2gem - Revision history

OCA at 00:58, 21 November 2024

2024-11-21T00:58:07Z

← Older revision		Revision as of 00:58, 21 November 2024
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	<StructureSection load='2gem' size='340' side='right'caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2gem' size='340' side='right'caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~2gel~~\|~~2gel~~]]~~</div>~~</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]] 2.1Å</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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [https://pdbe.org/2gem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [https://www.ebi.ac.uk/pdbsum/2gem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gem 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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [https://pdbe.org/2gem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [https://www.ebi.ac.uk/pdbsum/2gem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gem ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/TSAB_SALTY TSAB_SALTY]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.<ref>PMID:16213054</ref>		[https://www.uniprot.org/uniprot/TSAB_SALTY TSAB_SALTY] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.<ref>PMID:16213054</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/2gem_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/2gem_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Nichols, C E~~]]		[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
	[[Category: ~~Stammers, D K~~]]		[[Category: Nichols CE]]
	[[Category: ~~Actin-like-fold]]~~		[[Category: Stammers DK]]
	~~[[Category: Chaperone]]~~
	~~[[Category: Glycoprotease]]~~
	~~[[Category: M22]]~~
	~~[[Category: Yeaz~~]]

OCA at 09:58, 5 May 2021

2021-05-05T09:58:04Z

← Older revision		Revision as of 09:58, 5 May 2021
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	<StructureSection load='2gem' size='340' side='right'caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2gem' size='340' side='right'caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2GEM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gel\|2gel]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2gel\|2gel]]</div></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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [~~http~~://pdbe.org/2gem PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2gem PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2gem 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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [https://pdbe.org/2gem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [https://www.ebi.ac.uk/pdbsum/2gem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gem ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/TSAB_SALTY TSAB_SALTY]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.<ref>PMID:16213054</ref>		[[https://www.uniprot.org/uniprot/TSAB_SALTY TSAB_SALTY]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.<ref>PMID:16213054</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:18, 24 July 2019

2019-07-24T09:18:32Z

← Older revision		Revision as of 09:18, 24 July 2019
Line 1:		Line 1:

	==2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A==		==2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A==
	<StructureSection load='2gem' size='340' side='right' caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2gem' size='340' side='right'caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/2gem_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/2gem_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Nichols, C E]]		[[Category: Nichols, C E]]
	[[Category: Stammers, D K]]		[[Category: Stammers, D K]]

OCA at 11:13, 12 October 2017

2017-10-12T11:13:59Z

← Older revision		Revision as of 11:13, 12 October 2017
Line 1:		Line 1:

	==2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A==		==2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A==
	<StructureSection load='2gem' size='340' side='right' caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2gem' size='340' side='right' caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gel\|2gel]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gel\|2gel]]</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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [http://pdbe.org/2gem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [http://www.ebi.ac.uk/pdbsum/2gem PDBsum]</span></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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [http://pdbe.org/2gem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [http://www.ebi.ac.uk/pdbsum/2gem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gem ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2gem ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:42, 11 September 2015

2015-09-11T17:42:16Z

← Older revision		Revision as of 17:42, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2gem' size='340' side='right' caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2gem' size='340' side='right' caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gel\|2gel]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gel\|2gel]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yegS,YeaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [http://pdbe.org/2gem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [http://www.ebi.ac.uk/pdbsum/2gem PDBsum]</span></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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [http://www.ebi.ac.uk/pdbsum/2gem PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/~~Q7CQE0_SALTY Q7CQE0_SALTY~~]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance ~~(PubMed~~:16213054).		[[http://www.uniprot.org/uniprot/TSAB_SALTY TSAB_SALTY]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.<ref>PMID:16213054</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2gem" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]~~
	[[Category: Nichols, C E]]		[[Category: Nichols, C E]]
	[[Category: Stammers, D K]]		[[Category: Stammers, D K]]

OCA at 19:44, 25 December 2014

2014-12-25T19:44:34Z

← Older revision		Revision as of 19:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gel\|2gel]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gel\|2gel]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yegS,YeaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yegS,YeaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [http://www.ebi.ac.uk/pdbsum/2gem PDBsum]</span></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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [http://www.ebi.ac.uk/pdbsum/2gem PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q7CQE0_SALTY Q7CQE0_SALTY]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance (PubMed:16213054).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Nichols, C E.]]		[[Category: Nichols, C E]]
	[[Category: Stammers, D K.]]		[[Category: Stammers, D K]]
	[[Category: Actin-like-fold]]		[[Category: Actin-like-fold]]
	[[Category: Chaperone]]		[[Category: Chaperone]]

