1zfn - Revision history

OCA at 09:04, 14 February 2024

OCA — Wed, 14 Feb 2024 09:04:45 GMT

←Older revision		Revision as of 09:04, 14 February 2024
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	<StructureSection load='1zfn' size='340' side='right'caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='1zfn' size='340' side='right'caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ATP:ADENOSINE~~-~~5-TRIPHOSPHATE'>ATP</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.75Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [https://pdbe.org/1zfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [https://www.ebi.ac.uk/pdbsum/1zfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zfn 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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [~~http~~://pdbe.org/1zfn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1zfn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1zfn ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/THIF_ECOLI THIF_ECOLI]] Catalyzes the adenylation by ATP of the carboxyl group of the C-terminal glycine of sulfur carrier protein ThiS.	+	[https://www.uniprot.org/uniprot/THIF_ECOLI THIF_ECOLI] Catalyzes the adenylation by ATP of the carboxyl group of the C-terminal glycine of sulfur carrier protein ThiS.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1zfn 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=1zfn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Escherichia coli ThiF is an enzyme in the biosynthetic cascade for generating the essential cofactor thiamin pyrophosphate. In this cascade, ThiF catalyzes adenylation of the C terminus of ThiS. We report here the crystal structures of ThiF, alone and in complex with ATP. The structures provide insight into a preference for ATP during adenylation of the protein ThiS. Additionally, the structures reveal an ordered crossover loop predicted to clamp the flexible tail of ThiS into the ThiF active site during the adenylation reaction. The importance of the crossover loop for ThiF activity is highlighted by mutational analysis. Comparison of ThiF with the structural homologues MoeB, APPBP1-UBA3, and SAE1-SAE2 reveals that the ATP-binding site, including an arginine-finger, is maintained throughout evolution, and shows divergence occurring in protein substrate-binding sites and regions devoted to unique steps in the specific function of each enzyme.
-
-	Structural analysis of Escherichia coli ThiF.,Duda DM, Walden H, Sfondouris J, Schulman BA J Mol Biol. 2005 Jun 17;349(4):774-86. PMID:15896804<ref>PMID:15896804</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1zfn" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Duda~~, D M~~]]	+	[[Category: Duda DM]]
-	[[Category: Schulman~~, B A~~]]	+	[[Category: Schulman BA]]
-	[[Category: Sfondouris, J]]	+	[[Category: Sfondouris J]]
-	[[Category: Walden, H]]	+	[[Category: Walden H]]
-	~~[[Category: Adenylation]]~~	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: P-loop]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: These]]~~	+
-	~~[[Category: Thif]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:03, 20 January 2021

OCA — Wed, 20 Jan 2021 09:03:15 GMT

←Older revision		Revision as of 09:03, 20 January 2021
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	==Structural Analysis of Escherichia coli ThiF==		==Structural Analysis of Escherichia coli ThiF==
-	<StructureSection load='1zfn' size='340' side='right' caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='1zfn' size='340' side='right'caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://pdbe.org/1zfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zfn 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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://pdbe.org/1zfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zfn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Duda, D M]]		[[Category: Duda, D M]]
	[[Category: Schulman, B A]]		[[Category: Schulman, B A]]

OCA at 08:56, 2 May 2018

OCA — Wed, 02 May 2018 08:56:10 GMT

←Older revision		Revision as of 08:56, 2 May 2018
Line 1:		Line 1:
		+
	==Structural Analysis of Escherichia coli ThiF==		==Structural Analysis of Escherichia coli ThiF==
	<StructureSection load='1zfn' size='340' side='right' caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='1zfn' size='340' side='right' caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://pdbe.org/1zfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn 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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://pdbe.org/1zfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zfn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/zf/1zfn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zf/1zfn_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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	[[Category: P-loop]]		[[Category: P-loop]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
-	[[Category: Thif]]
	[[Category: These]]		[[Category: These]]
		+	[[Category: Thif]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 04:28, 7 February 2016

OCA — Sun, 07 Feb 2016 04:28:51 GMT

←Older revision		Revision as of 04:28, 7 February 2016
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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=1zfn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:50, 9 September 2015

OCA — Wed, 09 Sep 2015 21:50:50 GMT

←Older revision		Revision as of 21:50, 9 September 2015
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn 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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://pdbe.org/1zfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 1zfn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:51, 24 December 2014

OCA — Wed, 24 Dec 2014 07:51:56 GMT

←Older revision		Revision as of 07:51, 24 December 2014
Line 8:		Line 8:
	<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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn 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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THIF_ECOLI THIF_ECOLI]] Catalyzes the adenylation by ATP of the carboxyl group of the C-terminal glycine of sulfur carrier protein ThiS.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:20, 19 November 2014

OCA — Wed, 19 Nov 2014 09:20:15 GMT

←Older revision		Revision as of 09:20, 19 November 2014
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	<StructureSection load='1zfn' size='340' side='right' caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='1zfn' size='340' side='right' caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn 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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn PDBsum]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Duda, D M]]		[[Category: Duda, D M]]
	[[Category: Schulman, B A]]		[[Category: Schulman, B A]]

OCA at 07:15, 12 November 2014

OCA — Wed, 12 Nov 2014 07:15:13 GMT

←Older revision		Revision as of 07:15, 12 November 2014
Line 2:		Line 2:
	<StructureSection load='1zfn' size='340' side='right' caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='1zfn' size='340' side='right' caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn 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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn PDBsum]</span></td></tr>
	</table>		</table>
Line 30:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Escherichia coli]]~~	+	[[Category: Duda, D M]]
-	[[Category: Duda, D M.]]	+	[[Category: Schulman, B A]]
-	[[Category: Schulman, B A.]]	+	[[Category: Sfondouris, J]]
-	[[Category: Sfondouris, J.]]	+	[[Category: Walden, H]]
-	[[Category: Walden, H.]]	+
	[[Category: Adenylation]]		[[Category: Adenylation]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 14:16, 3 November 2014

OCA — Mon, 03 Nov 2014 14:16:50 GMT

←Older revision		Revision as of 14:16, 3 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn 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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 38:
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: P-loop]]		[[Category: P-loop]]
-	[[Category: ~~Rossman~~ fold]]	+	[[Category: Rossmann fold]]
	[[Category: Thif]]		[[Category: Thif]]
	[[Category: These]]		[[Category: These]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 18:58, 29 September 2014

OCA — Mon, 29 Sep 2014 18:58:54 GMT

←Older revision		Revision as of 18:58, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1zfn.~~png~~\|~~left~~\|200px]]	+	==Structural Analysis of Escherichia coli ThiF==
		+	<StructureSection load='1zfn' size='340' side='right' caption='[[1zfn]], [[Resolution\|resolution]] 2.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1zfn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZFN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jwa\|1jwa]], [[1jw9\|1jw9]], [[1jwb\|1jwb]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">thiF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1zfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zfn RCSB], [http://www.ebi.ac.uk/pdbsum/1zfn 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/zf/1zfn_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 ==
		+	Escherichia coli ThiF is an enzyme in the biosynthetic cascade for generating the essential cofactor thiamin pyrophosphate. In this cascade, ThiF catalyzes adenylation of the C terminus of ThiS. We report here the crystal structures of ThiF, alone and in complex with ATP. The structures provide insight into a preference for ATP during adenylation of the protein ThiS. Additionally, the structures reveal an ordered crossover loop predicted to clamp the flexible tail of ThiS into the ThiF active site during the adenylation reaction. The importance of the crossover loop for ThiF activity is highlighted by mutational analysis. Comparison of ThiF with the structural homologues MoeB, APPBP1-UBA3, and SAE1-SAE2 reveals that the ATP-binding site, including an arginine-finger, is maintained throughout evolution, and shows divergence occurring in protein substrate-binding sites and regions devoted to unique steps in the specific function of each enzyme.

-	~~{{STRUCTURE_1zfn\| PDB=1zfn \| SCENE= }}~~	+	Structural analysis of Escherichia coli ThiF.,Duda DM, Walden H, Sfondouris J, Schulman BA J Mol Biol. 2005 Jun 17;349(4):774-86. PMID:15896804<ref>PMID:15896804</ref>

-	~~===Structural Analysis~~ of ~~Escherichia coli ThiF===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15896804}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1zfn]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFN OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015896804<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Duda, D M.]]		[[Category: Duda, D M.]]