1f3t - Revision history

OCA at 07:10, 7 February 2024

OCA — Wed, 07 Feb 2024 07:10:23 GMT

←Older revision		Revision as of 07:10, 7 February 2024
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	<StructureSection load='1f3t' size='340' side='right'caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1f3t' size='340' side='right'caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3T 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>~~, ~~<scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</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]] 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;~~'>~~[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]~~</~~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>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [https://pdbe.org/1f3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [https://www.ebi.ac.uk/pdbsum/1f3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3t 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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [https://pdbe.org/1f3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [https://www.ebi.ac.uk/pdbsum/1f3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3t 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=1f3t 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=1f3t ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ornithine decarboxylase (ODC) catalyzes the first committed step in the biosynthesis of polyamines, and it has been identified as a drug target for the treatment of African sleeping sickness, caused by Trypanosoma brucei. ODC is a pyridoxal 5'-phosphate (PLP) dependent enzyme and an obligate homodimer. X-ray structural analysis of the complex of the T. brucei wild-type enzyme with the product putrescine reveals two structural changes that occur upon ligand binding: Lys-69 is displaced by putrescine and forms new interactions with Glu-94 and Asp-88, and the side chain of Cys-360 rotates into the active site to within 3.4 A of the imine bond. Mutation of Cys-360 to Ala or Ser reduces the k(cat) of the decarboxylation reaction by 50- and 1000-fold, respectively. However, HPLC analysis of the products demonstrates that the mutant enzymes almost exclusively catalyze a decarboxylation-dependent transamination reaction to form pyridoxamine 5-phosphate (PMP) and gamma-aminobutyraldehyde, instead of PLP and putrescine. This side reaction arises when the decarboxylated substrate intermediate is protonated at C4' of PLP instead of at the C(alpha) of substrate. For the reaction catalyzed by the wild-type enzyme, this side reaction occurs infrequently (<0.01% of the turnovers). Single turnover analysis and multiwavelength stopped-flow spectroscopic studies suggest that for the mutant ODCs protonation at C4' occurs either very rapidly or in a concerted reaction with decarboxylation and that the rate-limiting step in the steady-state reaction is Schiff base hydrolysis/product release. These studies demonstrate a role for Cys-360 in the control of the C(alpha) protonation step that catalyzes the formation of the physiological product putrescine. The results further provide insight into the mechanism by which this class of PLP-dependent enzymes controls reaction specificity.
-
-	Altering the reaction specificity of eukaryotic ornithine decarboxylase.,Jackson LK, Brooks HB, Osterman AL, Goldsmith EJ, Phillips MA Biochemistry. 2000 Sep 19;39(37):11247-57. PMID:10985770<ref>PMID:10985770</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1f3t" 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: Jackson~~, L K~~]]	+	[[Category: Jackson LK]]
-	[[Category: Osterman~~, A L~~]]	+	[[Category: Osterman AL]]
-	[[Category: Phillips~~, M A]]~~	+	[[Category: Phillips MA]]
-	~~[[Category: Beta-alpha-barrel]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Modified greek key beta-sheet~~]]	+

OCA at 09:46, 21 July 2021

OCA — Wed, 21 Jul 2021 09:46:05 GMT

←Older revision		Revision as of 09:46, 21 July 2021
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	<StructureSection load='1f3t' size='340' side='right'caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1f3t' size='340' side='right'caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1F3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3T 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>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</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>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [~~http~~://pdbe.org/1f3t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1f3t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3t 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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [https://pdbe.org/1f3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [https://www.ebi.ac.uk/pdbsum/1f3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3t ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 14:26, 16 October 2019

OCA — Wed, 16 Oct 2019 14:26:35 GMT

←Older revision		Revision as of 14:26, 16 October 2019
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	==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.==		==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.==
-	<StructureSection load='1f3t' size='340' side='right' caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1f3t' size='340' side='right'caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3T FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1f3t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1f3t" 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 09:32, 27 December 2017

OCA — Wed, 27 Dec 2017 09:32:06 GMT

←Older revision		Revision as of 09:32, 27 December 2017
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		+
	==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.==		==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.==
	<StructureSection load='1f3t' size='340' side='right' caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1f3t' size='340' side='right' caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [http://pdbe.org/1f3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [http://www.ebi.ac.uk/pdbsum/1f3t 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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [http://pdbe.org/1f3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [http://www.ebi.ac.uk/pdbsum/1f3t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3t 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/f3/1f3t_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/1f3t_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 1f3t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1f3t" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:47, 8 February 2016

OCA — Mon, 08 Feb 2016 06:47:21 GMT

←Older revision		Revision as of 06:47, 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=1f3t ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:57, 10 September 2015

