4wda - Revision history

OCA at 10:42, 10 January 2024

OCA — Wed, 10 Jan 2024 10:42:06 GMT

←Older revision		Revision as of 10:42, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wda]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WDA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wda]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WDA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2AM:ADENOSINE-2-MONOPHOSPHATE'>2AM</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]] 1.85Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2AM:ADENOSINE-2-MONOPHOSPHATE'>2AM</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=4wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wda OCA], [https://pdbe.org/4wda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wda RCSB], [https://www.ebi.ac.uk/pdbsum/4wda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wda 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=4wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wda OCA], [https://pdbe.org/4wda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wda RCSB], [https://www.ebi.ac.uk/pdbsum/4wda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wda ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:03, 7 April 2023

OCA — Fri, 07 Apr 2023 07:03:15 GMT

←Older revision		Revision as of 07:03, 7 April 2023
Line 1:		Line 1:

	==Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation P296G, complexed with 2'-AMP==		==Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation P296G, complexed with 2'-AMP==
-	<StructureSection load='4wda' size='340' side='right' caption='[[4wda]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='4wda' size='340' side='right'caption='[[4wda]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wda]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WDA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4WDA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wda]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WDA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2AM:ADENOSINE-2-MONOPHOSPHATE'>2AM</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2AM:ADENOSINE-2-MONOPHOSPHATE'>2AM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cnp, Cnp1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=4wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wda OCA], [https://pdbe.org/4wda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wda RCSB], [https://www.ebi.ac.uk/pdbsum/4wda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wda ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2',3'-cyclic-nucleotide_3'-phosphodiesterase 2',3'-cyclic-nucleotide 3'-phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.37 3.1.4.37] </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=4wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wda OCA], [~~http~~://pdbe.org/4wda PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4wda RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4wda PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4wda ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CN37_MOUSE CN37_MOUSE]] May participate in RNA metabolism in the myelinating cell, CNP is the third most abundant protein in central nervous system myelin.<ref>PMID:22393399</ref>	+	[https://www.uniprot.org/uniprot/CN37_MOUSE CN37_MOUSE] May participate in RNA metabolism in the myelinating cell, CNP is the third most abundant protein in central nervous system myelin.<ref>PMID:22393399</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]	+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~2',3'-cyclic-nucleotide 3'-phosphodiesterase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Kursula, P]]	+	[[Category: Kursula P]]
-	[[Category: Myllykoski, M]]	+	[[Category: Myllykoski M]]
-	[[Category: Raasakka, A]]	+	[[Category: Raasakka A]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Myelin]]~~	+
-	~~[[Category: Nervous system~~]]	+

OCA at 05:57, 8 March 2018

OCA — Thu, 08 Mar 2018 05:57:19 GMT

←Older revision		Revision as of 05:57, 8 March 2018
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4wda" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4wda" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase\|Phosphodiesterase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:15, 16 November 2017

OCA — Thu, 16 Nov 2017 15:15:49 GMT

←Older revision		Revision as of 15:15, 16 November 2017
Line 1:		Line 1:
		+
	==Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation P296G, complexed with 2'-AMP==		==Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation P296G, complexed with 2'-AMP==
	<StructureSection load='4wda' size='340' side='right' caption='[[4wda]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='4wda' size='340' side='right' caption='[[4wda]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wda]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WDA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WDA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wda]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WDA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WDA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2AM:ADENOSINE-2-MONOPHOSPHATE'>2AM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2AM:ADENOSINE-2-MONOPHOSPHATE'>2AM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cnp, Cnp1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2',3'-cyclic-nucleotide_3'-phosphodiesterase 2',3'-cyclic-nucleotide 3'-phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.37 3.1.4.37] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2',3'-cyclic-nucleotide_3'-phosphodiesterase 2',3'-cyclic-nucleotide 3'-phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.37 3.1.4.37] </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=4wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wda OCA], [http://pdbe.org/4wda PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wda RCSB], [http://www.ebi.ac.uk/pdbsum/4wda 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=4wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wda OCA], [http://pdbe.org/4wda PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wda RCSB], [http://www.ebi.ac.uk/pdbsum/4wda PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wda ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: 2',3'-cyclic-nucleotide 3'-phosphodiesterase]]		[[Category: 2',3'-cyclic-nucleotide 3'-phosphodiesterase]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Kursula, P]]		[[Category: Kursula, P]]
	[[Category: Myllykoski, M]]		[[Category: Myllykoski, M]]

