5gga - Revision history

OCA at 11:30, 2 August 2023

2023-08-02T11:30:47Z

←Older revision		Revision as of 11:30, 2 August 2023
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	<StructureSection load='5gga' size='340' side='right'caption='[[5gga]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5gga' size='340' side='right'caption='[[5gga]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gga]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycs2 Mycs2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GGA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gga]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GGA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8GM:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8GM</scene>, <scene name='pdbligand=G8D:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>G8D</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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]] 1.75Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gg5\|5gg5]], [[5gg6\|5gg6]], [[5gg7\|5gg7]], [[5gg8\|5gg8]], [[5gg9\|5gg9]], [[5ggb\|5ggb]], [[5ggc\|5ggc]], [[5ggd\|5ggd]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8GM:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8GM</scene>, <scene name='pdbligand=G8D:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>G8D</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_2390 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])~~</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=5gga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gga OCA], [https://pdbe.org/5gga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gga RCSB], [https://www.ebi.ac.uk/pdbsum/5gga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gga 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=5gga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gga OCA], [~~http~~://pdbe.org/5gga PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gga RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gga PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gga ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MUTT1_MYCS2 MUTT1_MYCS2] Catalyzes the conversion of 8-oxo-dGTP to 8-oxo-dGDP, and 8-oxo-GTP to 8-oxo-GDP (PubMed:16585780, PubMed:28375146). At high enzyme concentrations, can also catalyze the conversion of 8-oxo-dGDP to 8-oxo-dGMP, and 8-oxo-GDP to 8-oxo-GMP (PubMed:28375146). In addition, catalyzes the hydrolysis of the diadenosine polyphosphates diadenosine hexaphosphate (Ap6A), diadenosine pentaphosphate (Ap5A) and diadenosine tetraphosphate (Ap4A) (PubMed:28705712).<ref>PMID:16585780</ref> <ref>PMID:28375146</ref> <ref>PMID:28705712</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[~~Nudix hydrolase~~ 3D structures\|~~Nudix hydrolase~~ 3D structures]]	+	*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures\|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mycs2~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: Arif~~, S M~~]]	+	[[Category: Arif SM]]
-	[[Category: Patil~~, A G~~]]	+	[[Category: Patil AG]]
-	[[Category: Varshney, U]]	+	[[Category: Varshney U]]
-	[[Category: Vijayan, M]]	+	[[Category: Vijayan M]]
-	~~[[Category: 8-oxo-guanine nucleotide]]~~	+
-	~~[[Category: Binding sites at intermolecular interface]]~~	+
-	~~[[Category: Enzyme action]]~~	+
-	~~[[Category: Histidine phosphatase domain]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nudix enzyme]]~~	+
-	~~[[Category: Sanitization of nucleotide pool~~]]	+

OCA at 06:41, 13 May 2020

2020-05-13T06:41:53Z

←Older revision		Revision as of 06:41, 13 May 2020
Line 1:		Line 1:

	==Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GDP, 8-oxo-GMP and pyrophosphate==		==Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GDP, 8-oxo-GMP and pyrophosphate==
-	<StructureSection load='5gga' size='340' side='right' caption='[[5gga]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5gga' size='340' side='right'caption='[[5gga]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gga]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GGA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gga]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GGA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8GM:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8GM</scene>, <scene name='pdbligand=G8D:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>G8D</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8GM:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8GM</scene>, <scene name='pdbligand=G8D:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>G8D</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gg5\|5gg5]], [[5gg6\|5gg6]], [[5gg7\|5gg7]], [[5gg8\|5gg8]], [[5gg9\|5gg9]], [[5ggb\|5ggb]], [[5ggc\|5ggc]], [[5ggd\|5ggd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gg5\|5gg5]], [[5gg6\|5gg6]], [[5gg7\|5gg7]], [[5gg8\|5gg8]], [[5gg9\|5gg9]], [[5ggb\|5ggb]], [[5ggc\|5ggc]], [[5ggd\|5ggd]]</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=5gga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gga OCA], [http://pdbe.org/5gga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gga RCSB], [http://www.ebi.ac.uk/pdbsum/5gga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gga ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_2390 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</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=5gga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gga OCA], [http://pdbe.org/5gga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gga RCSB], [http://www.ebi.ac.uk/pdbsum/5gga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gga ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5gga" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gga" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nudix hydrolase 3D structures\|Nudix hydrolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mycs2]]
	[[Category: Arif, S M]]		[[Category: Arif, S M]]
	[[Category: Patil, A G]]		[[Category: Patil, A G]]

