7f71 - Revision history

OCA at 17:10, 29 November 2023

OCA — Wed, 29 Nov 2023 17:10:34 GMT

←Older revision		Revision as of 17:10, 29 November 2023
Line 1:		Line 1:

	==Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate==		==Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate==
-	<StructureSection load='7f71' size='340' side='right'caption='[[7f71]]' scene=''>	+	<StructureSection load='7f71' size='340' side='right'caption='[[7f71]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F71 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7f71]] 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=7F71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F71 FirstGlance]. <br>
-	</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=7f71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f71 OCA], [https://pdbe.org/7f71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f71 RCSB], [https://www.ebi.ac.uk/pdbsum/7f71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f71 ProSAT]</span></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]] 1.58Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=7f71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f71 OCA], [https://pdbe.org/7f71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f71 RCSB], [https://www.ebi.ac.uk/pdbsum/7f71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f71 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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;">
		+	== Publication Abstract from PubMed ==
		+	L,D-transpeptidase function predominates in atypical 3 --> 3 transpeptide networking of peptidoglycan (PG) layer in Mycobacterium tuberculosis. Prior studies of L,D-transpeptidases have identified only the catalytic site that binds to peptide moiety of the PG substrate or beta-lactam antibiotics. This insight was leveraged to develop mechanism of its activity and inhibition by beta-lactams. Here, we report identification of an allosteric site at a distance of 21 A from the catalytic site that binds the sugar moiety of PG substrates (hereafter referred to as the S-pocket). This site also binds a second beta-lactam molecule and influences binding at the catalytic site. We provide evidence that two beta-lactam molecules bind co-operatively to this enzyme, one non-covalently at the S-pocket and one covalently at the catalytic site. This dual beta-lactam-binding phenomenon is previously unknown and is an observation that may offer novel approaches for the structure-based design of new drugs against M. tuberculosis.
		+
		+	Allosteric cooperation in beta-lactam binding to a non-classical transpeptidase.,Ahmad N, Dugad S, Chauhan V, Ahmed S, Sharma K, Kachhap S, Zaidi R, Bishai WR, Lamichhane G, Kumar P Elife. 2022 Apr 27;11. pii: 73055. doi: 10.7554/eLife.73055. PMID:35475970<ref>PMID:35475970</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7f71" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Mycobacterium tuberculosis H37Rv]]
	[[Category: Kumar P]]		[[Category: Kumar P]]
	[[Category: Lamichhane G]]		[[Category: Lamichhane G]]

OCA at 14:31, 31 August 2022

OCA — Wed, 31 Aug 2022 14:31:36 GMT

←Older revision		Revision as of 14:31, 31 August 2022
Line 1:		Line 1:

	==Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate==		==Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate==
-	<StructureSection load='7f71' size='340' side='right'caption='[[7f71]]~~, [[Resolution\|resolution]] 1.58Å~~' scene=''>	+	<StructureSection load='7f71' size='340' side='right'caption='[[7f71]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7f71]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F71 FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F71 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</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=7f71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f71 OCA], [https://pdbe.org/7f71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f71 RCSB], [https://www.ebi.ac.uk/pdbsum/7f71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f71 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=7f71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f71 OCA], [https://pdbe.org/7f71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f71 RCSB], [https://www.ebi.ac.uk/pdbsum/7f71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f71 ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[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;">
-	== Publication Abstract from PubMed ==
-	L,D-transpeptidase function predominates in atypical 3 --> 3 transpeptide networking of peptidoglycan (PG) layer in Mycobacterium tuberculosis. Prior studies of L,D-transpeptidases have identified only the catalytic site that binds to peptide moiety of the PG substrate or beta-lactam antibiotics. This insight was leveraged to develop mechanism of its activity and inhibition by beta-lactams. Here, we report identification of an allosteric site at a distance of 21 A from the catalytic site that binds the sugar moiety of PG substrates (hereafter referred to as the S-pocket). This site also binds a second beta-lactam molecule and influences binding at the catalytic site. We provide evidence that two beta-lactam molecules bind co-operatively to this enzyme, one non-covalently at the S-pocket and one covalently at the catalytic site. This dual beta-lactam-binding phenomenon is previously unknown and is an observation that may offer novel approaches for the structure-based design of new drugs against M. tuberculosis.
-
-	Allosteric cooperation in beta-lactam binding to a non-classical transpeptidase.,Ahmad N, Dugad S, Chauhan V, Ahmed S, Sharma K, Kachhap S, Zaidi R, Bishai WR, Lamichhane G, Kumar P Elife. 2022 Apr 27;11. pii: 73055. doi: 10.7554/eLife.73055. PMID:35475970<ref>PMID:35475970</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7f71" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kumar, P]]	+	[[Category: Kumar P]]
-	[[Category: Lamichhane, G]]	+	[[Category: Lamichhane G]]
-	~~[[Category: Cysteine protease]]~~	+
-	~~[[Category: D-transpeptidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:11, 25 May 2022

