1qu4 - Revision history

OCA at 06:07, 17 April 2024

OCA — Wed, 17 Apr 2024 06:07:21 GMT

←Older revision		Revision as of 06:07, 17 April 2024
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	<StructureSection load='1qu4' size='340' side='right'caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1qu4' size='340' side='right'caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Trypanosoma_(trypanozoon)_brucei~~ Trypanosoma ~~(trypanozoon)~~ brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PLP:PYRIDOXAL~~-~~5-PHOSPHATE'>PLP</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]] 2.9Å</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]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [https://pdbe.org/1qu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [https://www.ebi.ac.uk/pdbsum/1qu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qu4 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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [https://pdbe.org/1qu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [https://www.ebi.ac.uk/pdbsum/1qu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qu4 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]]
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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=1qu4 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=1qu4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ornithine decarboxylase (ODC) is a pyridoxal 5'-phosphate (PLP) dependent homodimeric enzyme. It is a recognized drug target against African sleeping sickness, caused by Trypanosoma brucei. One of the currently used drugs, alpha-difluoromethylornithine (DFMO), is a suicide inhibitor of ODC. The structure of the T. brucei ODC (TbODC) mutant K69A bound to DFMO has been determined by X-ray crystallography to 2.0 A resolution. The protein crystallizes in the space group P2(1) (a = 66.8 A, b = 154.5 A, c = 77.1 A, beta = 90.58 degrees ), with two dimers per asymmetric unit. The initial phasing was done by molecular replacement with the mouse ODC structure. The structure of wild-type uncomplexed TbODC was also determined to 2.9 A resolution by molecular replacement using the TbODC DFMO-bound structure as the search model. The N-terminal domain of ODC is a beta/alpha-barrel, and the C-terminal domain of ODC is a modified Greek key beta-barrel. In comparison to structurally related alanine racemase, the two domains are rotated 27 degrees relative to each other. In addition, two of the beta-strands in the C-terminal domain have exchanged positions in order to maintain the location of essential active site residues in the context of the domain rotation. In ODC, the contacts in the dimer interface are formed primarily by the C-terminal domains, which interact through six aromatic rings that form stacking interactions across the domain boundary. The PLP binding site is formed by the C-termini of beta-strands and loops in the beta/alpha-barrel. In the native structure Lys69 forms a Schiff base with PLP. In both structures, the phosphate of PLP is bound between the seventh and eighth strands forming interactions with Arg277 and a Gly loop (residues 235-237). The pyridine nitrogen of PLP interacts with Glu274. DFMO forms a Schiff base with PLP and is covalently attached to Cys360. It is bound at the dimer interface and the delta-carbon amino group of DFMO is positioned between Asp361 of one subunit and Asp332 of the other. In comparison to the wild-type uncomplexed structure, Cys-360 has rotated 145 degrees toward the active site in the DFMO-bound structure. No domain, subunit rotations, or other significant structural changes are observed upon ligand binding. The structure offers insight into the enzyme mechanism by providing details of the enzyme/inhibitor binding site and allows for a detailed comparison between the enzymes from the host and parasite which will aid in selective inhibitor design.
-
-	X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine.,Grishin NV, Osterman AL, Brooks HB, Phillips MA, Goldsmith EJ Biochemistry. 1999 Nov 16;38(46):15174-84. PMID:10563800<ref>PMID:10563800</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qu4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]		*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ornithine decarboxylase~~]]	+	[[Category: Trypanosoma brucei]]
-	[[Category: Brooks~~, H B~~]]	+	[[Category: Brooks HB]]
-	[[Category: Goldsmith~~, E J~~]]	+	[[Category: Goldsmith EJ]]
-	[[Category: Grishin~~, N V~~]]	+	[[Category: Grishin NV]]
-	[[Category: Osterman~~, A L~~]]	+	[[Category: Osterman AL]]
-	[[Category: Phillips~~, M A]]~~	+	[[Category: Phillips MA]]
-	~~[[Category: Alpha-beta barrel]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Polyamine metabolism]]~~	+
-	~~[[Category: Pyridoxal 5'-phosphate~~]]	+