OCA at 12:56, 19 April 2017

2017-04-19T12:56:44Z

←Older revision		Revision as of 12:56, 19 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gga is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GDP, 8-oxo-GMP and pyrophosphate==
		+	<StructureSection load='5gga' size='340' side='right' caption='[[5gga]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gga]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GGA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8GM:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8GM</scene>, <scene name='pdbligand=G8D:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>G8D</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gg5\|5gg5]], [[5gg6\|5gg6]], [[5gg7\|5gg7]], [[5gg8\|5gg8]], [[5gg9\|5gg9]], [[5ggb\|5ggb]], [[5ggc\|5ggc]], [[5ggd\|5ggd]]</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=5gga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gga OCA], [http://pdbe.org/5gga PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gga RCSB], [http://www.ebi.ac.uk/pdbsum/5gga PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gga ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycobacterium smegmatis MutT1, which is made up of a Nudix domain (domain 1) and a histidine phosphatase domain (domain 2), efficiently hydrolyses 8-oxo-GTP and 8-oxo-dGTP to the corresponding nucleoside diphosphates and phosphate in the presence of magnesium ions. Domain 1 alone hydrolyses nucleoside triphosphates less efficiently. Under high concentrations and over long periods, the full-length enzyme as well as domain 1 catalyses the hydrolysis of the nucleoside triphosphates to the respective nucleoside monophosphates and pyrophosphate. The role of domain 2 appears to be limited to speeding up the reaction. Crystal structures of the apoenzyme and those of ligand-bound enzyme prepared in the presence of 8-oxo-GTP or 8-oxo-dGTP and different concentrations of magnesium were determined. In all of the structures except one, the molecules arrange themselves in a head-to-tail fashion in which domain 1 is brought into contact with domain 2 (trans domain 2) of a neighbouring molecule. The binding site for NTP (site A) is almost exclusively made up of residues from domain 1, while those for NDP (site B) and NMP (site C) are at the interface between domain 1 and trans domain 2 in an unusual instance of intermolecular interactions leading to binding sites. Protein-ligand interactions at site A lead to a proposal for the mechanism of hydrolysis of NTP to NDP and phosphate. A small modification in site A in the crystal which does not exhibit the head-to-tail arrangement appears to facilitate the production of NMP and pyrophosphate from NTP. The two arrangements could be in dynamic equilibrium in the cellular milieu.

-	~~Authors: Arif~~, ~~S.M~~., Patil~~, A.G.~~, Varshney, U., Vijayan, M.	+	Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association.,Arif SM, Patil AG, Varshney U, Vijayan M Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):349-364. doi:, 10.1107/S2059798317002534. Epub 2017 Mar 31. PMID:28375146<ref>PMID:28375146</ref>

-	~~Description: Crystal structure~~ of ~~Mycobacterium smegmatis MutT1 in complex with 8~~-~~oxo~~-~~GDP, 8-oxo-GMP and pyrophosphate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Vijayan~~, M]]	+	<div class="pdbe-citations 5gga" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arif, S M]]
		+	[[Category: Patil, A G]]
	[[Category: Varshney, U]]		[[Category: Varshney, U]]
-	[[Category: ~~Arif~~, S.M]]	+	[[Category: Vijayan, M]]
-	[[Category: ~~Patil, A.G~~]]	+	[[Category: 8-oxo-guanine nucleotide]]
		+	[[Category: Binding sites at intermolecular interface]]
		+	[[Category: Enzyme action]]
		+	[[Category: Histidine phosphatase domain]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nudix enzyme]]
		+	[[Category: Sanitization of nucleotide pool]]

OCA at 08:53, 9 March 2017

2017-03-09T08:53:30Z

←Older revision		Revision as of 08:53, 9 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Vijayan, M]]		[[Category: Vijayan, M]]
		+	[[Category: Varshney, U]]
	[[Category: Arif, S.M]]		[[Category: Arif, S.M]]
	[[Category: Patil, A.G]]		[[Category: Patil, A.G]]
-	[[Category: Varshney, U]]

OCA at 21:31, 12 July 2016

2016-07-12T21:31:04Z

←Older revision		Revision as of 21:31, 12 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5gga is ON HOLD	+	The entry 5gga is ON HOLD until Paper Publication

	Authors: Arif, S.M., Patil, A.G., Varshney, U., Vijayan, M.		Authors: Arif, S.M., Patil, A.G., Varshney, U., Vijayan, M.

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

2016-06-23T18:40:59Z

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

←Older revision

Revision as of 18:40, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5gga is ON HOLD Authors: Arif, S.M., Patil, A.G., Varshney, U., Vijayan, M. Description: Crystal structure of Mycobacterium smegmatis MutT1 in comp...

2016-06-23T18:40:57Z

New page: '''Unreleased structure''' The entry 5gga is ON HOLD Authors: Arif, S.M., Patil, A.G., Varshney, U., Vijayan, M. Description: Crystal structure of Mycobacterium smegmatis MutT1 in comp...

New page

'''Unreleased structure'''

The entry 5gga is ON HOLD

Authors: Arif, S.M., Patil, A.G., Varshney, U., Vijayan, M.

Description: Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GDP, 8-oxo-GMP and pyrophosphate
[[Category: Unreleased Structures]]
[[Category: Vijayan, M]]
[[Category: Arif, S.M]]
[[Category: Patil, A.G]]
[[Category: Varshney, U]]