7olb - Revision history

OCA at 12:52, 1 February 2024

OCA — Thu, 01 Feb 2024 12:52:10 GMT

←Older revision		Revision as of 12:52, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7olb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OLB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OLB FirstGlance]. <br>		<table><tr><td colspan='2'>[[7olb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OLB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OLB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7olb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7olb OCA], [https://pdbe.org/7olb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7olb RCSB], [https://www.ebi.ac.uk/pdbsum/7olb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7olb 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=7olb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7olb OCA], [https://pdbe.org/7olb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7olb RCSB], [https://www.ebi.ac.uk/pdbsum/7olb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7olb ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7olb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7olb" 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 07:45:19 GMT

←Older revision		Revision as of 07:45, 11 January 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 7olb is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase from Pyrococcus abyssi==
		+	<StructureSection load='7olb' size='340' side='right'caption='[[7olb]], [[Resolution\|resolution]] 1.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7olb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OLB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OLB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7olb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7olb OCA], [https://pdbe.org/7olb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7olb RCSB], [https://www.ebi.ac.uk/pdbsum/7olb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7olb ProSAT]</span></td></tr>
		+	</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.

-	~~Authors: Coste, F~~., ~~Goffinont~~, S., ~~Flament~~, D., ~~Castaing~~, B.	+	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>

-	~~Description: Crystal structure~~ of ~~Pab~~-~~AGOG, an 8~~-~~oxoguanine DNA glycosylase from Pyrococcus abyssi~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Castaing, B]]	+	<div class="pdbe-citations 7olb" style="background-color:#fffaf0;"></div>
-	[[Category: Coste, F]]	+	== References ==
-	[[Category: Flament, D]]	+	<references/>
-	[[Category: Goffinont, S]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrococcus abyssi GE5]]
		+	[[Category: Castaing B]]
		+	[[Category: Coste F]]
		+	[[Category: Flament D]]
		+	[[Category: Goffinont S]]

OCA at 13:36, 2 June 2021

OCA — Wed, 02 Jun 2021 13:36:59 GMT

←Older revision		Revision as of 13:36, 2 June 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7olb is ON HOLD	+	The entry 7olb 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 "7olb" [edit=sysop:move=sysop]

OCA — Wed, 26 May 2021 08:11:10 GMT

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

←Older revision

Revision as of 08:11, 26 May 2021

OCA: New page: '''Unreleased structure''' The entry 7olb is ON HOLD Authors: Coste, F., Goffinont, S., Flament, D., Castaing, B. Description: Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycos...

OCA — Wed, 26 May 2021 08:11:09 GMT

New page: '''Unreleased structure''' The entry 7olb is ON HOLD Authors: Coste, F., Goffinont, S., Flament, D., Castaing, B. Description: Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycos...

New page

'''Unreleased structure'''

The entry 7olb is ON HOLD

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

Description: Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase from Pyrococcus abyssi
[[Category: Unreleased Structures]]
[[Category: Castaing, B]]
[[Category: Coste, F]]
[[Category: Flament, D]]
[[Category: Goffinont, S]]