OCA at 10:04, 15 September 2021

OCA — Wed, 15 Sep 2021 10:04:28 GMT

←Older revision		Revision as of 10:04, 15 September 2021
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	<StructureSection load='1qu4' size='340' side='right'caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1qu4' size='340' side='right'caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]]</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]]</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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [~~http~~://pdbe.org/1qu4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qu4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qu4 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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [https://pdbe.org/1qu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [https://www.ebi.ac.uk/pdbsum/1qu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qu4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 11:26, 4 December 2019

OCA — Wed, 04 Dec 2019 11:26:48 GMT

←Older revision		Revision as of 11:26, 4 December 2019
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	==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE==		==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE==
-	<StructureSection load='1qu4' size='340' side='right' caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='1qu4' size='340' side='right'caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1qu4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qu4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
	[[Category: Brooks, H B]]		[[Category: Brooks, H B]]

OCA at 06:29, 31 January 2018

OCA — Wed, 31 Jan 2018 06:29:47 GMT

←Older revision		Revision as of 06:29, 31 January 2018
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		+
	==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE==		==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE==
	<StructureSection load='1qu4' size='340' side='right' caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1qu4' size='340' side='right' caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]]</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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [http://pdbe.org/1qu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [http://www.ebi.ac.uk/pdbsum/1qu4 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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [http://pdbe.org/1qu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [http://www.ebi.ac.uk/pdbsum/1qu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qu4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/qu/1qu4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qu/1qu4_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 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1qu4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qu4" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:09, 8 February 2016

OCA — Mon, 08 Feb 2016 13:09:21 GMT

←Older revision		Revision as of 13:09, 8 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=1qu4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:53, 10 September 2015

OCA — Thu, 10 Sep 2015 11:53:25 GMT

←Older revision		Revision as of 11:53, 10 September 2015
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	<StructureSection load='1qu4' size='340' side='right' caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='1qu4' size='340' side='right' caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Trypanosoma_brucei~~ Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]]</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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [http://www.ebi.ac.uk/pdbsum/1qu4 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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [http://pdbe.org/1qu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [http://www.ebi.ac.uk/pdbsum/1qu4 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 1qu4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
-	[[Category: Trypanosoma brucei]]
	[[Category: Brooks, H B]]		[[Category: Brooks, H B]]
	[[Category: Goldsmith, E J]]		[[Category: Goldsmith, E J]]

OCA at 07:03, 6 January 2015

OCA — Tue, 06 Jan 2015 07:03:35 GMT

←Older revision		Revision as of 07:03, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]]</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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [http://www.ebi.ac.uk/pdbsum/1qu4 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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [http://www.ebi.ac.uk/pdbsum/1qu4 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]]		[[Category: Trypanosoma brucei]]
-	[[Category: Brooks, H B.]]	+	[[Category: Brooks, H B]]
-	[[Category: Goldsmith, E J.]]	+	[[Category: Goldsmith, E J]]
-	[[Category: Grishin, N V.]]	+	[[Category: Grishin, N V]]
-	[[Category: Osterman, A L.]]	+	[[Category: Osterman, A L]]
-	[[Category: Phillips, M A.]]	+	[[Category: Phillips, M A]]
	[[Category: Alpha-beta barrel]]		[[Category: Alpha-beta barrel]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Polyamine metabolism]]		[[Category: Polyamine metabolism]]
	[[Category: Pyridoxal 5'-phosphate]]		[[Category: Pyridoxal 5'-phosphate]]

