1y6h - Revision history

OCA at 13:37, 13 March 2024

OCA — Wed, 13 Mar 2024 13:37:46 GMT

←Older revision		Revision as of 13:37, 13 March 2024
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	<StructureSection load='1y6h' size='340' side='right'caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1y6h' size='340' side='right'caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>~~, ~~<scene name='pdbligand=GLY:GLYCINE'>GLY</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='~~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=~~173~~ "~~Leptospira icteroides~~" ~~Noguchi 1919])~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [https://pdbe.org/1y6h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [https://www.ebi.ac.uk/pdbsum/1y6h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6h 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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [~~http~~://pdbe.org/1y6h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1y6h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6h ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DEF_LEPIN DEF_LEPIN]] 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 (By similarity).[HAMAP-Rule:MF_00163]	+	[https://www.uniprot.org/uniprot/DEF_LEPIN DEF_LEPIN] 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 (By similarity).[HAMAP-Rule:MF_00163]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1y6h 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=1y6h ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Peptide deformylase (PDF), which is essential for normal growth of bacteria but not for higher organisms, is explored as an attractive target for developing novel antibiotics. Here, we present the crystal structure of Leptospira interrogans PDF (LiPDF) at 2.2A resolution. To our knowledge, this is the first crystal structure of PDF associating in a stable dimer. The key loop (named the CD-loop: amino acid residues 66-76) near the active-site pocket adopts "closed" or "open" conformations in the two monomers forming the dimer. In the closed subunit, the CD-loop and residue Arg109 block the entry of the substrate-binding pocket, while the active-site pocket of the open subunit is occupied by the C-terminal tail from the neighbouring molecule. Moreover, a formate group, as one product of deformylisation, is observed bound with the active-site zinc ion. LiPDF displays significant structural differences in the C-terminal region compared to both type-I and type-II PDFs, suggesting a new family of PDFs.
-
-	Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans.,Zhou Z, Song X, Li Y, Gong W J Mol Biol. 2004 May 21;339(1):207-15. PMID:15123432<ref>PMID:15123432</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1y6h" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Leptospira icteroides noguchi 1919]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Peptide deformylase~~]]	+	[[Category: Leptospira interrogans]]
-	[[Category: Gong, W]]	+	[[Category: Gong W]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	[[Category: Song, X]]	+	[[Category: Song X]]
-	[[Category: Zhou, Z]]	+	[[Category: Zhou Z]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Open and close conformation]]~~	+
-	~~[[Category: Pdf~~]]	+

OCA at 10:36, 6 January 2021

OCA — Wed, 06 Jan 2021 10:36:33 GMT

←Older revision		Revision as of 10:36, 6 January 2021
Line 1:		Line 1:

	==Crystal structure of LIPDF==		==Crystal structure of LIPDF==
-	<StructureSection load='1y6h' size='340' side='right' caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1y6h' size='340' side='right'caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</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=173 "Leptospira icteroides" Noguchi 1919])</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=173 "Leptospira icteroides" Noguchi 1919])</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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://pdbe.org/1y6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6h 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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://pdbe.org/1y6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Leptospira icteroides noguchi 1919]]		[[Category: Leptospira icteroides noguchi 1919]]
		+	[[Category: Large Structures]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Gong, W]]		[[Category: Gong, W]]

OCA at 06:35, 25 April 2018

OCA — Wed, 25 Apr 2018 06:35:15 GMT

←Older revision		Revision as of 06:35, 25 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of LIPDF==		==Crystal structure of LIPDF==
	<StructureSection load='1y6h' size='340' side='right' caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1y6h' size='340' side='right' caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<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=173 "Leptospira icteroides" Noguchi 1919])</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=173 "Leptospira icteroides" Noguchi 1919])</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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://pdbe.org/1y6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h 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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://pdbe.org/1y6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y6/1y6h_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y6/1y6h_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 04:15, 9 February 2016

OCA — Tue, 09 Feb 2016 04:15:51 GMT

←Older revision		Revision as of 04:15, 9 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1y6h ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:32, 10 September 2015

OCA — Thu, 10 Sep 2015 18:32:18 GMT

←Older revision		Revision as of 18:32, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1y6h' size='340' side='right' caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1y6h' size='340' side='right' caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Leptospira_interrogans Leptospira interrogans~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</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=173 Leptospira ~~interrogans~~])</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=173 "Leptospira icteroides" Noguchi 1919])</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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h 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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://pdbe.org/1y6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1y6h" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Leptospira ~~interrogans~~]]	+	[[Category: Leptospira icteroides noguchi 1919]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Gong, W]]		[[Category: Gong, W]]

