5kqb - Revision history

OCA at 10:13, 14 June 2023

OCA — Wed, 14 Jun 2023 10:13:30 GMT

←Older revision		Revision as of 10:13, 14 June 2023
Line 1:		Line 1:

	==Identification and structural characterization of LytU==		==Identification and structural characterization of LytU==
-	<StructureSection load='5kqb' size='340' side='right'caption='[[5kqb~~]], [[NMR_Ensembles_of_Models \| 15 NMR models~~]]' scene=''>	+	<StructureSection load='5kqb' size='340' side='right'caption='[[5kqb]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kqb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KQB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kqb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KQB 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lytM_3, AS858_11005, ERS093009_01996 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=5kqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqb OCA], [https://pdbe.org/5kqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kqb RCSB], [https://www.ebi.ac.uk/pdbsum/5kqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqb 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/Lysostaphin Lysostaphin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.75 3.4.24.75] </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=5kqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqb OCA], [~~http~~://pdbe.org/5kqb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kqb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kqb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqb ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2G1F1_STAA8 Q2G1F1_STAA8]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lysostaphin~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: Permi, P]]	+	[[Category: Permi P]]
-	[[Category: Raulinaitis, V]]	+	[[Category: Raulinaitis V]]
-	[[Category: Tossavainen, H]]	+	[[Category: Tossavainen H]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lytu]]~~	+
-	~~[[Category: Peptidoglycan]]~~	+
-	~~[[Category: Zinc~~]]	+

OCA at 13:05, 10 May 2019

OCA — Fri, 10 May 2019 13:05:43 GMT

←Older revision		Revision as of 13:05, 10 May 2019
Line 1:		Line 1:

	==Identification and structural characterization of LytU==		==Identification and structural characterization of LytU==
-	<StructureSection load='5kqb' size='340' side='right' caption='[[5kqb]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>	+	<StructureSection load='5kqb' size='340' side='right'caption='[[5kqb]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kqb]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KQB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kqb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KQB 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lytM_3, AS858_11005, ERS093009_01996 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysostaphin Lysostaphin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.75 3.4.24.75] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysostaphin Lysostaphin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.75 3.4.24.75] </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=5kqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqb OCA], [http://pdbe.org/5kqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kqb RCSB], [http://www.ebi.ac.uk/pdbsum/5kqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqb ProSAT]</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=5kqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqb OCA], [http://pdbe.org/5kqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kqb RCSB], [http://www.ebi.ac.uk/pdbsum/5kqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqb ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lysostaphin]]		[[Category: Lysostaphin]]
	[[Category: Permi, P]]		[[Category: Permi, P]]

OCA at 03:59, 4 August 2017

OCA — Fri, 04 Aug 2017 03:59:26 GMT

←Older revision		Revision as of 03:59, 4 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kqb is ~~ON HOLD until Paper~~ Publication	+	==Identification and structural characterization of LytU==
		+	<StructureSection load='5kqb' size='340' side='right' caption='[[5kqb]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kqb]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KQB 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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysostaphin Lysostaphin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.75 3.4.24.75] </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=5kqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqb OCA], [http://pdbe.org/5kqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kqb RCSB], [http://www.ebi.ac.uk/pdbsum/5kqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqb ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the overall structure common to the lysostaphin family. Purified LytU lyses S. aureus cells and cleaves pentaglycine, a reaction conveniently monitored by NMR spectroscopy. Substituting the cofactor zinc ion with a copper or cobalt ion remarkably increases the rate of pentaglycine cleavage. NMR and isothermal titration calorimetry further reveal that, uniquely for its family, LytU is able to bind a second zinc ion which is coordinated by catalytic histidines and is therefore inhibitory. The pH-dependence and high affinity of binding carry further physiological implications.

-	~~Authors: Raulinaitis~~, V., ~~Tossavainen~~, H., ~~Permi~~, P.	+	Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family.,Raulinaitis V, Tossavainen H, Aitio O, Juuti JT, Hiramatsu K, Kontinen V, Permi P Sci Rep. 2017 Jul 20;7(1):6020. doi: 10.1038/s41598-017-06135-w. PMID:28729697<ref>PMID:28729697</ref>

-	~~Description: Identification and structural characterization~~ of ~~LytU~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5kqb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lysostaphin]]
		+	[[Category: Permi, P]]
	[[Category: Raulinaitis, V]]		[[Category: Raulinaitis, V]]
	[[Category: Tossavainen, H]]		[[Category: Tossavainen, H]]
-	[[Category: ~~Permi, P~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Lytu]]
		+	[[Category: Peptidoglycan]]
		+	[[Category: Zinc]]

OCA at 10:22, 9 March 2017

OCA — Thu, 09 Mar 2017 10:22:21 GMT

←Older revision		Revision as of 10:22, 9 March 2017
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	Description: Identification and structural characterization of LytU		Description: Identification and structural characterization of LytU
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Tossavainen, H]]
	[[Category: Raulinaitis, V]]		[[Category: Raulinaitis, V]]
		+	[[Category: Tossavainen, H]]
	[[Category: Permi, P]]		[[Category: Permi, P]]

OCA at 12:42, 26 July 2016

OCA — Tue, 26 Jul 2016 12:42:57 GMT

←Older revision		Revision as of 12:42, 26 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kqb is ON HOLD	+	The entry 5kqb is ON HOLD until Paper Publication

	Authors: Raulinaitis, V., Tossavainen, H., Permi, P.		Authors: Raulinaitis, V., Tossavainen, H., Permi, P.

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

OCA — Thu, 14 Jul 2016 09:34:52 GMT

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

←Older revision

Revision as of 09:34, 14 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kqb is ON HOLD Authors: Raulinaitis, V., Tossavainen, H., Permi, P. Description: Identification and structural characterization of LytU [[Category...

OCA — Thu, 14 Jul 2016 09:34:50 GMT

New page: '''Unreleased structure''' The entry 5kqb is ON HOLD Authors: Raulinaitis, V., Tossavainen, H., Permi, P. Description: Identification and structural characterization of LytU [[Category...

New page

'''Unreleased structure'''

The entry 5kqb is ON HOLD

Authors: Raulinaitis, V., Tossavainen, H., Permi, P.

Description: Identification and structural characterization of LytU
[[Category: Unreleased Structures]]
[[Category: Tossavainen, H]]
[[Category: Raulinaitis, V]]
[[Category: Permi, P]]