OCA at 18:49, 30 November 2015

OCA — Mon, 30 Nov 2015 18:49:22 GMT

←Older revision		Revision as of 18:49, 30 November 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation P296G, complexed with 2'-AMP==
		+	<StructureSection load='4wda' size='340' side='right' caption='[[4wda]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4wda]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WDA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WDA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2AM:ADENOSINE-2-MONOPHOSPHATE'>2AM</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2',3'-cyclic-nucleotide_3'-phosphodiesterase 2',3'-cyclic-nucleotide 3'-phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.37 3.1.4.37] </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=4wda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wda OCA], [http://pdbe.org/4wda PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wda RCSB], [http://www.ebi.ac.uk/pdbsum/4wda PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CN37_MOUSE CN37_MOUSE]] May participate in RNA metabolism in the myelinating cell, CNP is the third most abundant protein in central nervous system myelin.<ref>PMID:22393399</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an enzyme highly abundant in the central nervous system myelin of terrestrial vertebrates. The catalytic domain of CNPase belongs to the 2H phosphoesterase superfamily and catalyzes the hydrolysis of nucleoside 2',3'-cyclic monophosphates to nucleoside 2'-monophosphates. The detailed reaction mechanism and the essential catalytic amino acids involved have been described earlier, but the roles of many amino acids in the vicinity of the active site have remained unknown. Here, several CNPase catalytic domain mutants were studied using enzyme kinetics assays, thermal stability experiments, and X-ray crystallography. Additionally, the crystal structure of a perdeuterated CNPase catalytic domain was refined at atomic resolution to obtain a detailed view of the active site and the catalytic mechanism. The results specify determinants of ligand binding and novel essential residues required for CNPase catalysis. For example, the aromatic side chains of Phe235 and Tyr168 are crucial for substrate binding, and Arg307 may affect active site electrostatics and regulate loop dynamics. The beta5-alpha7 loop, unique for CNPase in the 2H phosphoesterase family, appears to have various functions in the CNPase reaction mechanism, from coordinating the nucleophilic water molecule to providing a binding pocket for the product and being involved in product release.

-	~~The entry 4wda is ON HOLD until Paper Publication~~	+	Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase.,Raasakka A, Myllykoski M, Laulumaa S, Lehtimaki M, Hartlein M, Moulin M, Kursula I, Kursula P Sci Rep. 2015 Nov 13;5:16520. doi: 10.1038/srep16520. PMID:26563764<ref>PMID:26563764</ref>

-	~~Authors: Myllykoski~~, M.~~, Raasakka, A~~.~~, Kursula, P~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Catalytic domain of mouse~~ 2',3'-cyclic nucleotide 3'-phosphodiesterase~~, with mutation P296G, complexed with 2'-AMP~~	+	<div class="pdbe-citations 4wda" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 2',3'-cyclic-nucleotide 3'-phosphodiesterase]]
		+	[[Category: Kursula, P]]
	[[Category: Myllykoski, M]]		[[Category: Myllykoski, M]]
	[[Category: Raasakka, A]]		[[Category: Raasakka, A]]
-	[[Category: ~~Kursula, P~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Myelin]]
		+	[[Category: Nervous system]]

OCA at 19:21, 24 December 2014

OCA — Wed, 24 Dec 2014 19:21:18 GMT

←Older revision		Revision as of 19:21, 24 December 2014
Line 6:		Line 6:

	Description: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase, with mutation P296G, complexed with 2'-AMP		Description: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase, with mutation P296G, complexed with 2'-AMP
		+	[[Category: Unreleased Structures]]
		+	[[Category: Myllykoski, M]]
		+	[[Category: Raasakka, A]]
		+	[[Category: Kursula, P]]

OCA: Protected "4wda" [edit=sysop:move=sysop]

OCA — Wed, 24 Sep 2014 09:09:28 GMT

Protected "4wda" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:09, 24 September 2014

OCA: New page: '''Unreleased structure''' The entry 4wda is ON HOLD until Paper Publication Authors: Myllykoski, M., Raasakka, A., Kursula, P. Description: Catalytic domain of mouse 2',3'-cyclic nucl...

OCA — Wed, 24 Sep 2014 09:09:27 GMT

New page: '''Unreleased structure''' The entry 4wda is ON HOLD until Paper Publication Authors: Myllykoski, M., Raasakka, A., Kursula, P. Description: Catalytic domain of mouse 2',3'-cyclic nucl...

New page

'''Unreleased structure'''

The entry 4wda is ON HOLD until Paper Publication

Authors: Myllykoski, M., Raasakka, A., Kursula, P.

Description: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase, with mutation P296G, complexed with 2'-AMP