3pn6 - Revision history

OCA at 09:57, 6 September 2023

OCA — Wed, 06 Sep 2023 09:57:14 GMT

←Older revision		Revision as of 09:57, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3pn6' size='340' side='right'caption='[[3pn6]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3pn6' size='340' side='right'caption='[[3pn6]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pn6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PN6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pn6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PN6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 2.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[3pn2\|3pn2]]~~, [[~~3pn3~~\|~~3pn3~~]]~~, [[3pn4\|3pn4]], [[3pn5\|3pn5]], [[3m6o\|3m6o]], [[3m6p\|3m6p]], [[3o3j\|3o3j]], [[3m6q\|3m6q]], [[3m6r\|3m6r]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DEF2, PDF1B ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3702 ARATH])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88]~~ </~~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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [https://pdbe.org/3pn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [https://www.ebi.ac.uk/pdbsum/3pn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pn6 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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [https://pdbe.org/3pn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [https://www.ebi.ac.uk/pdbsum/3pn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pn6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref>	+	[https://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peptide deformylase]]~~	+	[[Category: Fieulaine S]]
-	[[Category: Fieulaine, S]]	+	[[Category: Giglione C]]
-	[[Category: Giglione, C]]	+	[[Category: Meinnel T]]
-	[[Category: Meinnel, T]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Induced-fit]]~~	+
-	~~[[Category: N-terminal excision pathway]]~~	+
-	~~[[Category: Nme]]~~	+
-	~~[[Category: Pdf~~]]	+

OCA at 08:46, 25 May 2022

OCA — Wed, 25 May 2022 08:46:41 GMT

←Older revision		Revision as of 08:46, 25 May 2022
Line 1:		Line 1:

	==Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant==		==Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant==
-	<StructureSection load='3pn6' size='340' side='right' caption='[[3pn6]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3pn6' size='340' side='right'caption='[[3pn6]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pn6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PN6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pn6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PN6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pn2\|3pn2]], [[3pn3\|3pn3]], [[3pn4\|3pn4]], [[3pn5\|3pn5]], [[3m6o\|3m6o]], [[3m6p\|3m6p]], [[3o3j\|3o3j]], [[3m6q\|3m6q]], [[3m6r\|3m6r]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pn2\|3pn2]], [[3pn3\|3pn3]], [[3pn4\|3pn4]], [[3pn5\|3pn5]], [[3m6o\|3m6o]], [[3m6p\|3m6p]], [[3o3j\|3o3j]], [[3m6q\|3m6q]], [[3m6r\|3m6r]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF2, PDF1B ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF2, PDF1B ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [~~http~~://pdbe.org/3pn6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3pn6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3pn6 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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [https://pdbe.org/3pn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [https://www.ebi.ac.uk/pdbsum/3pn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pn6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref>	+	[[https://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Arath]]		[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Fieulaine, S]]		[[Category: Fieulaine, S]]

OCA at 15:24, 4 August 2016

OCA — Thu, 04 Aug 2016 15:24:31 GMT

←Older revision		Revision as of 15:24, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant==		==Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant==
	<StructureSection load='3pn6' size='340' side='right' caption='[[3pn6]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3pn6' size='340' side='right' caption='[[3pn6]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pn6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arabidopsis_thaliana Arabidopsis thaliana~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PN6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pn6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PN6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pn2\|3pn2]], [[3pn3\|3pn3]], [[3pn4\|3pn4]], [[3pn5\|3pn5]], [[3m6o\|3m6o]], [[3m6p\|3m6p]], [[3o3j\|3o3j]], [[3m6q\|3m6q]], [[3m6r\|3m6r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pn2\|3pn2]], [[3pn3\|3pn3]], [[3pn4\|3pn4]], [[3pn5\|3pn5]], [[3m6o\|3m6o]], [[3m6p\|3m6p]], [[3o3j\|3o3j]], [[3m6q\|3m6q]], [[3m6r\|3m6r]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF2, PDF1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ~~Arabidopsis thaliana~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF2, PDF1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [http://www.ebi.ac.uk/pdbsum/3pn6 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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [http://pdbe.org/3pn6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [http://www.ebi.ac.uk/pdbsum/3pn6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pn6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3pn6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arabidopsis thaliana~~]]	+	[[Category: Arath]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Fieulaine, S]]		[[Category: Fieulaine, S]]

OCA at 10:32, 25 December 2014

OCA — Thu, 25 Dec 2014 10:32:03 GMT

←Older revision		Revision as of 10:32, 25 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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [http://www.ebi.ac.uk/pdbsum/3pn6 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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [http://www.ebi.ac.uk/pdbsum/3pn6 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 11:01, 19 December 2014

OCA — Fri, 19 Dec 2014 11:01:29 GMT

←Older revision		Revision as of 11:01, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3pn6\| PDB=3pn6 \| SCENE= }}~~	+	==Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant==
-	===Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant===	+	<StructureSection load='3pn6' size='340' side='right' caption='[[3pn6]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21629676}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3pn6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PN6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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">[[3pn2\|3pn2]], [[3pn3\|3pn3]], [[3pn4\|3pn4]], [[3pn5\|3pn5]], [[3m6o\|3m6o]], [[3m6p\|3m6p]], [[3o3j\|3o3j]], [[3m6q\|3m6q]], [[3m6r\|3m6r]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DEF2, PDF1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=3pn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pn6 RCSB], [http://www.ebi.ac.uk/pdbsum/3pn6 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.