OCA at 15:04, 29 September 2014

OCA — Mon, 29 Sep 2014 15:04:48 GMT

←Older revision		Revision as of 15:04, 29 September 2014
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-	~~{{STRUCTURE_1qu4\| PDB=1qu4 \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE==
-	===CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE===	+	<StructureSection load='1qu4' size='340' side='right' caption='[[1qu4]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_10563800}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QU4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2tod\|2tod]]</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=1qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qu4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qu4 RCSB], [http://www.ebi.ac.uk/pdbsum/1qu4 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/qu/1qu4_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 a pyridoxal 5'-phosphate (PLP) dependent homodimeric enzyme. It is a recognized drug target against African sleeping sickness, caused by Trypanosoma brucei. One of the currently used drugs, alpha-difluoromethylornithine (DFMO), is a suicide inhibitor of ODC. The structure of the T. brucei ODC (TbODC) mutant K69A bound to DFMO has been determined by X-ray crystallography to 2.0 A resolution. The protein crystallizes in the space group P2(1) (a = 66.8 A, b = 154.5 A, c = 77.1 A, beta = 90.58 degrees ), with two dimers per asymmetric unit. The initial phasing was done by molecular replacement with the mouse ODC structure. The structure of wild-type uncomplexed TbODC was also determined to 2.9 A resolution by molecular replacement using the TbODC DFMO-bound structure as the search model. The N-terminal domain of ODC is a beta/alpha-barrel, and the C-terminal domain of ODC is a modified Greek key beta-barrel. In comparison to structurally related alanine racemase, the two domains are rotated 27 degrees relative to each other. In addition, two of the beta-strands in the C-terminal domain have exchanged positions in order to maintain the location of essential active site residues in the context of the domain rotation. In ODC, the contacts in the dimer interface are formed primarily by the C-terminal domains, which interact through six aromatic rings that form stacking interactions across the domain boundary. The PLP binding site is formed by the C-termini of beta-strands and loops in the beta/alpha-barrel. In the native structure Lys69 forms a Schiff base with PLP. In both structures, the phosphate of PLP is bound between the seventh and eighth strands forming interactions with Arg277 and a Gly loop (residues 235-237). The pyridine nitrogen of PLP interacts with Glu274. DFMO forms a Schiff base with PLP and is covalently attached to Cys360. It is bound at the dimer interface and the delta-carbon amino group of DFMO is positioned between Asp361 of one subunit and Asp332 of the other. In comparison to the wild-type uncomplexed structure, Cys-360 has rotated 145 degrees toward the active site in the DFMO-bound structure. No domain, subunit rotations, or other significant structural changes are observed upon ligand binding. The structure offers insight into the enzyme mechanism by providing details of the enzyme/inhibitor binding site and allows for a detailed comparison between the enzymes from the host and parasite which will aid in selective inhibitor design.

-	~~==About this Structure==~~	+	X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine.,Grishin NV, Osterman AL, Brooks HB, Phillips MA, Goldsmith EJ Biochemistry. 1999 Nov 16;38(46):15174-84. PMID:10563800<ref>PMID:10563800</ref>
-	~~[[1qu4]] is a 4 chain~~ structure ~~with sequence~~ from ~~[http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Trypanosoma_brucei Trypanosoma brucei]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1QU4 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:010563800<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
	[[Category: Trypanosoma brucei]]		[[Category: Trypanosoma brucei]]

OCA at 10:25, 11 March 2013

OCA — Mon, 11 Mar 2013 10:25:28 GMT

←Older revision		Revision as of 10:25, 11 March 2013
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-	[[Image:1qu4.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1qu4", 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_1qu4\| PDB=1qu4 \| SCENE= }}		{{STRUCTURE_1qu4\| PDB=1qu4 \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE===		===CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10563800}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10563800 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10563800}}		{{ABSTRACT_PUBMED_10563800}}

	==About this Structure==		==About this Structure==
	[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA].		[[1qu4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QU4 OCA].
		+
		+	==See Also==
		+	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]

	==Reference==		==Reference==

OCA: Protected "1qu4" [edit=sysop:move=sysop]

OCA — Sat, 02 Jun 2012 09:55:59 GMT

Protected "1qu4" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:55, 2 June 2012