5ldj - Revision history

OCA at 08:56, 11 October 2023

OCA — Wed, 11 Oct 2023 08:56:57 GMT

←Older revision		Revision as of 08:56, 11 October 2023
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	==Crystal structure of E.coli LigT complexed with phosphate==		==Crystal structure of E.coli LigT complexed with phosphate==
-	<StructureSection load='5ldj' size='340' side='right' caption='[[5ldj]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5ldj' size='340' side='right'caption='[[5ldj]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ldj]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecobd Ecobd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ldj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LDJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.802Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~thpR, ECBD_3472 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=469008 ECOBD])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5ldj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldj OCA], [~~http~~://pdbe.org/5ldj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ldj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ldj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldj 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=5ldj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldj OCA], [https://pdbe.org/5ldj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ldj RCSB], [https://www.ebi.ac.uk/pdbsum/5ldj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/A0A140NFI1_ECOBD A0A140NFI1_ECOBD]] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940]	+	[https://www.uniprot.org/uniprot/A0A140NFI1_ECOBD A0A140NFI1_ECOBD] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5ldj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ldj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecobd~~]]	+	[[Category: Large Structures]]
-	[[Category: Kursula, P]]	+	[[Category: Kursula P]]
-	[[Category: Myllykoski, M]]	+	[[Category: Myllykoski M]]
-	~~[[Category: 2h phosphoesterase/ligase]]~~	+
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:08, 17 January 2018

OCA — Wed, 17 Jan 2018 08:08:58 GMT

←Older revision		Revision as of 08:08, 17 January 2018
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	<StructureSection load='5ldj' size='340' side='right' caption='[[5ldj]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5ldj' size='340' side='right' caption='[[5ldj]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ldj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ldj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thpR, ECBD_3472 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=469008 ECOBD])</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=5ldj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldj OCA], [http://pdbe.org/5ldj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ldj RCSB], [http://www.ebi.ac.uk/pdbsum/5ldj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldj ProSAT]</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=5ldj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldj OCA], [http://pdbe.org/5ldj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ldj RCSB], [http://www.ebi.ac.uk/pdbsum/5ldj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldj ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecobd]]
	[[Category: Kursula, P]]		[[Category: Kursula, P]]
	[[Category: Myllykoski, M]]		[[Category: Myllykoski, M]]

OCA at 07:30, 9 March 2017

OCA — Thu, 09 Mar 2017 07:30:50 GMT

←Older revision		Revision as of 07:30, 9 March 2017
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/A0A140NFI1_ECOBD A0A140NFI1_ECOBD]] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940]		[[http://www.uniprot.org/uniprot/A0A140NFI1_ECOBD A0A140NFI1_ECOBD]] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The 2H phosphoesterase family contains enzymes with two His-X-Ser/Thr motifs in the active site. 2H enzymes are found in all kingdoms of life, sharing little sequence identity despite the conserved overall fold and active site. For many 2H enzymes, the physiological function is unknown. Here, we studied the structure of the 2H family member LigT from Escherichia coli both in the apo form and complexed with different active-site ligands, including ATP, 2'-AMP, 3'-AMP, phosphate, and NADP+. Comparisons to the well-characterized vertebrate myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) highlight specific features of the catalytic cycle and substrate recognition in both enzymes. The role played by the helix alpha7, unique to CNPases within the 2H family, is apparently taken over by Arg130 in the bacterial enzyme. Other residues and loops lining the active site groove are likely to be important for RNA substrate binding. We visualized conformational changes related to ligand binding, as well as the position of the nucleophilic water molecule. We also present a low-resolution model of E. coli LigT bound to tRNA in solution, and provide a model for RNA binding by LigT, involving flexible loops lining the active site cavity. Taken together, our results both aid in understanding the common features of 2H family enzymes and help highlight the distinct features in the 2H family members, which must result in different reaction mechanisms. Unique aspects in different 2H family members can be observed in ligand recognition and binding, and in the coordination of the nucleophilic water molecule and the reactive phosphate moiety.
		+
		+	Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.,Myllykoski M, Kursula P PLoS One. 2017 Jan 31;12(1):e0170355. doi: 10.1371/journal.pone.0170355., eCollection 2017. PMID:28141848<ref>PMID:28141848</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ldj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 00:44, 19 January 2017

OCA — Thu, 19 Jan 2017 00:44:28 GMT

←Older revision		Revision as of 00:44, 19 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ldj is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of E.coli LigT complexed with phosphate==
-		+	<StructureSection load='5ldj' size='340' side='right' caption='[[5ldj]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~: ~~Myllykoski~~, M., ~~Kursula~~, P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ldj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDJ FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of E~~.~~coli LigT complexed with phosphate~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5ldj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldj OCA], [http://pdbe.org/5ldj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ldj RCSB], [http://www.ebi.ac.uk/pdbsum/5ldj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldj ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A140NFI1_ECOBD A0A140NFI1_ECOBD]] Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.[HAMAP-Rule:MF_01940]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kursula, P]]
	[[Category: Myllykoski, M]]		[[Category: Myllykoski, M]]
-	[[Category: ~~Kursula, P~~]]	+	[[Category: 2h phosphoesterase/ligase]]
		+	[[Category: Enzyme]]
		+	[[Category: Hydrolase]]

OCA: Protected "5ldj" [edit=sysop:move=sysop]

OCA — Wed, 13 Jul 2016 01:01:05 GMT

Protected "5ldj" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:01, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5ldj is ON HOLD until Paper Publication Authors: Myllykoski, M., Kursula, P. Description: Crystal structure of E.coli LigT complexed with phosphate...

OCA — Wed, 13 Jul 2016 01:01:04 GMT

New page: '''Unreleased structure''' The entry 5ldj is ON HOLD until Paper Publication Authors: Myllykoski, M., Kursula, P. Description: Crystal structure of E.coli LigT complexed with phosphate...

New page

'''Unreleased structure'''

The entry 5ldj is ON HOLD until Paper Publication

Authors: Myllykoski, M., Kursula, P.

Description: Crystal structure of E.coli LigT complexed with phosphate
[[Category: Unreleased Structures]]
[[Category: Myllykoski, M]]
[[Category: Kursula, P]]