OCA at 08:47, 30 September 2014

2014-09-30T08:47:45Z

← Older revision		Revision as of 08:47, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2gem~~.~~png~~\|~~left~~\|~~200px~~]]		==2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A==
			<StructureSection load='2gem' size='340' side='right' caption='[[2gem]], [[Resolution\|resolution]] 2.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gel\|2gel]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yegS,YeaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [http://www.ebi.ac.uk/pdbsum/2gem PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/2gem_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The Salmonella typhimurium "yeaZ" gene (StyeaZ) encodes an essential protein of unknown function (StYeaZ), which has previously been annotated as a putative homolog of the Pasteurella haemolytica M22 O-sialoglycoprotein endopeptidase Gcp. YeaZ has also recently been reported as the first example of an RPF from a gram-negative bacterial species. To further characterize the properties of StYeaZ and the widely occurring MK-M22 family, we describe the purification, biochemical analysis, crystallization, and structure determination of StYeaZ. The crystal structure of StYeaZ reveals a classic two-lobed actin-like fold with structural features consistent with nucleotide binding. However, microcalorimetry experiments indicated that StYeaZ neither binds polyphosphates nor a wide range of nucleotides. Additionally, biochemical assays show that YeaZ is not an active O-sialoglycoprotein endopeptidase, consistent with the lack of the critical zinc binding motif. We present a detailed comparison of YeaZ with available structural homologs, the first reported structural analysis of an MK-M22 family member. The analysis indicates that StYeaZ has an unusual orientation of the A and B lobes which may require substantial relative movement or interaction with a partner protein in order to bind ligands. Comparison of the fold of YeaZ with that of a known RPF domain from a gram-positive species shows significant structural differences and therefore potentially distinctive RPF mechanisms for these two bacterial classes.

	~~{{STRUCTURE_2gem\| PDB=2gem \| SCENE= }}~~		Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog.,Nichols CE, Johnson C, Lockyer M, Charles IG, Lamb HK, Hawkins AR, Stammers DK Proteins. 2006 Jul 1;64(1):111-23. PMID:16617437<ref>PMID:16617437</ref>

	~~===2.1A crystal structure of Salmonella tyhpimurium YeaZ~~, a ~~putative Gram-negative RPF, form-A===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16617437}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2gem]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Salmonella_enterica_subsp~~.~~_enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016617437<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Nichols, C E.]]		[[Category: Nichols, C E.]]

OCA: Protected "2gem" [edit=sysop:move=sysop]

2013-01-07T11:08:54Z

Protected "2gem" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:08, 7 January 2013
(No difference)

OCA at 11:08, 7 January 2013

2013-01-07T11:08:52Z

← Older revision		Revision as of 11:08, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2gem.png\|left\|200px]]		[[Image:2gem.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2gem", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2gem\| PDB=2gem \| SCENE= }}		{{STRUCTURE_2gem\| PDB=2gem \| SCENE= }}

	===2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A===		===2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16617437}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16617437 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16617437}}		{{ABSTRACT_PUBMED_16617437}}

	==About this Structure==		==About this Structure==
	~~2GEM~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Salmonella_typhimurium~~ Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA].		[[2gem]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16617437~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016617437</ref><references group="xtra"/>
	[[Category: Salmonella typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Nichols, C E.]]		[[Category: Nichols, C E.]]
	[[Category: Stammers, D K.]]		[[Category: Stammers, D K.]]
	[[Category: Actin-like-fold]]		[[Category: Actin-like-fold]]
			[[Category: Chaperone]]
	[[Category: Glycoprotease]]		[[Category: Glycoprotease]]
	[[Category: M22]]		[[Category: M22]]
	[[Category: Yeaz]]		[[Category: Yeaz]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:57:18 2009''~~

OCA at 02:57, 18 February 2009

2009-02-18T02:57:21Z

← Older revision		Revision as of 02:57, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2GEM is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA].		2GEM is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA].

	==Reference==		==Reference==
	Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog., Nichols CE, Johnson C, Lockyer M, Charles IG, Lamb HK, Hawkins AR, Stammers DK, Proteins. 2006 Jul 1;64(1):111-23. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16617437 16617437]~~		<ref group="xtra">PMID:16617437</ref><references group="xtra"/>
	[[Category: Salmonella typhimurium]]		[[Category: Salmonella typhimurium]]
	~~[[Category: Single protein]]~~
	[[Category: Nichols, C E.]]		[[Category: Nichols, C E.]]
	[[Category: Stammers, D K.]]		[[Category: Stammers, D K.]]
Line 33:		Line 32:
	[[Category: Yeaz]]		[[Category: Yeaz]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 11~~:45:~~30 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:57:18 2009''