1bs8 - Revision history

OCA at 05:42, 9 August 2023

2023-08-09T05:42:06Z

← Older revision		Revision as of 05:42, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='1bs8' size='340' side='right'caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1bs8' size='340' side='right'caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bs4\|1bs4]]~~, [[~~1bs5~~\|~~1bs5]], [[1bs6\|1bs6]], [[1bs7\|1bs7]], [[1bsz\|1bsz~~]]</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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"~~>DEF ([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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [https://pdbe.org/1bs8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [https://www.ebi.ac.uk/pdbsum/1bs8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs8 ProSAT]</span></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31]~~ </~~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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [~~http~~://pdbe.org/1bs8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1bs8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]		[https://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~		[[Category: Escherichia coli]]
	~~[[Category: Formylmethionine deformylase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Becker, A]]		[[Category: Becker A]]
	[[Category: Groche, D]]		[[Category: Groche D]]
	[[Category: Kabsch, W]]		[[Category: Kabsch W]]
	[[Category: Schlichting, I]]		[[Category: Schlichting I]]
	[[Category: Schultz, S]]		[[Category: Schultz S]]
	[[Category: Wagner~~, A F.V]]~~		[[Category: Wagner AFV]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Iron metalloprotease]]~~
	~~[[Category: Protein synthesis~~]]

OCA at 10:15, 18 November 2020

2020-11-18T10:15:34Z

← Older revision		Revision as of 10:15, 18 November 2020
Line 1:		Line 1:

	==PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER==		==PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER==
	<StructureSection load='1bs8' size='340' side='right' caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1bs8' size='340' side='right'caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</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">[[1bs4\|1bs4]], [[1bs5\|1bs5]], [[1bs6\|1bs6]], [[1bs7\|1bs7]], [[1bsz\|1bsz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bs4\|1bs4]], [[1bs5\|1bs5]], [[1bs6\|1bs6]], [[1bs7\|1bs7]], [[1bsz\|1bsz]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF ([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">DEF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://pdbe.org/1bs8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs8 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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://pdbe.org/1bs8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bs/1bs8_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bs/1bs8_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>
Line 37:		Line 37:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Formylmethionine deformylase]]		[[Category: Formylmethionine deformylase]]
			[[Category: Large Structures]]
	[[Category: Becker, A]]		[[Category: Becker, A]]
	[[Category: Groche, D]]		[[Category: Groche, D]]

OCA at 08:06, 29 November 2017

2017-11-29T08:06:35Z

← Older revision		Revision as of 08:06, 29 November 2017
Line 1:		Line 1:

	==PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER==		==PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER==
	<StructureSection load='1bs8' size='340' side='right' caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1bs8' size='340' side='right' caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF ([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">DEF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://pdbe.org/1bs8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://pdbe.org/1bs8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 10:44, 8 February 2016

2016-02-08T10:44:29Z

← Older revision		Revision as of 10:44, 8 February 2016
Line 19:		Line 19:
	<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=1bs8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:46, 10 September 2015

2015-09-10T10:46:36Z

← Older revision		Revision as of 10:46, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1bs8' size='340' side='right' caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1bs8' size='340' side='right' caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</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">[[1bs4\|1bs4]], [[1bs5\|1bs5]], [[1bs6\|1bs6]], [[1bs7\|1bs7]], [[1bsz\|1bsz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bs4\|1bs4]], [[1bs5\|1bs5]], [[1bs6\|1bs6]], [[1bs7\|1bs7]], [[1bsz\|1bsz]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF ([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">DEF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://pdbe.org/1bs8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1bs8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Formylmethionine deformylase]]		[[Category: Formylmethionine deformylase]]
	[[Category: Becker, A]]		[[Category: Becker, A]]

OCA at 22:46, 24 December 2014

2014-12-24T22:46:20Z

← Older revision		Revision as of 22:46, 24 December 2014
Line 9:		Line 9:
	<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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:34, 22 December 2014