OCA — Wed, 25 May 2022 08:11:46 GMT

←Older revision		Revision as of 08:11, 25 May 2022
Line 1:		Line 1:

	==Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate==		==Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate==
-	<StructureSection load='7f71' size='340' side='right'caption='[[7f71]]' scene=''>	+	<StructureSection load='7f71' size='340' side='right'caption='[[7f71]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F71 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7f71]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F71 FirstGlance]. <br>
-	</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=7f71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f71 OCA], [https://pdbe.org/7f71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f71 RCSB], [https://www.ebi.ac.uk/pdbsum/7f71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f71 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=7f71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f71 OCA], [https://pdbe.org/7f71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f71 RCSB], [https://www.ebi.ac.uk/pdbsum/7f71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f71 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[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;">
		+	== Publication Abstract from PubMed ==
		+	L,D-transpeptidase function predominates in atypical 3 --> 3 transpeptide networking of peptidoglycan (PG) layer in Mycobacterium tuberculosis. Prior studies of L,D-transpeptidases have identified only the catalytic site that binds to peptide moiety of the PG substrate or beta-lactam antibiotics. This insight was leveraged to develop mechanism of its activity and inhibition by beta-lactams. Here, we report identification of an allosteric site at a distance of 21 A from the catalytic site that binds the sugar moiety of PG substrates (hereafter referred to as the S-pocket). This site also binds a second beta-lactam molecule and influences binding at the catalytic site. We provide evidence that two beta-lactam molecules bind co-operatively to this enzyme, one non-covalently at the S-pocket and one covalently at the catalytic site. This dual beta-lactam-binding phenomenon is previously unknown and is an observation that may offer novel approaches for the structure-based design of new drugs against M. tuberculosis.
		+
		+	Allosteric cooperation in beta-lactam binding to a non-classical transpeptidase.,Ahmad N, Dugad S, Chauhan V, Ahmed S, Sharma K, Kachhap S, Zaidi R, Bishai WR, Lamichhane G, Kumar P Elife. 2022 Apr 27;11. pii: 73055. doi: 10.7554/eLife.73055. PMID:35475970<ref>PMID:35475970</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7f71" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kumar P]]	+	[[Category: Kumar, P]]
-	[[Category: Lamichhane G]]	+	[[Category: Lamichhane, G]]
		+	[[Category: Cysteine protease]]
		+	[[Category: D-transpeptidase]]
		+	[[Category: Hydrolase]]

OCA at 06:17, 12 May 2022

OCA — Thu, 12 May 2022 06:17:28 GMT

←Older revision		Revision as of 06:17, 12 May 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7f71 is ON HOLD until Paper Publication~~	+	==Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate==
-		+	<StructureSection load='7f71' size='340' side='right'caption='[[7f71]]' scene=''>
-	~~Authors: Kumar, P., Lamichhane, G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F71 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate	+	</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=7f71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f71 OCA], [https://pdbe.org/7f71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f71 RCSB], [https://www.ebi.ac.uk/pdbsum/7f71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f71 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kumar, P]]	+	__TOC__
-	[[Category: Lamichhane, G]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kumar P]]
		+	[[Category: Lamichhane G]]

OCA at 05:05, 25 August 2021

OCA — Wed, 25 Aug 2021 05:05:33 GMT

←Older revision		Revision as of 05:05, 25 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7f71 is ON HOLD	+	The entry 7f71 is ON HOLD until Paper Publication

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

OCA: Protected "7f71" [edit=sysop:move=sysop]

OCA — Wed, 07 Jul 2021 08:40:46 GMT

Protected "7f71" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:40, 7 July 2021

OCA: New page: '''Unreleased structure''' The entry 7f71 is ON HOLD Authors: Kumar, P., Lamichhane, G. Description: Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) w...

OCA — Wed, 07 Jul 2021 08:40:45 GMT

New page: '''Unreleased structure''' The entry 7f71 is ON HOLD Authors: Kumar, P., Lamichhane, G. Description: Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) w...

New page

'''Unreleased structure'''

The entry 7f71 is ON HOLD

Authors: Kumar, P., Lamichhane, G.

Description: Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate
[[Category: Unreleased Structures]]
[[Category: Kumar, P]]
[[Category: Lamichhane, G]]