OCA — Thu, 10 Sep 2015 08:57:05 GMT

←Older revision		Revision as of 08:57, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1f3t' size='340' side='right' caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1f3t' size='340' side='right' caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3T 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>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</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>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [http://www.ebi.ac.uk/pdbsum/1f3t 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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [http://pdbe.org/1f3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [http://www.ebi.ac.uk/pdbsum/1f3t 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 1f3t" 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 23:58, 22 December 2014

OCA — Mon, 22 Dec 2014 23:58:52 GMT

←Older revision		Revision as of 23:58, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3T 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>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</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>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [http://www.ebi.ac.uk/pdbsum/1f3t 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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [http://www.ebi.ac.uk/pdbsum/1f3t 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: Jackson, L K.]]	+	[[Category: Jackson, L K]]
-	[[Category: Osterman, A L.]]	+	[[Category: Osterman, A L]]
-	[[Category: Phillips, M A.]]	+	[[Category: Phillips, M A]]
	[[Category: Beta-alpha-barrel]]		[[Category: Beta-alpha-barrel]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Modified greek key beta-sheet]]		[[Category: Modified greek key beta-sheet]]

OCA at 17:10, 29 September 2014

OCA — Mon, 29 Sep 2014 17:10:03 GMT

←Older revision		Revision as of 17:10, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1f3t\| PDB=1f3t \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.==
-	===CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.===	+	<StructureSection load='1f3t' size='340' side='right' caption='[[1f3t]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_10985770}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1f3t]] 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=1F3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3T 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>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qu4\|1qu4]], [[2tod\|2tod]], [[7odc\|7odc]]</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=1f3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f3t RCSB], [http://www.ebi.ac.uk/pdbsum/1f3t 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/f3/1f3t_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) catalyzes the first committed step in the biosynthesis of polyamines, and it has been identified as a drug target for the treatment of African sleeping sickness, caused by Trypanosoma brucei. ODC is a pyridoxal 5'-phosphate (PLP) dependent enzyme and an obligate homodimer. X-ray structural analysis of the complex of the T. brucei wild-type enzyme with the product putrescine reveals two structural changes that occur upon ligand binding: Lys-69 is displaced by putrescine and forms new interactions with Glu-94 and Asp-88, and the side chain of Cys-360 rotates into the active site to within 3.4 A of the imine bond. Mutation of Cys-360 to Ala or Ser reduces the k(cat) of the decarboxylation reaction by 50- and 1000-fold, respectively. However, HPLC analysis of the products demonstrates that the mutant enzymes almost exclusively catalyze a decarboxylation-dependent transamination reaction to form pyridoxamine 5-phosphate (PMP) and gamma-aminobutyraldehyde, instead of PLP and putrescine. This side reaction arises when the decarboxylated substrate intermediate is protonated at C4' of PLP instead of at the C(alpha) of substrate. For the reaction catalyzed by the wild-type enzyme, this side reaction occurs infrequently (<0.01% of the turnovers). Single turnover analysis and multiwavelength stopped-flow spectroscopic studies suggest that for the mutant ODCs protonation at C4' occurs either very rapidly or in a concerted reaction with decarboxylation and that the rate-limiting step in the steady-state reaction is Schiff base hydrolysis/product release. These studies demonstrate a role for Cys-360 in the control of the C(alpha) protonation step that catalyzes the formation of the physiological product putrescine. The results further provide insight into the mechanism by which this class of PLP-dependent enzymes controls reaction specificity.

-	~~==About this Structure==~~	+	Altering the reaction specificity of eukaryotic ornithine decarboxylase.,Jackson LK, Brooks HB, Osterman AL, Goldsmith EJ, Phillips MA Biochemistry. 2000 Sep 19;39(37):11247-57. PMID:10985770<ref>PMID:10985770</ref>
-	~~[[1f3t]] 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=1F3T 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:010985770<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
	[[Category: Trypanosoma brucei]]		[[Category: Trypanosoma brucei]]

OCA at 10:39, 11 March 2013

OCA — Mon, 11 Mar 2013 10:39:42 GMT

←Older revision		Revision as of 10:39, 11 March 2013
Line 1:		Line 1:
-	[[Image:1f3t.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1f3t", 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_1f3t\| PDB=1f3t \| SCENE= }}		{{STRUCTURE_1f3t\| PDB=1f3t \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.===		===CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10985770}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10985770 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10985770}}		{{ABSTRACT_PUBMED_10985770}}

	==About this Structure==		==About this Structure==
	[[1f3t]] 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=1F3T OCA].		[[1f3t]] 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=1F3T OCA].
		+
		+	==See Also==
		+	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]

	==Reference==		==Reference==

OCA: Protected "1f3t" [edit=sysop:move=sysop]

OCA — Sat, 02 Jun 2012 09:46:43 GMT

Protected "1f3t" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:46, 2 June 2012