1jh7 - Revision history

OCA at 06:03, 3 April 2024

OCA — Wed, 03 Apr 2024 06:03:38 GMT

←Older revision		Revision as of 06:03, 3 April 2024
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	<StructureSection load='1jh7' size='340' side='right'caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1jh7' size='340' side='right'caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~, ~~<scene name='pdbligand=UVC:URIDINE-~~2~~,3-VANADATE'>UVC</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1fsi\|1fsi]]~~, ~~[[1jh6\|1jh6]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene></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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [https://pdbe.org/1jh7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [https://www.ebi.ac.uk/pdbsum/1jh7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jh7 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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [https://pdbe.org/1jh7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [https://www.ebi.ac.uk/pdbsum/1jh7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jh7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CPD_ARATH CPD_ARATH]] Hydrolyzes ADP-ribose 1",2"-cyclic phosphate (Appr>1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p). Acts also on nucleoside 2',3'-cyclic phosphates.	+	[https://www.uniprot.org/uniprot/CPD_ARATH CPD_ARATH] Hydrolyzes ADP-ribose 1",2"-cyclic phosphate (Appr>1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p). Acts also on nucleoside 2',3'-cyclic phosphates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1jh7 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=1jh7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of the semireduced form of cyclic nucleotide phosphodiesterase (CPDase) from Arabidopsis thaliana has been solved by molecular replacement and refined at the resolution of 1.8 A. We have previously reported the crystal structure of the native form of this enzyme, whose main target is ADP-ribose 1",2"-cyclic phosphate, a product of the tRNA splicing reaction. CPDase possesses six cysteine residues, four of which are involved in forming two intra-molecular disulfide bridges. One of these bridges, between Cys-104 and Cys-110, is opened in the semireduced CPDase, whereas the other remains intact. This change of the redox state leads to a conformational rearrangement in the loop covering the active site of the protein. While the native structure shows this partially disordered loop in a coil conformation, in the semireduced enzyme the N-terminal lobe of this loop winds up and elongates the preceding alpha-helix. The semireduced state of CPDase also enabled co-crystallization with a putative inhibitor of its enzymatic activity, 2',3'-cyclic uridine vanadate. The ligand is bound within the active site, and the mode of binding is in agreement with the previously proposed enzymatic mechanism. Selected biophysical properties of the oxidized and the semireduced CPDase are also discussed.
-
-	Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana.,Hofmann A, Grella M, Botos I, Filipowicz W, Wlodawer A J Biol Chem. 2002 Jan 11;277(2):1419-25. Epub 2001 Nov 1. PMID:11694509<ref>PMID:11694509</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1jh7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]		*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Botos, I]]	+	[[Category: Botos I]]
-	[[Category: Filipowicz, W]]	+	[[Category: Filipowicz W]]
-	[[Category: Grella, M]]	+	[[Category: Grella M]]
-	[[Category: Hofmann, A]]	+	[[Category: Hofmann A]]
-	[[Category: Wlodawer, A]]	+	[[Category: Wlodawer A]]
-	~~[[Category: 2''-cyclic phosphate]]~~	+
-	~~[[Category: 2ss']]~~	+
-	~~[[Category: 3'-cyclic nucleotide phosphodiesterase]]~~	+
-	~~[[Category: 3'-cyclic uridine vanadate]]~~	+
-	~~[[Category: Adp-ribose 1'ss']]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rna processing~~]]	+

