5fsi - Revision history

OCA at 13:21, 26 July 2023

OCA — Wed, 26 Jul 2023 13:21:41 GMT

←Older revision		Revision as of 13:21, 26 July 2023
Line 3:		Line 3:
	<StructureSection load='5fsi' size='340' side='right'caption='[[5fsi]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='5fsi' size='340' side='right'caption='[[5fsi]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fsi]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FSI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FSI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fsi]] 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=5FSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FSI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=8DG:8~~-~~OXO-2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>8DG</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]] 1.63Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5fsk\|5fsk]], [[5fsl\|5fsl]], [[5fsm\|5fsm]], [[5fsn\|5fsn]], [[5fso\|5fso]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8DG:8-OXO-2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>8DG</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5fsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fsi OCA], [~~http~~://pdbe.org/5fsi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fsi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fsi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fsi 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=5fsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fsi OCA], [https://pdbe.org/5fsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fsi RCSB], [https://www.ebi.ac.uk/pdbsum/5fsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fsi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/8ODP_HUMAN 8ODP_HUMAN]] Antimutagenic. Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress. Hydrolyzes 8-oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions. Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP.<ref>PMID:10373420</ref> <ref>PMID:10608900</ref> <ref>PMID:11139615</ref> <ref>PMID:12857738</ref> <ref>PMID:22556419</ref>	+	[https://www.uniprot.org/uniprot/8ODP_HUMAN 8ODP_HUMAN] Antimutagenic. Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress. Hydrolyzes 8-oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions. Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP.<ref>PMID:10373420</ref> <ref>PMID:10608900</ref> <ref>PMID:11139615</ref> <ref>PMID:12857738</ref> <ref>PMID:22556419</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bista, M]]	+	[[Category: Bista M]]
-	[[Category: Breed, J]]	+	[[Category: Breed J]]
-	[[Category: Carter, N]]	+	[[Category: Carter N]]
-	[[Category: Embrey, K]]	+	[[Category: Embrey K]]
-	[[Category: Nissink~~, J W.M~~]]	+	[[Category: Nissink JWM]]
-	[[Category: Phillips, C]]	+	[[Category: Phillips C]]
-	[[Category: Read, J]]	+	[[Category: Read J]]
-	[[Category: Winter~~, J J]]~~	+	[[Category: Winter JJ]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nudt1~~]]	+

OCA at 07:34, 6 May 2020

OCA — Wed, 06 May 2020 07:34:45 GMT

←Older revision		Revision as of 07:34, 6 May 2020
Line 1:		Line 1:

	==MTH1 substrate recognition: Complex with 8-oxo-dGTP.==		==MTH1 substrate recognition: Complex with 8-oxo-dGTP.==
-	<StructureSection load='5fsi' size='340' side='right' caption='[[5fsi]], [[Resolution\|resolution]] 1.63Å' scene=''>	+	<StructureSection load='5fsi' size='340' side='right'caption='[[5fsi]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fsi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FSI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FSI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fsi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FSI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FSI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8DG:8-OXO-2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>8DG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8DG:8-OXO-2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>8DG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fsk\|5fsk]], [[5fsl\|5fsl]], [[5fsm\|5fsm]], [[5fsn\|5fsn]], [[5fso\|5fso]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fsk\|5fsk]], [[5fsl\|5fsl]], [[5fsm\|5fsm]], [[5fsn\|5fsn]], [[5fso\|5fso]]</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=5fsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fsi OCA], [http://pdbe.org/5fsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fsi RCSB], [http://www.ebi.ac.uk/pdbsum/5fsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fsi ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5fsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fsi OCA], [http://pdbe.org/5fsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fsi RCSB], [http://www.ebi.ac.uk/pdbsum/5fsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fsi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[7%2C8-dihydro-8-oxoguanine triphosphatase\|7%2C8-dihydro-8-oxoguanine triphosphatase]]	+	*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures\|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bista, M]]		[[Category: Bista, M]]
	[[Category: Breed, J]]		[[Category: Breed, J]]

