8a5f - Revision history

OCA at 19:26, 8 September 2026

2026-09-08T19:26:20Z

← Older revision		Revision as of 19:26, 8 September 2026
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	<table><tr><td colspan='2'>[[8a5f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5F FirstGlance]. <br>		<table><tr><td colspan='2'>[[8a5f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5F FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.38Å</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]] 1.38Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG~~</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4~~</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=8a5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5f OCA], [https://pdbe.org/8a5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5f RCSB], [https://www.ebi.ac.uk/pdbsum/8a5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5f 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=8a5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5f OCA], [https://pdbe.org/8a5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5f RCSB], [https://www.ebi.ac.uk/pdbsum/8a5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5f ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:56, 1 May 2024

2024-05-01T07:56:14Z

← Older revision		Revision as of 07:56, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8a5f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5F FirstGlance]. <br>		<table><tr><td colspan='2'>[[8a5f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.38Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=8a5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5f OCA], [https://pdbe.org/8a5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5f RCSB], [https://www.ebi.ac.uk/pdbsum/8a5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5f 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=8a5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5f OCA], [https://pdbe.org/8a5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5f RCSB], [https://www.ebi.ac.uk/pdbsum/8a5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/Q9RRQ0_DEIRA Q9RRQ0_DEIRA]] DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity.[PIRNR:PIRNR001435]		[https://www.uniprot.org/uniprot/Q9RRQ0_DEIRA Q9RRQ0_DEIRA] DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity.[PIRNR:PIRNR001435]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Endonuclease III (EndoIII) is a bifunctional DNA glycosylase with specificity for a broad range of oxidized DNA lesions. The genome of an extremely radiation- and desiccation-resistant bacterium, Deinococcus radiodurans, possesses three genes encoding for EndoIII-like enzymes (DrEndoIII1, DrEndoIII2 and DrEndoIII3), which reveal different types of catalytic activities. DrEndoIII2 acts as the main EndoIII in this organism, while DrEndoIII1 and 3 demonstrate unusual and no EndoIII activity, respectively. In order to understand the role of DrEndoIII1 and DrEndoIII3 in D. radiodurans, we have generated mutants which target non-conserved residues in positions considered essential for classic EndoIII activity. In parallel, we have substituted residues coordinating the iron atoms in the [4Fe-4S] cluster in DrEndoIII2, aiming at elucidating the role of the cluster in these enzymes. Our results demonstrate that the amino acid substitutions in DrEndoIII1 reduce the enzyme activity without altering the overall structure, revealing that the residues found in the wild-type enzyme are essential for its unusual activity. The attempt to generate catalytic activity of DrEndoIII3 by re-designing its catalytic pocket was unsuccessful. A mutation of the iron-coordinating cysteine 199 in DrEndoIII2 appears to compromise the structural integrity and induce the formation of a [3Fe-4S] cluster, but apparently without affecting the activity. Taken together, we provide important structural and mechanistic insights into the three EndoIIIs, which will help us disentangle the open questions related to their presence in D. radiodurans and their particularities.

	Disentangling Unusual Catalytic Properties and the Role of the [4Fe-4S] Cluster of Three Endonuclease III from the Extremophile D. radiodurans.,Rollo F, Borges PT, Silveira CM, Rosa MTG, Todorovic S, Moe E Molecules. 2022 Jul 2;27(13). pii: molecules27134270. doi:, 10.3390/molecules27134270. PMID:35807515<ref>PMID:35807515</ref>		==See Also==
			*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 8a5f" style="background-color:#fffaf0;"></div>~~
	== ~~References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:26, 8 September 2022

2022-09-08T03:26:07Z

← Older revision		Revision as of 03:26, 8 September 2022
Line 1:		Line 1:

	==Crystal structure of Deinococcus radiodurans Endonuclease III-1 R61Q variant==		==Crystal structure of Deinococcus radiodurans Endonuclease III-1 R61Q variant==
	<StructureSection load='8a5f' size='340' side='right'caption='[[8a5f]]' scene=''>		<StructureSection load='8a5f' size='340' side='right'caption='[[8a5f]], [[Resolution\|resolution]] 1.38Å' 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=8A5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5F FirstGlance]. <br>		<table><tr><td colspan='2'>[[8a5f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5F 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=8a5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5f OCA], [https://pdbe.org/8a5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5f RCSB], [https://www.ebi.ac.uk/pdbsum/8a5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5f 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=8a5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5f OCA], [https://pdbe.org/8a5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5f RCSB], [https://www.ebi.ac.uk/pdbsum/8a5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5f ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/Q9RRQ0_DEIRA Q9RRQ0_DEIRA]] DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity.[PIRNR:PIRNR001435]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Endonuclease III (EndoIII) is a bifunctional DNA glycosylase with specificity for a broad range of oxidized DNA lesions. The genome of an extremely radiation- and desiccation-resistant bacterium, Deinococcus radiodurans, possesses three genes encoding for EndoIII-like enzymes (DrEndoIII1, DrEndoIII2 and DrEndoIII3), which reveal different types of catalytic activities. DrEndoIII2 acts as the main EndoIII in this organism, while DrEndoIII1 and 3 demonstrate unusual and no EndoIII activity, respectively. In order to understand the role of DrEndoIII1 and DrEndoIII3 in D. radiodurans, we have generated mutants which target non-conserved residues in positions considered essential for classic EndoIII activity. In parallel, we have substituted residues coordinating the iron atoms in the [4Fe-4S] cluster in DrEndoIII2, aiming at elucidating the role of the cluster in these enzymes. Our results demonstrate that the amino acid substitutions in DrEndoIII1 reduce the enzyme activity without altering the overall structure, revealing that the residues found in the wild-type enzyme are essential for its unusual activity. The attempt to generate catalytic activity of DrEndoIII3 by re-designing its catalytic pocket was unsuccessful. A mutation of the iron-coordinating cysteine 199 in DrEndoIII2 appears to compromise the structural integrity and induce the formation of a [3Fe-4S] cluster, but apparently without affecting the activity. Taken together, we provide important structural and mechanistic insights into the three EndoIIIs, which will help us disentangle the open questions related to their presence in D. radiodurans and their particularities.

			Disentangling Unusual Catalytic Properties and the Role of the [4Fe-4S] Cluster of Three Endonuclease III from the Extremophile D. radiodurans.,Rollo F, Borges PT, Silveira CM, Rosa MTG, Todorovic S, Moe E Molecules. 2022 Jul 2;27(13). pii: molecules27134270. doi:, 10.3390/molecules27134270. PMID:35807515<ref>PMID:35807515</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 8a5f" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Borges PT]]		[[Category: Borges PT]]
	[[Category: Moe E]]		[[Category: Moe E]]
	[[Category: Rollo F]]		[[Category: Rollo F]]

OCA at 04:55, 3 August 2022

2022-08-03T04:55:55Z

← Older revision		Revision as of 04:55, 3 August 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 8a5f is ~~ON HOLD until Paper Publication~~		==Crystal structure of Deinococcus radiodurans Endonuclease III-1 R61Q variant==
			<StructureSection load='8a5f' size='340' side='right'caption='[[8a5f]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5F FirstGlance]. <br>
	~~Description~~:		</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=8a5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5f OCA], [https://pdbe.org/8a5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5f RCSB], [https://www.ebi.ac.uk/pdbsum/8a5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5f ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Borges PT]]
			[[Category: Moe E]]
			[[Category: Rollo F]]

OCA at 06:20, 29 June 2022

2022-06-29T06:20:06Z

← Older revision		Revision as of 06:20, 29 June 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8a5f is ON HOLD		The entry 8a5f is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8a5f" [edit=sysop:move=sysop]

2022-06-22T07:21:26Z

Protected "8a5f" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:21, 22 June 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8a5f is ON HOLD Authors: Description: Category: Unreleased Structures

2022-06-22T07:21:25Z

New page: '''Unreleased structure''' The entry 8a5f is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8a5f is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]