4ryt - Revision history

OCA at 17:59, 20 September 2023

OCA — Wed, 20 Sep 2023 17:59:03 GMT

←Older revision		Revision as of 17:59, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ryt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RYT FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ryt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RYT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.09Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4ryt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryt OCA], [https://pdbe.org/4ryt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ryt RCSB], [https://www.ebi.ac.uk/pdbsum/4ryt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ryt 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=4ryt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryt OCA], [https://pdbe.org/4ryt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ryt RCSB], [https://www.ebi.ac.uk/pdbsum/4ryt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ryt ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:34, 15 March 2023

OCA — Wed, 15 Mar 2023 10:34:32 GMT

←Older revision		Revision as of 10:34, 15 March 2023
Line 1:		Line 1:

	==Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium==		==Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium==
-	<StructureSection load='4ryt' size='340' side='right' caption='[[4ryt]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='4ryt' size='340' side='right'caption='[[4ryt]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ryt]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Salty Salty~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RYT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ryt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RYT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2v4n\|2v4n]], [[2v4o\|2v4o]], [[4gad\|4gad]], [[4g9o\|4g9o]], [[4ryu\|4ryu]]</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=4ryt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryt OCA], [https://pdbe.org/4ryt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ryt RCSB], [https://www.ebi.ac.uk/pdbsum/4ryt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ryt ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">surE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])~~</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=4ryt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryt OCA], [~~http~~://pdbe.org/4ryt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ryt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ryt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ryt ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SURE_SALTY SURE_SALTY]] Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs.[HAMAP-Rule:MF_00060]	+	[https://www.uniprot.org/uniprot/SURE_SALTY SURE_SALTY] Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs.[HAMAP-Rule:MF_00060]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Salty~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mathiharan, Y K]]~~	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-	~~[[Category: Murthy, M R~~.N]]	+	[[Category: Mathiharan YK]]
-	[[Category: ~~Domain swapping~~]]	+	[[Category: Murthy MRN]]
-	[[Category: ~~Hydrolase]]~~	+
-	~~[[Category: Phosphatase]]~~	+
-	~~[[Category: Rossmann fold like]]~~	+
-	~~[[Category: Stationary phase survival protein~~]]	+

OCA at 06:10, 18 April 2018

OCA — Wed, 18 Apr 2018 06:10:04 GMT

←Older revision		Revision as of 06:10, 18 April 2018
Line 1:		Line 1:
		+
	==Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium==		==Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium==
	<StructureSection load='4ryt' size='340' side='right' caption='[[4ryt]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='4ryt' size='340' side='right' caption='[[4ryt]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ryt]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RYT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ryt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RYT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2v4n\|2v4n]], [[2v4o\|2v4o]], [[4gad\|4gad]], [[4g9o\|4g9o]], [[4ryu\|4ryu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2v4n\|2v4n]], [[2v4o\|2v4o]], [[4gad\|4gad]], [[4g9o\|4g9o]], [[4ryu\|4ryu]]</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=4ryt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ryt RCSB], [http://www.ebi.ac.uk/pdbsum/4ryt PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">surE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=4ryt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryt OCA], [http://pdbe.org/4ryt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ryt RCSB], [http://www.ebi.ac.uk/pdbsum/4ryt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ryt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SURE_SALTY SURE_SALTY]] Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs.[HAMAP-Rule:MF_00060]		[[http://www.uniprot.org/uniprot/SURE_SALTY SURE_SALTY]] Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs.[HAMAP-Rule:MF_00060]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The survival protein SurE from Salmonella typhimurium (StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of beta-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167 degrees . New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11 degrees between the B chains upon superposition of the A chains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.
		+
		+	Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein.,Mathiharan YK, Savithri HS, Murthy MR Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1812-23. doi:, 10.1107/S1399004715011992. Epub 2015 Aug 25. PMID:26327371<ref>PMID:26327371</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4ryt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Salty]]
	[[Category: Mathiharan, Y K]]		[[Category: Mathiharan, Y K]]
	[[Category: Murthy, M R.N]]		[[Category: Murthy, M R.N]]

OCA at 11:18, 9 September 2015

OCA — Wed, 09 Sep 2015 11:18:05 GMT

←Older revision		Revision as of 11:18, 9 September 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium==
-		+	<StructureSection load='4ryt' size='340' side='right' caption='[[4ryt]], [[Resolution\|resolution]] 2.09Å' scene=''>
-	~~The entry~~ 4ryt is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ryt]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RYT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RYT FirstGlance]. <br>
-	~~Authors~~: ~~Mathiharan~~, Y.K., ~~Murthy~~, M.R.N.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2v4n\|2v4n]], [[2v4o\|2v4o]], [[4gad\|4gad]], [[4g9o\|4g9o]], [[4ryu\|4ryu]]</td></tr>
-	~~Description~~: ~~Crystal Structure~~ of ~~F222 form of E112A Mutant~~ of ~~Stationary Phase Survival Protein~~ (~~SurE~~) ~~from Salmonella typhimurium~~	+	<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=4ryt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ryt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ryt RCSB], [http://www.ebi.ac.uk/pdbsum/4ryt PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Murthy, M.R.N]]	+	== Function ==
-	[[Category: ~~Mathiharan, Y.K~~]]	+	[[http://www.uniprot.org/uniprot/SURE_SALTY SURE_SALTY]] Nucleotidase with a broad substrate specificity as it can dephosphorylate various ribo- and deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates with highest affinity to 3'-AMP. Also hydrolyzes polyphosphate (exopolyphosphatase activity) with the preference for short-chain-length substrates (P20-25). Might be involved in the regulation of dNTP and NTP pools, and in the turnover of 3'-mononucleotides produced by numerous intracellular RNases (T1, T2, and F) during the degradation of various RNAs.[HAMAP-Rule:MF_00060]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mathiharan, Y K]]
		+	[[Category: Murthy, M R.N]]
		+	[[Category: Domain swapping]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phosphatase]]
		+	[[Category: Rossmann fold like]]
		+	[[Category: Stationary phase survival protein]]

OCA at 10:28, 25 February 2015

OCA — Wed, 25 Feb 2015 10:28:33 GMT

←Older revision		Revision as of 10:28, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ryt is ON HOLD	+	The entry 4ryt is ON HOLD until Paper Publication

	Authors: Mathiharan, Y.K., Murthy, M.R.N.		Authors: Mathiharan, Y.K., Murthy, M.R.N.

OCA at 17:38, 24 December 2014

OCA — Wed, 24 Dec 2014 17:38:31 GMT

←Older revision		Revision as of 17:38, 24 December 2014
Line 6:		Line 6:

	Description: Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium		Description: Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium
		+	[[Category: Unreleased Structures]]
		+	[[Category: Murthy, M.R.N]]
		+	[[Category: Mathiharan, Y.K]]

OCA: Protected "4ryt" [edit=sysop:move=sysop]

OCA — Wed, 24 Dec 2014 09:33:11 GMT

Protected "4ryt" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:33, 24 December 2014

OCA: New page: '''Unreleased structure''' The entry 4ryt is ON HOLD Authors: Mathiharan, Y.K., Murthy, M.R.N. Description: Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival ...

OCA — Wed, 24 Dec 2014 09:33:10 GMT

New page: '''Unreleased structure''' The entry 4ryt is ON HOLD Authors: Mathiharan, Y.K., Murthy, M.R.N. Description: Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival ...

New page

'''Unreleased structure'''

The entry 4ryt is ON HOLD

Authors: Mathiharan, Y.K., Murthy, M.R.N.

Description: Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium