3ieu - Revision history

OCA at 13:09, 30 August 2023

2023-08-30T13:09:37Z

←Older revision		Revision as of 13:09, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3ieu' size='340' side='right'caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3ieu' size='340' side='right'caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.8Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [https://pdbe.org/3ieu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [https://www.ebi.ac.uk/pdbsum/3ieu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieu 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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [https://pdbe.org/3ieu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [https://www.ebi.ac.uk/pdbsum/3ieu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ERA_ECOLI ERA_ECOLI]] An essential GTPase that binds both GDP and GTP, with nucleotide exchange occurring on the order of seconds whereas hydrolysis occurs on the order of minutes. Plays a role in numerous processes, including cell cycle regulation, energy metabolism, as a chaperone for 16S rRNA processing and 30S ribosomal subunit biogenesis. Its presence in the 30S subunit may prevent translation initiation. Seems to be critical for maintaining cell growth and cell divison rates; a dramatic reduction in Era protein levels temporarily arrests cell growth just before cytokinesis (at the predivisional two-cell stage) and delays cell division. Era mutant era1 suppresses some temperature-sensitive mutations that affect DNA replication and chromosome partitioning and segregation. The dominant-negative Era-de mutant which is missing residues in a putative effector region, is unable to complement the disruption mutant; upon overproduction it shows a significant decrease in cell viability and a synthetic lethal phenotype in the presence of acetate. Era function probably overlaps RbfA. Binds to the pre-30S subunit through several stages of protein assembly.<ref>PMID:9515700</ref> <ref>PMID:12125819</ref> <ref>PMID:12753192</ref> <ref>PMID:16825789</ref> <ref>PMID:20188109</ref>	+	[https://www.uniprot.org/uniprot/ERA_ECOLI ERA_ECOLI] An essential GTPase that binds both GDP and GTP, with nucleotide exchange occurring on the order of seconds whereas hydrolysis occurs on the order of minutes. Plays a role in numerous processes, including cell cycle regulation, energy metabolism, as a chaperone for 16S rRNA processing and 30S ribosomal subunit biogenesis. Its presence in the 30S subunit may prevent translation initiation. Seems to be critical for maintaining cell growth and cell divison rates; a dramatic reduction in Era protein levels temporarily arrests cell growth just before cytokinesis (at the predivisional two-cell stage) and delays cell division. Era mutant era1 suppresses some temperature-sensitive mutations that affect DNA replication and chromosome partitioning and segregation. The dominant-negative Era-de mutant which is missing residues in a putative effector region, is unable to complement the disruption mutant; upon overproduction it shows a significant decrease in cell viability and a synthetic lethal phenotype in the presence of acetate. Era function probably overlaps RbfA. Binds to the pre-30S subunit through several stages of protein assembly.<ref>PMID:9515700</ref> <ref>PMID:12125819</ref> <ref>PMID:12753192</ref> <ref>PMID:16825789</ref> <ref>PMID:20188109</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ji, X]]	+	[[Category: Ji X]]
-	[[Category: Tu, C]]	+	[[Category: Tu C]]
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Era]]~~	+
-	~~[[Category: Gdp]]~~	+
-	~~[[Category: Gtp-binding]]~~	+
-	~~[[Category: Gtpase]]~~	+
-	~~[[Category: Kh domain]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Nucleotide binding protein]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Rna-binding~~]]	+

OCA at 03:30, 21 April 2022

2022-04-21T03:30:56Z

←Older revision		Revision as of 03:30, 21 April 2022
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	<StructureSection load='3ieu' size='340' side='right'caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3ieu' size='340' side='right'caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IEU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [~~http~~://pdbe.org/3ieu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ieu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieu 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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [https://pdbe.org/3ieu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [https://www.ebi.ac.uk/pdbsum/3ieu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ERA_ECOLI ERA_ECOLI]] An essential GTPase that binds both GDP and GTP, with nucleotide exchange occurring on the order of seconds whereas hydrolysis occurs on the order of minutes. Plays a role in numerous processes, including cell cycle regulation, energy metabolism, as a chaperone for 16S rRNA processing and 30S ribosomal subunit biogenesis. Its presence in the 30S subunit may prevent translation initiation. Seems to be critical for maintaining cell growth and cell divison rates; a dramatic reduction in Era protein levels temporarily arrests cell growth just before cytokinesis (at the predivisional two-cell stage) and delays cell division. Era mutant era1 suppresses some temperature-sensitive mutations that affect DNA replication and chromosome partitioning and segregation. The dominant-negative Era-de mutant which is missing residues in a putative effector region, is unable to complement the disruption mutant; upon overproduction it shows a significant decrease in cell viability and a synthetic lethal phenotype in the presence of acetate. Era function probably overlaps RbfA. Binds to the pre-30S subunit through several stages of protein assembly.<ref>PMID:9515700</ref> <ref>PMID:12125819</ref> <ref>PMID:12753192</ref> <ref>PMID:16825789</ref> <ref>PMID:20188109</ref>	+	[[https://www.uniprot.org/uniprot/ERA_ECOLI ERA_ECOLI]] An essential GTPase that binds both GDP and GTP, with nucleotide exchange occurring on the order of seconds whereas hydrolysis occurs on the order of minutes. Plays a role in numerous processes, including cell cycle regulation, energy metabolism, as a chaperone for 16S rRNA processing and 30S ribosomal subunit biogenesis. Its presence in the 30S subunit may prevent translation initiation. Seems to be critical for maintaining cell growth and cell divison rates; a dramatic reduction in Era protein levels temporarily arrests cell growth just before cytokinesis (at the predivisional two-cell stage) and delays cell division. Era mutant era1 suppresses some temperature-sensitive mutations that affect DNA replication and chromosome partitioning and segregation. The dominant-negative Era-de mutant which is missing residues in a putative effector region, is unable to complement the disruption mutant; upon overproduction it shows a significant decrease in cell viability and a synthetic lethal phenotype in the presence of acetate. Era function probably overlaps RbfA. Binds to the pre-30S subunit through several stages of protein assembly.<ref>PMID:9515700</ref> <ref>PMID:12125819</ref> <ref>PMID:12753192</ref> <ref>PMID:16825789</ref> <ref>PMID:20188109</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:24, 24 July 2019

2019-07-24T08:24:39Z

←Older revision		Revision as of 08:24, 24 July 2019
Line 1:		Line 1:

	==Crystal Structure of ERA in Complex with GDP==		==Crystal Structure of ERA in Complex with GDP==
-	<StructureSection load='3ieu' size='340' side='right' caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='3ieu' size='340' side='right'caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEU FirstGlance]. <br>
Line 33:		Line 33:
	==See Also==		==See Also==
	*[[GTP-binding protein\|GTP-binding protein]]		*[[GTP-binding protein\|GTP-binding protein]]
		+	*[[GTP-binding protein 3D structures\|GTP-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Ji, X]]		[[Category: Ji, X]]
	[[Category: Tu, C]]		[[Category: Tu, C]]

OCA at 10:06, 19 December 2018

2018-12-19T10:06:19Z

←Older revision		Revision as of 10:06, 19 December 2018
Line 1:		Line 1:
		+
	==Crystal Structure of ERA in Complex with GDP==		==Crystal Structure of ERA in Complex with GDP==
	<StructureSection load='3ieu' size='340' side='right' caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3ieu' size='340' side='right' caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [http://pdbe.org/3ieu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [http://www.ebi.ac.uk/pdbsum/3ieu 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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [http://pdbe.org/3ieu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [http://www.ebi.ac.uk/pdbsum/3ieu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ieu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ie/3ieu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ie/3ieu_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>

OCA at 10:13, 8 February 2016

2016-02-08T10:13:43Z

←Older revision		Revision as of 10:13, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3ieu' size='340' side='right' caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3ieu' size='340' side='right' caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [http://www.ebi.ac.uk/pdbsum/3ieu 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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [http://pdbe.org/3ieu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [http://www.ebi.ac.uk/pdbsum/3ieu PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3ieu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3ieu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Ji, X]]		[[Category: Ji, X]]
	[[Category: Tu, C]]		[[Category: Tu, C]]

OCA at 22:36, 24 December 2014

2014-12-24T22:36:11Z

←Older revision		Revision as of 22:36, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [http://www.ebi.ac.uk/pdbsum/3ieu 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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [http://www.ebi.ac.uk/pdbsum/3ieu PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ERA_ECOLI ERA_ECOLI]] An essential GTPase that binds both GDP and GTP, with nucleotide exchange occurring on the order of seconds whereas hydrolysis occurs on the order of minutes. Plays a role in numerous processes, including cell cycle regulation, energy metabolism, as a chaperone for 16S rRNA processing and 30S ribosomal subunit biogenesis. Its presence in the 30S subunit may prevent translation initiation. Seems to be critical for maintaining cell growth and cell divison rates; a dramatic reduction in Era protein levels temporarily arrests cell growth just before cytokinesis (at the predivisional two-cell stage) and delays cell division. Era mutant era1 suppresses some temperature-sensitive mutations that affect DNA replication and chromosome partitioning and segregation. The dominant-negative Era-de mutant which is missing residues in a putative effector region, is unable to complement the disruption mutant; upon overproduction it shows a significant decrease in cell viability and a synthetic lethal phenotype in the presence of acetate. Era function probably overlaps RbfA. Binds to the pre-30S subunit through several stages of protein assembly.<ref>PMID:9515700</ref> <ref>PMID:12125819</ref> <ref>PMID:12753192</ref> <ref>PMID:16825789</ref> <ref>PMID:20188109</ref>
	== 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: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
-	[[Category: Ji, X.]]	+	[[Category: Ji, X]]
-	[[Category: Tu, C.]]	+	[[Category: Tu, C]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Era]]		[[Category: Era]]

OCA at 11:18, 29 September 2014

2014-09-29T11:18:53Z

←Older revision		Revision as of 11:18, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3ieu.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of ERA in Complex with GDP==
		+	<StructureSection load='3ieu' size='340' side='right' caption='[[3ieu]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ieu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ega\|1ega]], [[1wf3\|1wf3]], [[1x1l\|1x1l]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2566, era, Escherichia coli, JW2550, rbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=3ieu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ieu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ieu RCSB], [http://www.ebi.ac.uk/pdbsum/3ieu 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/ie/3ieu_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 ==
		+	ERA, composed of an N-terminal GTPase domain followed by an RNA-binding KH domain, is essential for bacterial cell viability. It binds to 16S rRNA and the 30S ribosomal subunit. However, its RNA-binding site, the functional relationship between the two domains, and its role in ribosome biogenesis remain unclear. We have determined two crystal structures of ERA, a binary complex with GDP and a ternary complex with a GTP-analog and the 1531AUCACCUCCUUA1542 sequence at the 3' end of 16S rRNA. In the ternary complex, the first nine of the 12 nucleotides are recognized by the protein. We show that GTP binding is a prerequisite for RNA recognition by ERA and that RNA recognition stimulates its GTP-hydrolyzing activity. Based on these and other data, we propose a functional cycle of ERA, suggesting that the protein serves as a chaperone for processing and maturation of 16S rRNA and a checkpoint for assembly of the 30S ribosomal subunit. The AUCA sequence is highly conserved among bacteria, archaea, and eukaryotes, whereas the CCUCC, known as the anti-Shine-Dalgarno sequence, is conserved in noneukaryotes only. Therefore, these data suggest a common mechanism for a highly conserved ERA function in all three kingdoms of life by recognizing the AUCA, with a "twist" for noneukaryotic ERA proteins by also recognizing the CCUCC.

-	~~{{STRUCTURE_3ieu\| PDB=3ieu \| SCENE= }}~~	+	Structure of ERA in complex with the 3' end of 16S rRNA: implications for ribosome biogenesis.,Tu C, Zhou X, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14843-8. Epub 2009 Aug 17. PMID:19706445<ref>PMID:19706445</ref>

-	~~===Crystal Structure~~ of ~~ERA in Complex with GDP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19706445}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ieu]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA].~~	+

	==See Also==		==See Also==
	*[[GTP-binding protein\|GTP-binding protein]]		*[[GTP-binding protein\|GTP-binding protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019706445<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Ji, X.]]		[[Category: Ji, X.]]

OCA at 09:49, 20 October 2012

2012-10-20T09:49:29Z

←Older revision		Revision as of 09:49, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3ieu]] is a 2 chain structure ~~of [[GTP-binding protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA].	+	[[3ieu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA].

	==See Also==		==See Also==

OCA: Protected "3ieu" [edit=sysop:move=sysop]

2012-07-26T00:04:11Z

Protected "3ieu" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:04, 26 July 2012

OCA at 00:04, 26 July 2012

2012-07-26T00:04:10Z

←Older revision		Revision as of 00:04, 26 July 2012
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-	{{Seed}}
	[[Image:3ieu.png\|left\|200px]]		[[Image:3ieu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ieu", 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_3ieu\| PDB=3ieu \| SCENE= }}		{{STRUCTURE_3ieu\| PDB=3ieu \| SCENE= }}

	===Crystal Structure of ERA in Complex with GDP===		===Crystal Structure of ERA in Complex with GDP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19706445}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19706445 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19706445}}		{{ABSTRACT_PUBMED_19706445}}

	==About this Structure==		==About this Structure==
-	~~3IEU~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA].	+	[[3ieu]] is a 2 chain structure of [[GTP-binding protein]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEU OCA].
		+
		+	==See Also==
		+	*[[GTP-binding protein\|GTP-binding protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19706445~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019706445</ref><references group="xtra"/>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Ji, X.]]		[[Category: Ji, X.]]
Line 38:		Line 29:
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 14 09:54:44 2009''