]		[[Category: Baldwin, J]]
	[[Category: Goldsmith, E J]]		[[Category: Goldsmith, E J]]

OCA at 08:07, 6 January 2015

2015-01-06T08:07:33Z

←Older revision		Revision as of 08:07, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SZR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SZR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [http://www.ebi.ac.uk/pdbsum/1szr 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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [http://www.ebi.ac.uk/pdbsum/1szr PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
	[[Category: Trypanosoma brucei brucei]]		[[Category: Trypanosoma brucei brucei]]
-	[[Category: Baldwin, J.]]	+	[[Category: Baldwin, J]]
-	[[Category: Goldsmith, E J.]]	+	[[Category: Goldsmith, E J]]
-	[[Category: Jackson, L K.]]	+	[[Category: Jackson, L K]]
-	[[Category: Phillips, M A.]]	+	[[Category: Phillips, M A]]
	[[Category: Beta-alpha-barrel]]		[[Category: Beta-alpha-barrel]]
	[[Category: Carbinolamine]]		[[Category: Carbinolamine]]
Line 46:		Line 46:
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Odc]]		[[Category: Odc]]
-	[[Category: Ornithine decarboxylase]]
	[[Category: Pxp]]		[[Category: Pxp]]
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]

OCA at 14:38, 29 September 2014

2014-09-29T14:38:49Z

←Older revision		Revision as of 14:38, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1szr\| PDB=1szr \| SCENE= }}~~	+	==A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate==
-	===A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate===	+	<StructureSection load='1szr' size='340' side='right' caption='[[1szr]], [[Resolution\|resolution]] 2.15Å' scene=''>
-	{~~{ABSTRACT_PUBMED_15476392}~~}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SZR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PXP:PYRIDOXINE-5-PHOSPHATE'>PXP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]], [[1qu4\|1qu4]], [[1f3t\|1f3t]], [[1njj\|1njj]], [[7odc\|7odc]], [[1d7k\|1d7k]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1szr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1szr RCSB], [http://www.ebi.ac.uk/pdbsum/1szr 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/sz/1szr_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 ==
		+	Ornithine decarboxylase (ODC) is an obligate homodimer that catalyzes the pyridoxal 5'-phosphate-dependent decarboxylation of l-ornithine to putrescine, a vital step in polyamine biosynthesis. A previous mutagenic analysis of the ODC dimer interface identified several residues that were distant from the active site yet had a greater impact on catalytic activity than on dimer stability [Myers, D. P., et al. (2001) Biochemistry 40, 13230-13236]. To better understand the basis of this phenomenon, the structure of the Trypanosoma brucei ODC mutant K294A was determined to 2.15 A resolution in complex with the substrate analogue d-ornithine. This residue is distant from the reactive center (>10 A from the PLP Schiff base), and its mutation reduced catalytic efficiency by 3 kcal/mol. The X-ray structure demonstrates that the mutation increases the disorder of residues Leu-166-Ala-172 (Lys-169 loop), which normally form interactions with Lys-294 across the dimer interface. In turn, the Lys-169 loop forms interactions with the active site, suggesting that the reduced catalytic efficiency is mediated by the decreased stability of this loop. The extent of disorder varies in the four Lys-169 loops in the asymmetric unit, suggesting that the mutation has led to an increase in the population of inactive conformations. The structure also reveals that the mutation has affected the nature of the ligand-bound species. Each of the four active sites contains unusual ligands. The electron density suggests one active site contains a gem-diamine intermediate with d-ornithine; the second has density consistent with a tetrahedral adduct with glycine, and the remaining two contain tetrahedral adducts of PLP, Lys-69, and water (or hydroxide). These data also suggest that the structure is less constrained in the mutant enzyme. The observation of a gem-diamine intermediate provides insight into the conformational changes that occur during the ODC catalytic cycle.

-	~~==About this Structure==~~	+	Multiple active site conformations revealed by distant site mutation in ornithine decarboxylase.,Jackson LK, Baldwin J, Akella R, Goldsmith EJ, Phillips MA Biochemistry. 2004 Oct 19;43(41):12990-9. PMID:15476392<ref>PMID:15476392</ref>
-	~~[[1szr]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1SZR OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]		*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015476392<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
	[[Category: Trypanosoma brucei brucei]]		[[Category: Trypanosoma brucei brucei]]

OCA at 09:57, 11 March 2013

2013-03-11T09:57:31Z

←Older revision		Revision as of 09:57, 11 March 2013
Line 1:		Line 1:
-	[[Image:1szr.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1szr", 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_1szr\| PDB=1szr \| SCENE= }}		{{STRUCTURE_1szr\| PDB=1szr \| SCENE= }}
-
	===A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate===		===A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15476392}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15476392 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15476392}}		{{ABSTRACT_PUBMED_15476392}}

	==About this Structure==		==About this Structure==
	[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA].		[[1szr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SZR OCA].
		+
		+	==See Also==
		+	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]

	==Reference==		==Reference==

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

2012-06-02T08:54:26Z

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

←Older revision

Revision as of 08:54, 2 June 2012