OCA at 04:21, 25 December 2014

OCA — Thu, 25 Dec 2014 04:21:52 GMT

←Older revision		Revision as of 04:21, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=173 Leptospira interrogans])</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=173 Leptospira interrogans])</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h 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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEF_LEPIN DEF_LEPIN]] 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 (By similarity).[HAMAP-Rule:MF_00163]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Leptospira interrogans]]		[[Category: Leptospira interrogans]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Gong, W.]]	+	[[Category: Gong, W]]
-	[[Category: Li, Y.]]	+	[[Category: Li, Y]]
-	[[Category: Song, X.]]	+	[[Category: Song, X]]
-	[[Category: Zhou, Z.]]	+	[[Category: Zhou, Z]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Open and close conformation]]		[[Category: Open and close conformation]]
	[[Category: Pdf]]		[[Category: Pdf]]

OCA at 19:56, 29 September 2014

OCA — Mon, 29 Sep 2014 19:56:17 GMT

←Older revision		Revision as of 19:56, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1y6h.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of LIPDF==
		+	<StructureSection load='1y6h' size='340' side='right' caption='[[1y6h]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<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=173 Leptospira interrogans])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [http://www.ebi.ac.uk/pdbsum/1y6h 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/y6/1y6h_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 ==
		+	Peptide deformylase (PDF), which is essential for normal growth of bacteria but not for higher organisms, is explored as an attractive target for developing novel antibiotics. Here, we present the crystal structure of Leptospira interrogans PDF (LiPDF) at 2.2A resolution. To our knowledge, this is the first crystal structure of PDF associating in a stable dimer. The key loop (named the CD-loop: amino acid residues 66-76) near the active-site pocket adopts "closed" or "open" conformations in the two monomers forming the dimer. In the closed subunit, the CD-loop and residue Arg109 block the entry of the substrate-binding pocket, while the active-site pocket of the open subunit is occupied by the C-terminal tail from the neighbouring molecule. Moreover, a formate group, as one product of deformylisation, is observed bound with the active-site zinc ion. LiPDF displays significant structural differences in the C-terminal region compared to both type-I and type-II PDFs, suggesting a new family of PDFs.

-	~~{{STRUCTURE_1y6h\| PDB=1y6h \| SCENE= }}~~	+	Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans.,Zhou Z, Song X, Li Y, Gong W J Mol Biol. 2004 May 21;339(1):207-15. PMID:15123432<ref>PMID:15123432</ref>

-	~~===Crystal structure~~ of ~~LIPDF===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15123432}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015123432<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Leptospira interrogans]]		[[Category: Leptospira interrogans]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]

OCA: Protected "1y6h" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 13:22:14 GMT

Protected "1y6h" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:22, 5 January 2013

OCA at 13:22, 5 January 2013

OCA — Sat, 05 Jan 2013 13:22:10 GMT

←Older revision		Revision as of 13:22, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1y6h.png\|left\|200px]]		[[Image:1y6h.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1y6h", 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_1y6h\| PDB=1y6h \| SCENE= }}		{{STRUCTURE_1y6h\| PDB=1y6h \| SCENE= }}

	===Crystal structure of LIPDF===		===Crystal structure of LIPDF===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15123432}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15123432 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15123432}}		{{ABSTRACT_PUBMED_15123432}}

	==About this Structure==		==About this Structure==
-	~~1Y6H~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA].	+	[[1y6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15123432~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015123432</ref><references group="xtra"/>
	[[Category: Leptospira interrogans]]		[[Category: Leptospira interrogans]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
Line 30:		Line 18:
	[[Category: Song, X.]]		[[Category: Song, X.]]
	[[Category: Zhou, Z.]]		[[Category: Zhou, Z.]]
		+	[[Category: Hydrolase]]
	[[Category: Open and close conformation]]		[[Category: Open and close conformation]]
	[[Category: Pdf]]		[[Category: Pdf]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:23:49 2009''

OCA at 04:23, 17 February 2009

OCA — Tue, 17 Feb 2009 04:23:50 GMT

←Older revision		Revision as of 04:23, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1Y6H is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA].	+	1Y6H is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA].

	==Reference==		==Reference==
-	~~Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans., Zhou Z, Song X, Li Y, Gong W, J Mol Biol. 2004 May 21;339(1):207-15.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15123432 15123432]~~	+	<ref group="xtra">PMID:15123432</ref><references group="xtra"/>
	[[Category: Leptospira interrogans]]		[[Category: Leptospira interrogans]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Single protein]]
	[[Category: Gong, W.]]		[[Category: Gong, W.]]
	[[Category: Li, Y.]]		[[Category: Li, Y.]]
Line 34:		Line 33:
	[[Category: Pdf]]		[[Category: Pdf]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 09~~:57:~~33 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:23:49 2009''