-	~~==Function==~~	+	Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis.,Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C PLoS Biol. 2011 May;9(5):e1001066. Epub 2011 May 24. PMID:21629676<ref>PMID:21629676</ref>
-	~~[[http~~:~~//www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH]] Removes~~ the ~~formyl group from the N-terminal Met~~ of ~~newly synthesized proteins~~. ~~Has a preferred substrate specificity towards the photosystem II~~ (~~PS II~~) ~~D1 polypeptide~~.<ref>PMID:~~11060042~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3pn6]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021629676</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Fieulaine, S.]]	+	[[Category: Fieulaine, S]]
-	[[Category: Giglione, C.]]	+	[[Category: Giglione, C]]
-	[[Category: Meinnel, T~~.]]~~	+	[[Category: Meinnel, T]]
-	~~[[Category: 1b~~]]	+
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Induced-fit]]		[[Category: Induced-fit]]
Line 22:		Line 31:
	[[Category: Nme]]		[[Category: Nme]]
	[[Category: Pdf]]		[[Category: Pdf]]
-	[[Category: Peptide deformylase]]

OCA at 08:02, 16 May 2013

OCA — Thu, 16 May 2013 08:02:18 GMT

←Older revision		Revision as of 08:02, 16 May 2013
Line 1:		Line 1:
-	[[Image:3pn6.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3pn6", 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_3pn6\| PDB=3pn6 \| SCENE= }}		{{STRUCTURE_3pn6\| PDB=3pn6 \| SCENE= }}
-
	===Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant===		===Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant===
		+	{{ABSTRACT_PUBMED_21629676}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21629676}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 21629676 is~~ the ~~PubMed ID number.~~	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21629676}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021629676</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021629676</ref><references group="xtra"/><references/>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]

OCA at 07:29, 13 July 2011

OCA — Wed, 13 Jul 2011 07:29:11 GMT

←Older revision		Revision as of 07:29, 13 July 2011
Line 1:		Line 1:
-	[[Image:3pn6.~~jpg~~\|left\|200px]]	+	[[Image:3pn6.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant===		===Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21629676}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21629676 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21629676}}

	==About this Structure==		==About this Structure==
	[[3pn6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA].		[[3pn6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021629676</ref><references group="xtra"/>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
Line 19:		Line 28:
	[[Category: Giglione, C.]]		[[Category: Giglione, C.]]
	[[Category: Meinnel, T.]]		[[Category: Meinnel, T.]]
		+	[[Category: 1b]]
		+	[[Category: Hydrolase]]
		+	[[Category: Induced-fit]]
		+	[[Category: N-terminal excision pathway]]
		+	[[Category: Nme]]
		+	[[Category: Pdf]]
		+	[[Category: Peptide deformylase]]

OCA: Protected "3pn6" [edit=sysop:move=sysop]

OCA — Wed, 08 Jun 2011 05:21:50 GMT

Protected "3pn6" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:21, 8 June 2011

OCA at 05:21, 8 June 2011

OCA — Wed, 08 Jun 2011 05:21:47 GMT

←Older revision		Revision as of 05:21, 8 June 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3pn6.jpg\|left\|200px]]

-	The ~~entry 3pn6~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3pn6", 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_3pn6\| PDB=3pn6 \| SCENE= }}

-	~~Authors: Fieulaine, S., Meinnel, T., Giglione, C.~~	+	===Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant===

-	Description: Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Dec 15 08~~:24:~~24 2010''~~	+	==About this Structure==
		+	[[3pn6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN6 OCA].
		+	[[Category: Arabidopsis thaliana]]
		+	[[Category: Peptide deformylase]]
		+	[[Category: Fieulaine, S.]]
		+	[[Category: Giglione, C.]]
		+	[[Category: Meinnel, T.]]

OCA at 05:12, 15 December 2010

OCA — Wed, 15 Dec 2010 05:12:04 GMT

←Older revision		Revision as of 05:12, 15 December 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3pn6 is ON HOLD	+	The entry 3pn6 is ON HOLD until Paper Publication

	Authors: Fieulaine, S., Meinnel, T., Giglione, C.		Authors: Fieulaine, S., Meinnel, T., Giglione, C.
Line 7:		Line 7:
	Description: Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant		Description: Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec ~~1 11~~:14:21 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 15 08:24:24 2010''