2014-12-22T09:34:31Z

← Older revision		Revision as of 09:34, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bs4\|1bs4]], [[1bs5\|1bs5]], [[1bs6\|1bs6]], [[1bs7\|1bs7]], [[1bsz\|1bsz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bs4\|1bs4]], [[1bs5\|1bs5]], [[1bs6\|1bs6]], [[1bs7\|1bs7]], [[1bsz\|1bsz]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF ([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">DEF ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </span></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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 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 33:		Line 33:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Formylmethionine deformylase]]		[[Category: Formylmethionine deformylase]]
	[[Category: Becker, A.]]		[[Category: Becker, A]]
	[[Category: Groche, D.]]		[[Category: Groche, D]]
	[[Category: Kabsch, W.]]		[[Category: Kabsch, W]]
	[[Category: Schlichting, I.]]		[[Category: Schlichting, I]]
	[[Category: Schultz, S.]]		[[Category: Schultz, S]]
	[[Category: Wagner, A F.V.]]		[[Category: Wagner, A F.V]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Iron metalloprotease]]		[[Category: Iron metalloprotease]]
	[[Category: Protein synthesis]]		[[Category: Protein synthesis]]

OCA at 09:37, 13 August 2014

2014-08-13T09:37:12Z

← Older revision		Revision as of 09:37, 13 August 2014
Line 1:		Line 1:
	[[Image:~~1bs8~~.~~png~~\|~~left~~\|~~200px~~]]		==PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER==
			<StructureSection load='1bs8' size='340' side='right' caption='[[1bs8]], [[Resolution\|resolution]] 2.20Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1bs8]] is a 6 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=1BS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BS8 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bs4\|1bs4]], [[1bs5\|1bs5]], [[1bs6\|1bs6]], [[1bs7\|1bs7]], [[1bsz\|1bsz]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </span></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=1bs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bs8 RCSB], [http://www.ebi.ac.uk/pdbsum/1bs8 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/bs/1bs8_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 ==
			Eubacterial proteins are synthesized with a formyl group at the N-terminus which is hydrolytically removed from the nascent chain by the mononuclear iron enzyme peptide deformylase. Catalytic efficiency strongly depends on the identity of the bound metal. We have determined by X-ray crystallography the Fe2+, Ni2+ and Zn2+ forms of the Escherichia coli enzyme and a structure in complex with the reaction product Met-Ala-Ser. The structure of the complex, with the tripeptide bound at the active site, suggests detailed models for the mechanism of substrate recognition and catalysis. Differences of the protein structures due to the identity of the bound metal are extremely small and account only for the observation that Zn2+ binds more tightly than Fe2+ or Ni2+. The striking loss of catalytic activity of the Zn2+ form could be caused by its reluctance to change between tetrahedral and five-fold metal coordination believed to occur during catalysis. N-terminal formylation and subsequent deformylation

	~~{{STRUCTURE_1bs8\| PDB=1bs8 \| SCENE= }}~~		Iron center, substrate recognition and mechanism of peptide deformylase.,Becker A, Schlichting I, Kabsch W, Groche D, Schultz S, Wagner AF Nat Struct Biol. 1998 Dec;5(12):1053-8. PMID:9846875<ref>PMID:9846875</ref>

	~~===PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_9846875}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[1bs8]] is~~ a ~~6 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=1BS8 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:009846875<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Formylmethionine deformylase]]		[[Category: Formylmethionine deformylase]]

OCA: Protected "1bs8" [edit=sysop:move=sysop]

2012-10-21T20:02:51Z

Protected "1bs8" [edit=sysop:move=sysop]

← Older revision	Revision as of 20:02, 21 October 2012
(No difference)

OCA at 20:02, 21 October 2012

2012-10-21T20:02:49Z

← Older revision		Revision as of 20:02, 21 October 2012
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:1bs8.png\|left\|200px]]		[[Image:1bs8.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1bs8", 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_1bs8\| PDB=1bs8 \| SCENE= }}		{{STRUCTURE_1bs8\| PDB=1bs8 \| SCENE= }}

	===PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER===		===PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_9846875}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 9846875 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_9846875}}		{{ABSTRACT_PUBMED_9846875}}

	==About this Structure==		==About this Structure==
	~~1BS8~~ is a 6 ~~chains~~ structure ~~of sequences~~ 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=1BS8 OCA].		[[1bs8]] is a 6 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=1BS8 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~9846875~~</ref><references group="xtra"/>		<ref group="xtra">PMID:009846875</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Formylmethionine deformylase]]		[[Category: Formylmethionine deformylase]]
Line 35:		Line 23:
	[[Category: Iron metalloprotease]]		[[Category: Iron metalloprotease]]
	[[Category: Protein synthesis]]		[[Category: Protein synthesis]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:25:50 2009''~~