6d4k - Revision history

OCA at 15:17, 4 October 2023

2023-10-04T15:17:58Z

←Older revision		Revision as of 15:17, 4 October 2023
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	<StructureSection load='6d4k' size='340' side='right'caption='[[6d4k]], [[Resolution\|resolution]] 1.32Å' scene=''>		<StructureSection load='6d4k' size='340' side='right'caption='[[6d4k]], [[Resolution\|resolution]] 1.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d4k]] is a 1 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=6D4K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6D4K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d4k]] is a 1 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=6D4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D4K FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</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]] 1.32Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Rv1433, RVBD_1433, P425_01489 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=6d4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d4k OCA], [~~http~~://pdbe.org/6d4k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6d4k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6d4k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6d4k 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=6d4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d4k OCA], [https://pdbe.org/6d4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d4k RCSB], [https://www.ebi.ac.uk/pdbsum/6d4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d4k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LDT3_MYCTU LDT3_MYCTU]] Probable L,D-transpeptidase that may perform as-yet-unknown cross-linking reactions in M.tuberculosis. Is not able to generate 3->3 cross-links in peptidoglycan, using tetrapeptide stems as acyl donor substrates. May function in the anchoring of proteins to peptidoglycan.<ref>PMID:24041897</ref>	+	[https://www.uniprot.org/uniprot/LDT3_MYCTU LDT3_MYCTU] Probable L,D-transpeptidase that may perform as-yet-unknown cross-linking reactions in M.tuberculosis. Is not able to generate 3->3 cross-links in peptidoglycan, using tetrapeptide stems as acyl donor substrates. May function in the anchoring of proteins to peptidoglycan.<ref>PMID:24041897</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Dias~~, M V.B~~]]	+	[[Category: Dias MVB]]
-	[[Category: Libreros~~, G A]]~~	+	[[Category: Libreros GA]]
-	~~[[Category: Apo-form]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:45, 6 November 2019

2019-11-06T07:45:23Z

←Older revision		Revision as of 07:45, 6 November 2019
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	==Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.32 A resolution==		==Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.32 A resolution==
-	<StructureSection load='6d4k' size='340' side='right' caption='[[6d4k]], [[Resolution\|resolution]] 1.32Å' scene=''>	+	<StructureSection load='6d4k' size='340' side='right'caption='[[6d4k]], [[Resolution\|resolution]] 1.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d4k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D4K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d4k]] is a 1 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=6D4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D4K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv1433, RVBD_1433, P425_01489 ([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=6d4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d4k OCA], [http://pdbe.org/6d4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d4k RCSB], [http://www.ebi.ac.uk/pdbsum/6d4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d4k 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=6d4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d4k OCA], [http://pdbe.org/6d4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d4k RCSB], [http://www.ebi.ac.uk/pdbsum/6d4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d4k ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Dias, M V.B]]		[[Category: Dias, M V.B]]
	[[Category: Libreros, G A]]		[[Category: Libreros, G A]]
	[[Category: Apo-form]]		[[Category: Apo-form]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 15:16, 27 February 2019

2019-02-27T15:16:01Z

←Older revision		Revision as of 15:16, 27 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6d4k is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.32 A resolution==
		+	<StructureSection load='6d4k' size='340' side='right' caption='[[6d4k]], [[Resolution\|resolution]] 1.32Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6d4k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D4K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=6d4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d4k OCA], [http://pdbe.org/6d4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d4k RCSB], [http://www.ebi.ac.uk/pdbsum/6d4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d4k ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LDT3_MYCTU LDT3_MYCTU]] Probable L,D-transpeptidase that may perform as-yet-unknown cross-linking reactions in M.tuberculosis. Is not able to generate 3->3 cross-links in peptidoglycan, using tetrapeptide stems as acyl donor substrates. May function in the anchoring of proteins to peptidoglycan.<ref>PMID:24041897</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Targeting Mycobacterium tuberculosis peptidoglycans with beta-lactam antibiotics represents a strategy to address increasing resistance to antitubercular drugs. beta-Lactams inhibit peptidoglycan synthases such as l,d-transpeptidases, a group of carbapenem-sensitive enzymes that stabilize peptidoglycans through 3 --> 3 cross-links. M. tuberculosis encodes five l,d-transpeptidases (LdtMt1-5), of which LdtMt3 is one of the less understood. Herein, we structurally characterized the apo and faropenem-acylated forms of LdtMt3 at 1.3 and 1.8 A resolution, respectively. These structures revealed a fold and catalytic diad similar to those of other LdtsMt enzymes, supporting its involvement in transpeptidation reactions despite divergences in active site size and charges. The LdtMt3-faropenem structure indicated that faropenem is degraded after Cys-246 acylation, and possibly only a beta-OH-butyrate or an acetyl group (C2H3O) covalently attached to the enzyme remains, an observation that strongly supports the notion that LdtMt3 is inactivated by beta-lactams. Docking simulations with intact beta-lactams predicted key LdtMt3 residues that interact with these antibiotics. We also characterized the heat of acylation involved in the binding and reaction of LdtMt3 for ten beta-lactams belonging to four different classes, and imipenem had the highest inactivation constant. This work provides key insights into the structure, binding mechanisms, and degradation of beta-lactams by LdtMt3, which may be useful for the development of additional beta-lactams with potential antitubercular activity.

-	~~Authors: Libreros~~, ~~G.A~~., ~~Dias~~, M.V.B.	+	Structural Basis for the Interaction and Processing of beta-Lactam Antibiotics by l,d-Transpeptidase 3 (LdtMt3) from Mycobacterium tuberculosis.,Libreros-Zuniga GA, Dos Santos Silva C, Salgado Ferreira R, Dias MVB ACS Infect Dis. 2019 Feb 8;5(2):260-271. doi: 10.1021/acsinfecdis.8b00244. Epub, 2018 Dec 28. PMID:30556998<ref>PMID:30556998</ref>

-	~~Description: Crystal structure~~ of ~~L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1~~.~~32 A resolution~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Libreros, G.A]]	+	<div class="pdbe-citations 6d4k" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Dias, M.V.B~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dias, M V.B]]
		+	[[Category: Libreros, G A]]
		+	[[Category: Apo-form]]
		+	[[Category: Transferase]]

OCA at 04:00, 16 May 2018

2018-05-16T04:00:47Z

←Older revision		Revision as of 04:00, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6d4k is ON HOLD	+	The entry 6d4k is ON HOLD until Paper Publication

	Authors: Libreros, G.A., Dias, M.V.B.		Authors: Libreros, G.A., Dias, M.V.B.

OCA: Protected "6d4k" [edit=sysop:move=sysop]

2018-04-25T04:11:52Z

Protected "6d4k" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:11, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 6d4k is ON HOLD Authors: Libreros, G.A., Dias, M.V.B. Description: Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.3...

2018-04-25T04:11:50Z

New page: '''Unreleased structure''' The entry 6d4k is ON HOLD Authors: Libreros, G.A., Dias, M.V.B. Description: Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.3...

New page

'''Unreleased structure'''

The entry 6d4k is ON HOLD

Authors: Libreros, G.A., Dias, M.V.B.

Description: Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.32 A resolution
[[Category: Unreleased Structures]]
[[Category: Libreros, G.A]]
[[Category: Dias, M.V.B]]