8efg - Revision history

OCA at 19:48, 29 May 2024

OCA — Wed, 29 May 2024 19:48:33 GMT

←Older revision		Revision as of 19:48, 29 May 2024
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[8efg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8EFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8EFG FirstGlance]. <br>		<table><tr><td colspan='2'>[[8efg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8EFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8EFG 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]] 1.5Å</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]] 1.5Å</td></tr>
-	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene>, <scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene>, <scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=D5M:2-DEOXYADENOSINE-5-MONOPHOSPHATE'>D5M</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8efg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8efg OCA], [https://pdbe.org/8efg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8efg RCSB], [https://www.ebi.ac.uk/pdbsum/8efg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8efg 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=8efg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8efg OCA], [https://pdbe.org/8efg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8efg RCSB], [https://www.ebi.ac.uk/pdbsum/8efg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8efg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TATD1_HUMAN TATD1_HUMAN] Putative deoxyribonuclease (By similarity).		[https://www.uniprot.org/uniprot/TATD1_HUMAN TATD1_HUMAN] Putative deoxyribonuclease (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	TatD enzymes are evolutionarily conserved deoxyribonucleases associated with DNA repair, apoptosis, development, and parasite virulence. Three TatD paralogs exist in humans, but their nuclease functions are unknown. Here, we describe the nuclease activities of two of the three human TatD paralogs, TATDN1 and TATDN3, which represent two phylogenetically distinct clades based on unique active site motifs. We found that in addition to 3'-5' exonuclease activity associated with other TatD proteins, both TATDN1 and TATDN3 exhibited apurinic/apyrimidinic (AP) endonuclease activity. The AP endonuclease activity was observed only in double-stranded DNA, whereas exonuclease activity was operative primarily in single-stranded DNA. Both nuclease activities were observed in the presence of Mg2+ or Mn2+, and we identified several divalent metal cofactors that inhibited exonuclease and supported AP endonuclease activity. Biochemical analysis and a crystal structure of TATDN1 bound to 2'-deoxyadenosine 5'-monophosphate in the active site are consistent with two-metal ion catalysis, and we identify several residues that differentiate nuclease activities in the two proteins. In addition, we show that the three Escherichia coli TatD paralogs are also AP endonucleases, indicating that this activity is conserved across evolution. Together, these results indicate that TatD enzymes constitute a family of ancient AP endonucleases.
		+
		+	Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity.,Dorival J, Eichman BF Nucleic Acids Res. 2023 Apr 11;51(6):2838-2849. doi: 10.1093/nar/gkad133. PMID:36881763<ref>PMID:36881763</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 8efg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:20, 25 October 2023

OCA — Wed, 25 Oct 2023 10:20:53 GMT

←Older revision		Revision as of 10:20, 25 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8efg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8EFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8EFG FirstGlance]. <br>		<table><tr><td colspan='2'>[[8efg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8EFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8EFG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene>, <scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene>, <scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8efg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8efg OCA], [https://pdbe.org/8efg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8efg RCSB], [https://www.ebi.ac.uk/pdbsum/8efg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8efg 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=8efg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8efg OCA], [https://pdbe.org/8efg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8efg RCSB], [https://www.ebi.ac.uk/pdbsum/8efg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8efg ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:43, 22 February 2023

OCA — Wed, 22 Feb 2023 12:43:29 GMT

←Older revision		Revision as of 12:43, 22 February 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8efg is ~~ON HOLD~~	+	==Crystal structure of human TATDN1 bound to dAMP and two zinc ions==
-		+	<StructureSection load='8efg' size='340' side='right'caption='[[8efg]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[8efg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8EFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8EFG FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene>, <scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8efg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8efg OCA], [https://pdbe.org/8efg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8efg RCSB], [https://www.ebi.ac.uk/pdbsum/8efg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8efg ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TATD1_HUMAN TATD1_HUMAN] Putative deoxyribonuclease (By similarity).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Dorival J]]
		+	[[Category: Eichman BF]]

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

OCA — Wed, 14 Sep 2022 05:52:15 GMT

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

←Older revision

Revision as of 05:52, 14 September 2022

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

OCA — Wed, 14 Sep 2022 05:52:14 GMT

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

New page

'''Unreleased structure'''

The entry 8efg is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]