OCA at 06:40, 11 August 2021

OCA — Wed, 11 Aug 2021 06:40:36 GMT

←Older revision		Revision as of 06:40, 11 August 2021
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	<StructureSection load='1jh7' size='340' side='right'caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1jh7' size='340' side='right'caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fsi\|1fsi]], [[1jh6\|1jh6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fsi\|1fsi]], [[1jh6\|1jh6]]</div></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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [~~http~~://pdbe.org/1jh7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1jh7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1jh7 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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [https://pdbe.org/1jh7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [https://www.ebi.ac.uk/pdbsum/1jh7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jh7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CPD_ARATH CPD_ARATH]] Hydrolyzes ADP-ribose 1",2"-cyclic phosphate (Appr>1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p). Acts also on nucleoside 2',3'-cyclic phosphates.	+	[[https://www.uniprot.org/uniprot/CPD_ARATH CPD_ARATH]] Hydrolyzes ADP-ribose 1",2"-cyclic phosphate (Appr>1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p). Acts also on nucleoside 2',3'-cyclic phosphates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]	+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:25, 6 November 2019

OCA — Wed, 06 Nov 2019 09:25:09 GMT

←Older revision		Revision as of 09:25, 6 November 2019
Line 1:		Line 1:

	==Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana==		==Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana==
-	<StructureSection load='1jh7' size='340' side='right' caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1jh7' size='340' side='right'caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1jh7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jh7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase\|Phosphodiesterase]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Arath]]		[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Botos, I]]		[[Category: Botos, I]]
	[[Category: Filipowicz, W]]		[[Category: Filipowicz, W]]
Line 39:		Line 43:
	[[Category: Hofmann, A]]		[[Category: Hofmann, A]]
	[[Category: Wlodawer, A]]		[[Category: Wlodawer, A]]
-	[[Category: 2s']]
	[[Category: 2''-cyclic phosphate]]		[[Category: 2''-cyclic phosphate]]
		+	[[Category: 2ss']]
	[[Category: 3'-cyclic nucleotide phosphodiesterase]]		[[Category: 3'-cyclic nucleotide phosphodiesterase]]
	[[Category: 3'-cyclic uridine vanadate]]		[[Category: 3'-cyclic uridine vanadate]]
-	[[Category: Adp-ribose 1's']]	+	[[Category: Adp-ribose 1'ss']]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Rna processing]]		[[Category: Rna processing]]

OCA at 09:00, 17 January 2018

OCA — Wed, 17 Jan 2018 09:00:10 GMT

←Older revision		Revision as of 09:00, 17 January 2018
Line 1:		Line 1:
		+
	==Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana==		==Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana==
	<StructureSection load='1jh7' size='340' side='right' caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1jh7' size='340' side='right' caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fsi\|1fsi]], [[1jh6\|1jh6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fsi\|1fsi]], [[1jh6\|1jh6]]</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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [http://pdbe.org/1jh7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [http://www.ebi.ac.uk/pdbsum/1jh7 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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [http://pdbe.org/1jh7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [http://www.ebi.ac.uk/pdbsum/1jh7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jh7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jh/1jh7_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jh/1jh7_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 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1jh7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jh7" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:22, 9 February 2016

OCA — Tue, 09 Feb 2016 22:22:57 GMT

←Older revision		Revision as of 22:22, 9 February 2016
Line 17:		Line 17:
	<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=1jh7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:36, 11 September 2015

OCA — Fri, 11 Sep 2015 02:36:47 GMT

←Older revision		Revision as of 02:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1jh7' size='340' side='right' caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1jh7' size='340' side='right' caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arabidopsis_thaliana Arabidopsis thaliana~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fsi\|1fsi]], [[1jh6\|1jh6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fsi\|1fsi]], [[1jh6\|1jh6]]</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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [http://www.ebi.ac.uk/pdbsum/1jh7 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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [http://pdbe.org/1jh7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [http://www.ebi.ac.uk/pdbsum/1jh7 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1jh7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arabidopsis thaliana~~]]	+	[[Category: Arath]]
	[[Category: Botos, I]]		[[Category: Botos, I]]
	[[Category: Filipowicz, W]]		[[Category: Filipowicz, W]]

