7p9z - Revision history

OCA at 13:03, 1 February 2024

OCA — Thu, 01 Feb 2024 13:03:01 GMT

←Older revision		Revision as of 13:03, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7p9z]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P9Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[7p9z]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P9Z FirstGlance]. <br>
-	</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>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</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]] 1.33Å</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>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</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=7p9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p9z OCA], [https://pdbe.org/7p9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p9z RCSB], [https://www.ebi.ac.uk/pdbsum/7p9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p9z 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=7p9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p9z OCA], [https://pdbe.org/7p9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p9z RCSB], [https://www.ebi.ac.uk/pdbsum/7p9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p9z ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7p9z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7p9z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:45, 11 January 2023

OCA — Wed, 11 Jan 2023 07:45:42 GMT

←Older revision		Revision as of 07:45, 11 January 2023
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-	====	+	==Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing adenine opposite to lesion)==
-	<StructureSection load='7p9z' size='340' side='right'caption='[[7p9z]]' scene=''>	+	<StructureSection load='7p9z' size='340' side='right'caption='[[7p9z]], [[Resolution\|resolution]] 1.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7p9z]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P9Z FirstGlance]. <br>
-	</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=7p9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p9z OCA], [https://pdbe.org/7p9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p9z RCSB], [https://www.ebi.ac.uk/pdbsum/7p9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p9z ProSAT]</span></td></tr>	+	</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>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</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=7p9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p9z OCA], [https://pdbe.org/7p9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p9z RCSB], [https://www.ebi.ac.uk/pdbsum/7p9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p9z ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AGOG_PYRAB AGOG_PYRAB] DNA repair enzyme that is part of the base excision repair (BER) pathway; protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	8-Oxoguanine (GO) is a major purine oxidation product in DNA. Because of its highly mutagenic properties, GO absolutely must be eliminated from DNA. To do this, aerobic and anaerobic organisms from the three kingdoms of life have evolved repair mechanisms to prevent its deleterious effect on genetic integrity. The major way to remove GO is the base excision repair pathway, usually initiated by a GO-DNA glycosylase. First identified in bacteria (Fpg) and eukaryotes (OGG1), GO-DNA glycosylases were more recently identified in archaea (OGG2 and AGOG). AGOG is the less documented enzyme and its mode of damage recognition and removing remains to be clarified at the molecular and atomic levels. This study presents a complete structural characterisation of apo AGOGs from Pyrococcus abyssi (Pab) and Thermococcus gammatolerans (Tga) and the first structure of Pab-AGOG bound to lesion-containing single- or double-stranded DNA. By combining X-ray structure analysis, site directed mutagenesis and biochemistry experiments, we identified key amino acid residues of AGOGs responsible for the specific recognition of the lesion and the base opposite the lesion and for catalysis. Moreover, a unique binding mode of GO, involving double base flipping, never observed for any other DNA glycosylases, is revealed. In addition to unravelling the properties of AGOGs, our study, through comparative biochemical and structural analysis, offers new insights into the evolutionary plasticity of DNA glycosylases across all three kingdoms of life.
		+
		+	Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing.,Franck C, Stephane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C Nucleic Acids Res. 2022 Oct 28;50(19):11072-11092. doi: 10.1093/nar/gkac932. PMID:36300625<ref>PMID:36300625</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7p9z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Pyrococcus abyssi]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Castaing B]]
		+	[[Category: Coste F]]
		+	[[Category: Flament D]]
		+	[[Category: Goffinont S]]

OCA at 04:58, 10 August 2022

OCA — Wed, 10 Aug 2022 04:58:33 GMT

←Older revision		Revision as of 04:58, 10 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7p9z ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7p9z' size='340' side='right'caption='[[7p9z]]' scene=''>
-	~~Authors~~: ~~Coste, F~~.~~, Goffinont, S~~.~~, Flament, D~~.~~, Castaing, B~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Crystal~~ structure ~~of a trapped Pab-AGOG~~/~~double-standed DNA covalent intermediate (DNA containing adenine opposite to lesion)~~	+	</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=7p9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p9z OCA], [https://pdbe.org/7p9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p9z RCSB], [https://www.ebi.ac.uk/pdbsum/7p9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p9z ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures]~~]	+	</table>
-	[[~~Category~~: ~~Castaing~~, B]]	+	__TOC__
-	[~~[Category~~: ~~Coste~~, F]]	+	</StructureSection>
-	[[Category: ~~Flament, D~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Goffinont, S~~]]	+	[[Category: Z-disk]]

OCA at 07:27, 8 September 2021

OCA — Wed, 08 Sep 2021 07:27:25 GMT

←Older revision		Revision as of 07:27, 8 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7p9z is ON HOLD	+	The entry 7p9z is ON HOLD until Paper Publication

	Authors: Coste, F., Goffinont, S., Flament, D., Castaing, B.		Authors: Coste, F., Goffinont, S., Flament, D., Castaing, B.

OCA: Protected "7p9z" [edit=sysop:move=sysop]

OCA — Wed, 04 Aug 2021 09:15:52 GMT

Protected "7p9z" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:15, 4 August 2021

OCA: New page: '''Unreleased structure''' The entry 7p9z is ON HOLD Authors: Coste, F., Goffinont, S., Flament, D., Castaing, B. Description: Crystal structure of a trapped Pab-AGOG/double-standed DN...

OCA — Wed, 04 Aug 2021 09:15:51 GMT

New page: '''Unreleased structure''' The entry 7p9z is ON HOLD Authors: Coste, F., Goffinont, S., Flament, D., Castaing, B. Description: Crystal structure of a trapped Pab-AGOG/double-standed DN...

New page

'''Unreleased structure'''

The entry 7p9z is ON HOLD

Authors: Coste, F., Goffinont, S., Flament, D., Castaing, B.

Description: Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing adenine opposite to lesion)
[[Category: Unreleased Structures]]
[[Category: Castaing, B]]
[[Category: Coste, F]]
[[Category: Flament, D]]
[[Category: Goffinont, S]]