OCA at 16:02, 25 January 2017

OCA — Wed, 25 Jan 2017 16:02:31 GMT

←Older revision		Revision as of 16:02, 25 January 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/8ODP_HUMAN 8ODP_HUMAN]] Antimutagenic. Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress. Hydrolyzes 8-oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions. Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP.<ref>PMID:10373420</ref> <ref>PMID:10608900</ref> <ref>PMID:11139615</ref> <ref>PMID:12857738</ref> <ref>PMID:22556419</ref>		[[http://www.uniprot.org/uniprot/8ODP_HUMAN 8ODP_HUMAN]] Antimutagenic. Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress. Hydrolyzes 8-oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions. Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP.<ref>PMID:10373420</ref> <ref>PMID:10608900</ref> <ref>PMID:11139615</ref> <ref>PMID:12857738</ref> <ref>PMID:22556419</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	MTH1 (NUDT1) is an oncologic target involved in the prevention of DNA damage. We investigate the way MTH1 recognises its substrates and present substrate-bound structures of MTH1 for 8-oxo-dGTP and 8-oxo-rATP as examples of novel strong and weak binding substrate motifs. Investigation of a small set of purine-like fragments using 2D NMR resulted in identification of a fragment with weak potency. The protein-ligand X-Ray structure of this fragment provides insight into the role of water molecules in substrate selectivity. Wider fragment screening by NMR resulted in three new protein structures exhibiting alternative binding configurations to the key Asp-Asp recognition element of the protein. These inhibitor binding modes demonstrate that MTH1 employs an intricate yet promiscuous mechanism of substrate anchoring through its Asp-Asp pharmacophore. The structures suggest that water-mediated interactions convey selectivity towards oxidized substrates over their non-oxidised counterparts, in particular by stabilization of a water molecule in a hydrophobic environment through hydrogen bonding. These findings may be useful in the design of inhibitors of MTH1.
		+
		+	MTH1 Substrate Recognition--An Example of Specific Promiscuity.,Nissink JW, Bista M, Breed J, Carter N, Embrey K, Read J, Winter-Holt JJ PLoS One. 2016 Mar 21;11(3):e0151154. doi: 10.1371/journal.pone.0151154., eCollection 2016. PMID:26999531<ref>PMID:26999531</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fsi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[7%2C8-dihydro-8-oxoguanine triphosphatase\|7%2C8-dihydro-8-oxoguanine triphosphatase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:32, 26 July 2016

OCA — Tue, 26 Jul 2016 15:32:47 GMT

←Older revision		Revision as of 15:32, 26 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fsi ~~is ON HOLD~~	+	==MTH1 substrate recognition: Complex with 8-oxo-dGTP.==
-		+	<StructureSection load='5fsi' size='340' side='right' caption='[[5fsi]], [[Resolution\|resolution]] 1.63Å' scene=''>
-	~~Authors~~: ~~Nissink, J~~.W.M.~~, Bista, M~~.~~, Breed, J~~.~~, Carter, N~~.~~, Embrey, K~~.~~, Read, J~~.~~, Phillips, C., Winter, J.J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fsi]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FSI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FSI FirstGlance]. <br>
-	~~Description~~: ~~MTH1 substrate recognition~~: ~~Complex with~~ 8-~~oxo~~-~~dGTP.~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8DG:8-OXO-2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>8DG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fsk\|5fsk]], [[5fsl\|5fsl]], [[5fsm\|5fsm]], [[5fsn\|5fsn]], [[5fso\|5fso]]</td></tr>
-	[[~~Category~~: ~~Winter~~, J.J]]	+	<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=5fsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fsi OCA], [http://pdbe.org/5fsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fsi RCSB], [http://www.ebi.ac.uk/pdbsum/5fsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fsi ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Nissink, J~~.W.M]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/8ODP_HUMAN 8ODP_HUMAN]] Antimutagenic. Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress. Hydrolyzes 8-oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions. Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP.<ref>PMID:10373420</ref> <ref>PMID:10608900</ref> <ref>PMID:11139615</ref> <ref>PMID:12857738</ref> <ref>PMID:22556419</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bista, M]]		[[Category: Bista, M]]
		+	[[Category: Breed, J]]
		+	[[Category: Carter, N]]
	[[Category: Embrey, K]]		[[Category: Embrey, K]]
-	[[Category: ~~Carter~~, N]]	+	[[Category: Nissink, J W.M]]
	[[Category: Phillips, C]]		[[Category: Phillips, C]]
-	[[Category: Breed, J]]
	[[Category: Read, J]]		[[Category: Read, J]]
		+	[[Category: Winter, J J]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nudt1]]

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

OCA — Wed, 13 Jan 2016 18:37:09 GMT

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

←Older revision

Revision as of 18:37, 13 January 2016

OCA: New page: '''Unreleased structure''' The entry 5fsi is ON HOLD Authors: Nissink, J.W.M., Bista, M., Breed, J., Carter, N., Embrey, K., Read, J., Phillips, C., Winter, J.J. Description: MTH1 subs...

OCA — Wed, 13 Jan 2016 18:37:07 GMT

New page: '''Unreleased structure''' The entry 5fsi is ON HOLD Authors: Nissink, J.W.M., Bista, M., Breed, J., Carter, N., Embrey, K., Read, J., Phillips, C., Winter, J.J. Description: MTH1 subs...

New page

'''Unreleased structure'''

The entry 5fsi is ON HOLD

Authors: Nissink, J.W.M., Bista, M., Breed, J., Carter, N., Embrey, K., Read, J., Phillips, C., Winter, J.J.

Description: MTH1 substrate recognition: Complex with 8-oxo-dGTP.
[[Category: Unreleased Structures]]
[[Category: Winter, J.J]]
[[Category: Nissink, J.W.M]]
[[Category: Bista, M]]
[[Category: Embrey, K]]
[[Category: Carter, N]]
[[Category: Phillips, C]]
[[Category: Breed, J]]
[[Category: Read, J]]