OCA at 09:55, 25 December 2014

OCA — Thu, 25 Dec 2014 09:55:44 GMT

←Older revision		Revision as of 09:55, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fsi\|1fsi]], [[1jh6\|1jh6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fsi\|1fsi]], [[1jh6\|1jh6]]</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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [http://www.ebi.ac.uk/pdbsum/1jh7 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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [http://www.ebi.ac.uk/pdbsum/1jh7 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CPD_ARATH CPD_ARATH]] Hydrolyzes ADP-ribose 1",2"-cyclic phosphate (Appr>1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p). Acts also on nucleoside 2',3'-cyclic phosphates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
-	[[Category: Botos, I.]]	+	[[Category: Botos, I]]
-	[[Category: Filipowicz, W.]]	+	[[Category: Filipowicz, W]]
-	[[Category: Grella, M.]]	+	[[Category: Grella, M]]
-	[[Category: Hofmann, A.]]	+	[[Category: Hofmann, A]]
-	[[Category: Wlodawer, A.]]	+	[[Category: Wlodawer, A]]
	[[Category: 2s']]		[[Category: 2s']]
	[[Category: 2''-cyclic phosphate]]		[[Category: 2''-cyclic phosphate]]

OCA at 12:42, 28 September 2014

OCA — Sun, 28 Sep 2014 12:42:50 GMT

←Older revision		Revision as of 12:42, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1jh7.~~png~~\|~~left~~\|200px]]	+	==Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana==
		+	<StructureSection load='1jh7' size='340' side='right' caption='[[1jh7]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1jh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JH7 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UVC:URIDINE-2,3-VANADATE'>UVC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fsi\|1fsi]], [[1jh6\|1jh6]]</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=1jh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jh7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jh7 RCSB], [http://www.ebi.ac.uk/pdbsum/1jh7 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/jh/1jh7_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the semireduced form of cyclic nucleotide phosphodiesterase (CPDase) from Arabidopsis thaliana has been solved by molecular replacement and refined at the resolution of 1.8 A. We have previously reported the crystal structure of the native form of this enzyme, whose main target is ADP-ribose 1",2"-cyclic phosphate, a product of the tRNA splicing reaction. CPDase possesses six cysteine residues, four of which are involved in forming two intra-molecular disulfide bridges. One of these bridges, between Cys-104 and Cys-110, is opened in the semireduced CPDase, whereas the other remains intact. This change of the redox state leads to a conformational rearrangement in the loop covering the active site of the protein. While the native structure shows this partially disordered loop in a coil conformation, in the semireduced enzyme the N-terminal lobe of this loop winds up and elongates the preceding alpha-helix. The semireduced state of CPDase also enabled co-crystallization with a putative inhibitor of its enzymatic activity, 2',3'-cyclic uridine vanadate. The ligand is bound within the active site, and the mode of binding is in agreement with the previously proposed enzymatic mechanism. Selected biophysical properties of the oxidized and the semireduced CPDase are also discussed.

-	~~{{STRUCTURE_1jh7\| PDB=1jh7 \| SCENE= }}~~	+	Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana.,Hofmann A, Grella M, Botos I, Filipowicz W, Wlodawer A J Biol Chem. 2002 Jan 11;277(2):1419-25. Epub 2001 Nov 1. PMID:11694509<ref>PMID:11694509</ref>

-	~~===Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11694509}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1jh7]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA].~~	+

	==See Also==		==See Also==
	*[[Phosphodiesterase\|Phosphodiesterase]]		*[[Phosphodiesterase\|Phosphodiesterase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011694509<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Botos, I.]]		[[Category: Botos, I.]]

OCA at 15:20, 20 October 2012

OCA — Sat, 20 Oct 2012 15:20:38 GMT

←Older revision		Revision as of 15:20, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1jh7]] is a 1 chain structure ~~of [[Phosphodiesterase]]~~ with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA].	+	[[1jh7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JH7 OCA].

	==See Also==		==See Also==

OCA: Protected "1jh7" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 18:04:59 GMT

Protected "1jh7" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:04, 26 July 2012