5zbk - Revision history

OCA at 08:51, 22 November 2023

OCA — Wed, 22 Nov 2023 08:51:10 GMT

←Older revision		Revision as of 08:51, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5zbk' size='340' side='right'caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5zbk' size='340' side='right'caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.3Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA4923 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbk OCA], [~~http~~://pdbe.org/5zbk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zbk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zbk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbk 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=5zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbk OCA], [https://pdbe.org/5zbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zbk RCSB], [https://www.ebi.ac.uk/pdbsum/5zbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LOGH_PSEAE LOGH_PSEAE]] Catalyzes the hydrolytic removal of ribose 5'-monophosphate from nitrogen N6-modified adenosines, the final step of bioactive cytokinin synthesis.[UniProtKB:O05306]	+	[https://www.uniprot.org/uniprot/LOGH_PSEAE LOGH_PSEAE] Catalyzes the hydrolytic removal of ribose 5'-monophosphate from nitrogen N6-modified adenosines, the final step of bioactive cytokinin synthesis.[UniProtKB:O05306]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Kim, K J]]	+	[[Category: Kim K-J]]
-	[[Category: Seo, H]]	+	[[Category: Seo H]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:00, 16 September 2020

OCA — Wed, 16 Sep 2020 10:00:34 GMT

←Older revision		Revision as of 10:00, 16 September 2020
Line 1:		Line 1:

-	==Crystal ~~strcuture~~ of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP==	+	==Crystal structure of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP==
	<StructureSection load='5zbk' size='340' side='right'caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5zbk' size='340' side='right'caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA4923 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA4923 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=5zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbk OCA], [http://pdbe.org/5zbk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zbk RCSB], [http://www.ebi.ac.uk/pdbsum/5zbk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbk ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbk OCA], [http://pdbe.org/5zbk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zbk RCSB], [http://www.ebi.ac.uk/pdbsum/5zbk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:01, 16 October 2019

OCA — Wed, 16 Oct 2019 07:01:15 GMT

←Older revision		Revision as of 07:01, 16 October 2019
Line 1:		Line 1:

	==Crystal strcuture of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP==		==Crystal strcuture of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP==
-	<StructureSection load='5zbk' size='340' side='right' caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5zbk' size='340' side='right'caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>		<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pseae]]		[[Category: Pseae]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Seo, H]]		[[Category: Seo, H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:31, 17 October 2018

OCA — Wed, 17 Oct 2018 08:31:11 GMT

←Older revision		Revision as of 08:31, 17 October 2018
Line 3:		Line 3:
	<StructureSection load='5zbk' size='340' side='right' caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5zbk' size='340' side='right' caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA4923 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=5zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbk OCA], [http://pdbe.org/5zbk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zbk RCSB], [http://www.ebi.ac.uk/pdbsum/5zbk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbk 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=5zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbk OCA], [http://pdbe.org/5zbk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zbk RCSB], [http://www.ebi.ac.uk/pdbsum/5zbk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbk ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pseae]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Seo, H]]		[[Category: Seo, H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 05:32, 27 June 2018

OCA — Wed, 27 Jun 2018 05:32:32 GMT

←Older revision		Revision as of 05:32, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zbk is ~~ON HOLD until Paper~~ Publication	+	==Crystal strcuture of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP==
		+	<StructureSection load='5zbk' size='340' side='right' caption='[[5zbk]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zbk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZBK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5zbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbk OCA], [http://pdbe.org/5zbk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zbk RCSB], [http://www.ebi.ac.uk/pdbsum/5zbk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LOGH_PSEAE LOGH_PSEAE]] Catalyzes the hydrolytic removal of ribose 5'-monophosphate from nitrogen N6-modified adenosines, the final step of bioactive cytokinin synthesis.[UniProtKB:O05306]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cytokinin (CK)-activating enzyme, called LOG, is a phosphoribohydrolase that hydrolyzes nucleotides into nucleobases and phosphoriboses. This reaction is a fascinating target for regulation of cellular active CK. However, misannotation of LOG as a lysine decarboxylase and the lack of detailed catalytic and substrate-binding mechanisms have prevented studies of LOG at a protein-level. In this study, we determined the crystal structure of PA4923 from Pseudomonas aeruginosa PAO1. The overall structure of PA4923 resembles those of type-I LOGs, and it exhibited phosphoribohydrolase activity against AMP. These observations indicated that PA4923 functions as an LOG. We also determined the PaLOG structure in complex with AMP and elucidated the detailed binding mode of LOG against the AMP substrate. Interestingly, PaLOG undergoes an open/closed conformational change upon binding AMP, during which the Glu74 residue located on the beta3-beta4 connecting loop flips 180 degrees and moves 13 A toward the AMP molecule. Structural and amino acid sequence comparisons of LOGs suggest that this conformational change upon substrate binding might be a common phenomenon in LOGs. In addition, based on our structural studies and the reported catalytic mechanism of nucleoside hydrolases, we proposed a catalytic mechanism for LOG in which an oxocarbenium ion-like transition state is formed. This article is protected by copyright. All rights reserved.

-	~~Authors: Seo~~, H., Kim~~, K~~.-J.	+	Structural insight into molecular mechanism of cytokinin activating protein from Pseudomonas aeruginosa PAO1.,Seo H, Kim KJ Environ Microbiol. 2018 Jun 14. doi: 10.1111/1462-2920.14287. PMID:29901273<ref>PMID:29901273</ref>

-	~~Description: Crystal strcuture~~ of ~~type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Kim, K.-J]]	+	<div class="pdbe-citations 5zbk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, K J]]
	[[Category: Seo, H]]		[[Category: Seo, H]]
		+	[[Category: Hydrolase]]

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

OCA — Wed, 21 Mar 2018 05:56:28 GMT

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

←Older revision

Revision as of 05:56, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zbk is ON HOLD until Paper Publication Authors: Seo, H., Kim, K.-J. Description: Crystal strcuture of type-I LOG from Pseudomonas aeruginosa PAO1 ...

OCA — Wed, 21 Mar 2018 05:56:26 GMT

New page: '''Unreleased structure''' The entry 5zbk is ON HOLD until Paper Publication Authors: Seo, H., Kim, K.-J. Description: Crystal strcuture of type-I LOG from Pseudomonas aeruginosa PAO1 ...

New page

'''Unreleased structure'''

The entry 5zbk is ON HOLD until Paper Publication

Authors: Seo, H., Kim, K.-J.

Description: Crystal strcuture of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP
[[Category: Unreleased Structures]]
[[Category: Kim, K.-J]]
[[Category: Seo, H]]