5zj4 - Revision history

OCA at 08:57, 22 November 2023

OCA — Wed, 22 Nov 2023 08:57:12 GMT

←Older revision		Revision as of 08:57, 22 November 2023
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	==Guanine-specific ADP-ribosyltransferase==		==Guanine-specific ADP-ribosyltransferase==
-	<StructureSection load='5zj4' size='340' side='right' caption='[[5zj4]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5zj4' size='340' side='right'caption='[[5zj4]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zj4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strco Strco~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zj4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZJ4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MPD:(4S)~~-~~2-METHYL-2~~,~~4-PENTANEDIOL'>MPD</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]] 1.4973928Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SCO5461 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=100226 STRCO]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=5zj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zj4 OCA], [~~http~~://pdbe.org/5zj4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zj4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zj4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zj4 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=5zj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zj4 OCA], [https://pdbe.org/5zj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zj4 RCSB], [https://www.ebi.ac.uk/pdbsum/5zj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zj4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SCARP_STRCO SCARP_STRCO] ADP-ribosylates the N2 amino group of guanosine, deoxyguanosine, GMP, dGMP, cGMP, GTP and dGTP; oligo-guanosine, oligo-deoxyguanosine and tRNA are ADP-ribosylated less efficiently, while dsDNA is a very poor substrate (PubMed:23212047). Also acts on GDP (PubMed:30072382).<ref>PMID:23212047</ref> <ref>PMID:30072382</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Strco~~]]	+	[[Category: Large Structures]]
-	[[Category: Tsuge, H]]	+	[[Category: Tsuge H]]
-	[[Category: Yoshida, T]]	+	[[Category: Yoshida T]]
-	~~[[Category: Adp-ribosyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:24, 5 September 2018

OCA — Wed, 05 Sep 2018 10:24:12 GMT

←Older revision		Revision as of 10:24, 5 September 2018
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	<StructureSection load='5zj4' size='340' side='right' caption='[[5zj4]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5zj4' size='340' side='right' caption='[[5zj4]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zj4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zj4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZJ4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SCO5461 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=100226 STRCO])</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=5zj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zj4 OCA], [http://pdbe.org/5zj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zj4 RCSB], [http://www.ebi.ac.uk/pdbsum/5zj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zj4 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=5zj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zj4 OCA], [http://pdbe.org/5zj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zj4 RCSB], [http://www.ebi.ac.uk/pdbsum/5zj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zj4 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ScARP from the bacterium Streptomyces coelicolor belongs to the pierisin family of DNA-targeting ADP-ribosyltransferases (ARTs). These enzymes ADP-ribosylate the N(2) amino groups of guanine residues in DNA to yield N(2)-(ADP-ribos-1-yl)-2'-deoxyguanosine. Although the structures of pierisin-1 and Scabin were revealed recently, the substrate recognition mechanisms remain poorly understood because of the lack of a substrate-binding structure. Here, we report the apo structure of ScARP and of ScARP bound to NADH and its GDP substrate at 1.50 and 1.57 A resolutions, respectively. The bound structure revealed that the guanine of GDP is trapped between N-ribose of NADH and Trp159. Interestingly, N(2) and N(3) of guanine formed hydrogen bonds with the OE1 and NE2 atoms of Gln162, respectively. We directly observed that the ADP-ribosylating toxin turn-turn (ARTT)-loop including Trp159 and Gln162 plays a key role in the specificity of DNA-targeting guanine-specific ART as well as protein-targeting ARTs such as C3 exoenzyme. We propose that the ARTT-loop recognition is a common substrate recognition mechanism in the pierisin family. Furthermore, this complex structure sheds light on similarities and differences among two subclasses that are distinguished by conserved structural motifs: H-Y-E in the ARTD subfamily and R-S-E in the ARTC subfamily. The spatial arrangements of the electrophile and nucleophile were the same, providing the first evidence for a common reaction mechanism in these ARTs. ARTC (including ScARP) uses the ARTT-loop for substrate recognition, whereas ARTD (represented by Arr) uses the C-terminal helix instead of the ARTT-loop. These observations could help inform efforts to improve ART inhibitors.
		+
		+	Substrate N(2) atom recognition mechanism in pierisin family DNA-targeting guanine-specific ADP-ribosyltransferase ScARP.,Yoshida T, Tsuge H J Biol Chem. 2018 Aug 2. pii: AC118.004412. doi: 10.1074/jbc.AC118.004412. PMID:30072382<ref>PMID:30072382</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zj4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Strco]]
	[[Category: Tsuge, H]]		[[Category: Tsuge, H]]
	[[Category: Yoshida, T]]		[[Category: Yoshida, T]]
	[[Category: Adp-ribosyltransferase]]		[[Category: Adp-ribosyltransferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 21:44, 9 August 2018

OCA — Thu, 09 Aug 2018 21:44:40 GMT

←Older revision		Revision as of 21:44, 9 August 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5zj4 is ~~ON HOLD until Paper Publication~~	+	==Guanine-specific ADP-ribosyltransferase==
-		+	<StructureSection load='5zj4' size='340' side='right' caption='[[5zj4]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zj4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZJ4 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=5zj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zj4 OCA], [http://pdbe.org/5zj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zj4 RCSB], [http://www.ebi.ac.uk/pdbsum/5zj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zj4 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Tsuge, H]]
		+	[[Category: Yoshida, T]]
		+	[[Category: Adp-ribosyltransferase]]
		+	[[Category: Transferase]]

OCA at 04:30, 4 April 2018

OCA — Wed, 04 Apr 2018 04:30:34 GMT

←Older revision		Revision as of 04:30, 4 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zj4 is ON HOLD	+	The entry 5zj4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5zj4" [edit=sysop:move=sysop]

OCA — Wed, 28 Mar 2018 05:10:41 GMT

Protected "5zj4" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:10, 28 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zj4 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 28 Mar 2018 05:10:40 GMT

New page: '''Unreleased structure''' The entry 5zj4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5zj4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]