5jez - Revision history

OCA at 11:01, 6 September 2023

2023-09-06T11:01:42Z

←Older revision		Revision as of 11:01, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='5jez' size='340' side='right'caption='[[5jez]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5jez' size='340' side='right'caption='[[5jez]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jez]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JEZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jez]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Streptococcus_agalactiae Streptococcus agalactiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JEZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 1.7Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~OCS~~:~~CYSTEINESULFONIC~~+~~ACID~~'>~~OCS~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5jez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jez OCA], [https://pdbe.org/5jez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jez RCSB], [https://www.ebi.ac.uk/pdbsum/5jez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jez 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=5jez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jez OCA], [~~http~~://pdbe.org/5jez PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jez RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jez PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jez ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DEF_STRA3 DEF_STRA3]] 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.	+	[https://www.uniprot.org/uniprot/DEF_STRA3 DEF_STRA3] 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Peptide deformylase]]
-	[[Category: Fieulaine, S]]
-	[[Category: Giglione, C]]
-	[[Category: Meinnel, T]]
-	[[Category: Hydrolase]]
-	[[Category: Inhibitor]]
-	[[Category: N-terminal methionine excision]]
-	[[Category: Nme]]
-	[[Category: Pdf]]
	[[Category: Streptococcus agalactiae]]		[[Category: Streptococcus agalactiae]]
-	[[Category: ~~Tripeptide~~]]	+	[[Category: Fieulaine S]]
-	[[Category: ~~Type 2~~]]	+	[[Category: Giglione C]]
		+	[[Category: Meinnel T]]

OCA at 07:45, 10 June 2020

2020-06-10T07:45:54Z

←Older revision		Revision as of 07:45, 10 June 2020
Line 1:		Line 1:

	==Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Ser==		==Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Ser==
-	<StructureSection load='5jez' size='340' side='right' caption='[[5jez]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5jez' size='340' side='right'caption='[[5jez]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jez]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JEZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jez]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JEZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></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=5jez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jez OCA], [http://pdbe.org/5jez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jez RCSB], [http://www.ebi.ac.uk/pdbsum/5jez PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jez 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=5jez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jez OCA], [http://pdbe.org/5jez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jez RCSB], [http://www.ebi.ac.uk/pdbsum/5jez PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jez ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Fieulaine, S]]		[[Category: Fieulaine, S]]

OCA at 18:34, 10 December 2016

2016-12-10T18:34:41Z

←Older revision		Revision as of 18:34, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jez is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Ser==
		+	<StructureSection load='5jez' size='340' side='right' caption='[[5jez]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jez]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JEZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></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=5jez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jez OCA], [http://pdbe.org/5jez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jez RCSB], [http://www.ebi.ac.uk/pdbsum/5jez PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jez ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEF_STRA3 DEF_STRA3]] 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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae PDF could be used as PDF prototype as it allowed to get complete sets of 3-dimensional, biophysical and kinetic data with virtually any inhibitor compound. Structure-activity relationship analysis with this single reference system allowed us to reveal distinct binding modes for different PDF inhibitors and the key role of a hydrogen bond in potentiating the interaction between ligand and target. We propose this protein as an irreplaceable tool, allowing easy and relevant fine comparisons between series, to design, challenge and validate novel series of inhibitors. As proof-of-concept, we report here the design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug resistant clinical isolate.

-	~~Authors: Fieulaine~~, S., ~~Giglione~~, C., ~~Meinnel~~, T.	+	A unique peptide deformylase platform to rationally design and challenge novel active compounds.,Fieulaine S, Alves de Sousa R, Maigre L, Hamiche K, Alimi M, Bolla JM, Taleb A, Denis A, Pages JM, Artaud I, Meinnel T, Giglione C Sci Rep. 2016 Oct 20;6:35429. doi: 10.1038/srep35429. PMID:27762275<ref>PMID:27762275</ref>

-	~~Description: Crystal structure~~ of ~~type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met~~-~~Ala~~-~~Ser~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Meinnel, T~~]]	+	<div class="pdbe-citations 5jez" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Peptide deformylase]]
	[[Category: Fieulaine, S]]		[[Category: Fieulaine, S]]
	[[Category: Giglione, C]]		[[Category: Giglione, C]]
		+	[[Category: Meinnel, T]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor]]
		+	[[Category: N-terminal methionine excision]]
		+	[[Category: Nme]]
		+	[[Category: Pdf]]
		+	[[Category: Streptococcus agalactiae]]
		+	[[Category: Tripeptide]]
		+	[[Category: Type 2]]

OCA: Protected "5jez" [edit=sysop:move=sysop]

2016-05-11T01:56:54Z

Protected "5jez" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:56, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jez is ON HOLD until Paper Publication Authors: Fieulaine, S., Giglione, C., Meinnel, T. Description: Crystal structure of type 2 PDF from Strepto...

2016-05-11T01:56:52Z

New page: '''Unreleased structure''' The entry 5jez is ON HOLD until Paper Publication Authors: Fieulaine, S., Giglione, C., Meinnel, T. Description: Crystal structure of type 2 PDF from Strepto...

New page

'''Unreleased structure'''

The entry 5jez is ON HOLD until Paper Publication

Authors: Fieulaine, S., Giglione, C., Meinnel, T.

Description: Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Ser
[[Category: Unreleased Structures]]
[[Category: Meinnel, T]]
[[Category: Fieulaine, S]]
[[Category: Giglione, C]]