5dvp - Revision history

OCA at 22:01, 28 June 2023

OCA — Wed, 28 Jun 2023 22:01:53 GMT

←Older revision		Revision as of 22:01, 28 June 2023
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	==Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct==		==Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct==
-	<StructureSection load='5dvp' size='340' side='right' caption='[[5dvp]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='5dvp' size='340' side='right'caption='[[5dvp]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dvp]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DVP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dvp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DVP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DRW:(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>DRW</scene>, <scene name='pdbligand=POA:PHOSPHONOACETALDEHYDE'>POA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.18Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5duj\|5duj]], [[5du7\|5du7]], [[5dvq\|5dvq]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DRW:(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>DRW</scene>, <scene name='pdbligand=POA:PHOSPHONOACETALDEHYDE'>POA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=5dvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvp OCA], [https://pdbe.org/5dvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dvp RCSB], [https://www.ebi.ac.uk/pdbsum/5dvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dvp 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=5dvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvp OCA], [~~http~~://pdbe.org/5dvp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dvp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dvp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dvp ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LDT2_MYCTU LDT2_MYCTU]] Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems.<ref>PMID:24041897</ref>	+	[https://www.uniprot.org/uniprot/LDT2_MYCTU LDT2_MYCTU] Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems.<ref>PMID:24041897</ref>
	<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: ~~Myctu~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kumar, P~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: ~~Lamichhane, G~~]]	+	[[Category: Kumar P]]
-	[[Category: ~~Cell wall enzyme]]~~	+	[[Category: Lamichhane G]]
-	~~[[Category: Peptidoglycan synthesis enzyme]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 16:58, 15 November 2017

OCA — Wed, 15 Nov 2017 16:58:45 GMT

←Older revision		Revision as of 16:58, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5dvp' size='340' side='right' caption='[[5dvp]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='5dvp' size='340' side='right' caption='[[5dvp]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dvp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DVP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DVP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DRW:(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>DRW</scene>, <scene name='pdbligand=POA:PHOSPHONOACETALDEHYDE'>POA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DRW:(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>DRW</scene>, <scene name='pdbligand=POA:PHOSPHONOACETALDEHYDE'>POA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5duj\|5duj]], [[5du7\|5du7]], [[5dvq\|5dvq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5duj\|5duj]], [[5du7\|5du7]], [[5dvq\|5dvq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=5dvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvp OCA], [http://pdbe.org/5dvp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dvp RCSB], [http://www.ebi.ac.uk/pdbsum/5dvp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dvp 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=5dvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvp OCA], [http://pdbe.org/5dvp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dvp RCSB], [http://www.ebi.ac.uk/pdbsum/5dvp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dvp ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Myctu]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]
	[[Category: Lamichhane, G]]		[[Category: Lamichhane, G]]

OCA at 20:04, 9 December 2016

OCA — Fri, 09 Dec 2016 20:04:25 GMT

←Older revision		Revision as of 20:04, 9 December 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/LDT2_MYCTU LDT2_MYCTU]] Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems.<ref>PMID:24041897</ref>		[[http://www.uniprot.org/uniprot/LDT2_MYCTU LDT2_MYCTU]] Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems.<ref>PMID:24041897</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial survival requires an intact peptidoglycan layer, a three-dimensional exoskeleton that encapsulates the cytoplasmic membrane. Historically, the final steps of peptidoglycan synthesis are known to be carried out by D,D-transpeptidases, enzymes that are inhibited by the beta-lactams, which constitute >50% of all antibacterials in clinical use. Here, we show that the carbapenem subclass of beta-lactams are distinctly effective not only because they inhibit D,D-transpeptidases and are poor substrates for beta-lactamases, but primarily because they also inhibit non-classical transpeptidases, namely the L,D-transpeptidases, which generate the majority of linkages in the peptidoglycan of mycobacteria. We have characterized the molecular mechanisms responsible for inhibition of L,D-transpeptidases of Mycobacterium tuberculosis and a range of bacteria including ESKAPE pathogens, and used this information to design, synthesize and test simplified carbapenems with potent antibacterial activity.
		+
		+	Non-classical transpeptidases yield insight into new antibacterials.,Kumar P, Kaushik A, Lloyd EP, Li SG, Mattoo R, Ammerman NC, Bell DT, Perryman AL, Zandi TA, Ekins S, Ginell SL, Townsend CA, Freundlich JS, Lamichhane G Nat Chem Biol. 2016 Nov 7. doi: 10.1038/nchembio.2237. PMID:27820797<ref>PMID:27820797</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5dvp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:05, 3 October 2016

OCA — Mon, 03 Oct 2016 17:05:55 GMT

←Older revision		Revision as of 17:05, 3 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5dvp is ON HOLD until Paper Publication~~	+	==Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct==
-		+	<StructureSection load='5dvp' size='340' side='right' caption='[[5dvp]], [[Resolution\|resolution]] 2.18Å' scene=''>
-	~~Authors: Kumar, P., Lamichhane, G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5dvp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DVP FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DRW:(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>DRW</scene>, <scene name='pdbligand=POA:PHOSPHONOACETALDEHYDE'>POA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5duj\|5duj]], [[5du7\|5du7]], [[5dvq\|5dvq]]</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=5dvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvp OCA], [http://pdbe.org/5dvp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dvp RCSB], [http://www.ebi.ac.uk/pdbsum/5dvp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dvp ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LDT2_MYCTU LDT2_MYCTU]] Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems.<ref>PMID:24041897</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kumar, P]]		[[Category: Kumar, P]]
	[[Category: Lamichhane, G]]		[[Category: Lamichhane, G]]
		+	[[Category: Cell wall enzyme]]
		+	[[Category: Peptidoglycan synthesis enzyme]]
		+	[[Category: Transferase]]

OCA at 02:13, 1 December 2015

OCA — Tue, 01 Dec 2015 02:13:05 GMT

←Older revision		Revision as of 02:13, 1 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kumar, P., Lamichhane, G.		Authors: Kumar, P., Lamichhane, G.

-	Description: Crystal structure of ~~ldtMt2~~ with Doripenem adduct	+	Description: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]
	[[Category: Lamichhane, G]]		[[Category: Lamichhane, G]]

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

OCA — Wed, 30 Sep 2015 13:35:51 GMT

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

←Older revision

Revision as of 13:35, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dvp is ON HOLD Authors: Kumar, P., Lamichhane, G. Description: Crystal structure of ldtMt2 with Doripenem adduct [[Category: Unreleased Structures...

OCA — Wed, 30 Sep 2015 13:35:49 GMT

New page: '''Unreleased structure''' The entry 5dvp is ON HOLD Authors: Kumar, P., Lamichhane, G. Description: Crystal structure of ldtMt2 with Doripenem adduct [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 5dvp is ON HOLD

Authors: Kumar, P., Lamichhane, G.

Description: Crystal structure of ldtMt2 with Doripenem adduct
[[Category: Unreleased Structures]]
[[Category: Kumar, P]]
[[Category: Lamichhane, G]]