5z01 - Revision history

OCA at 10:26, 27 March 2024

OCA — Wed, 27 Mar 2024 10:26:03 GMT

←Older revision		Revision as of 10:26, 27 March 2024
Line 1:		Line 1:

	==Native Escherichia coli L,D-carboxypeptidase A (LdcA)==		==Native Escherichia coli L,D-carboxypeptidase A (LdcA)==
-	<StructureSection load='5z01' size='340' side='right' caption='[[5z01]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5z01' size='340' side='right'caption='[[5z01]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z01]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z01 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z01 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z01]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z01 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.75Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">ldcA, ycgQ, b1192, JW1181 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=83333 ECOLI])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>[http://en.wikipedia.org/wiki/Muramoyltetrapeptide_carboxypeptidase Muramoyltetrapeptide carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.13 3.4.17.13] </~~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=5z01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z01 OCA], [https://pdbe.org/5z01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z01 RCSB], [https://www.ebi.ac.uk/pdbsum/5z01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z01 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=5z01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z01 OCA], [~~http~~://pdbe.org/5z01 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z01 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z01 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z01 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LDCA_ECOLI LDCA_ECOLI]] Releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso-Dap-D-Ala. To a lesser extent, can also cleave D-Ala from murein derivatives containing the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide, GlcNAc-MurNAc-tetrapeptide, and GlcNAc-anhMurNAc-tetrapeptide. Does not act on murein sacculi or cross-linked muropeptides. The tripeptides produced by the LcdA reaction can then be reused as peptidoglycan building blocks; LcdA is thereby involved in murein recycling. Is also essential for viability during stationary phase.<ref>PMID:10428950</ref> <ref>PMID:18535144</ref>	+	[https://www.uniprot.org/uniprot/LDCA_ECOLI LDCA_ECOLI] Releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso-Dap-D-Ala. To a lesser extent, can also cleave D-Ala from murein derivatives containing the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide, GlcNAc-MurNAc-tetrapeptide, and GlcNAc-anhMurNAc-tetrapeptide. Does not act on murein sacculi or cross-linked muropeptides. The tripeptides produced by the LcdA reaction can then be reused as peptidoglycan building blocks; LcdA is thereby involved in murein recycling. Is also essential for viability during stationary phase.<ref>PMID:10428950</ref> <ref>PMID:18535144</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Bacterial peptidoglycan is constructed by cross-linking sugar chains carrying pentapeptide building blocks with two d-alanine residues at the C-terminus. Incorporation into the polymer and subsequent breakdown of peptidoglycan releases a tetrapeptide with a single d-alanine residue. Removal of this residue is necessary for the tripeptide to receive a new D-Ala-D-Ala dipeptide in the synthetic pathway, but proteases are generally unable to work with substrates having residues of unusual chirality close to the scissile bond. Processing of the tetrapeptide is carried out by a dedicated ld-carboxypeptidase, which is of interest as a novel drug target. We describe the high resolution crystal structure of the enzyme from E. coli, and demonstrate the dimeric structure is highly conserved.	+
-		+
-	The crystal structure and oligomeric form of Escherichia colil,d-carboxypeptidase A.,Meyer K, Addy C, Akashi S, Roper DI, Tame JRH Biochem Biophys Res Commun. 2018 May 15;499(3):594-599. doi:, 10.1016/j.bbrc.2018.03.195. Epub 2018 Apr 5. PMID:29601819<ref>PMID:29601819</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5z01" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Muramoyltetrapeptide carboxypeptidase~~]]	+	[[Category: Large Structures]]
-	[[Category: Meyer, K]]	+	[[Category: Meyer K]]
-	[[Category: Tame~~, J R.H]]~~	+	[[Category: Tame JRH]]
-	~~[[Category: Cell-wall]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidoglycan]]~~	+
-	~~[[Category: Recycling~~]]	+

OCA at 08:27, 2 May 2018

OCA — Wed, 02 May 2018 08:27:50 GMT

←Older revision		Revision as of 08:27, 2 May 2018
Line 3:		Line 3:
	<StructureSection load='5z01' size='340' side='right' caption='[[5z01]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5z01' size='340' side='right' caption='[[5z01]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z01]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z01 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z01]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z01 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ldcA, ycgQ, b1192, JW1181 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Muramoyltetrapeptide_carboxypeptidase Muramoyltetrapeptide carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.13 3.4.17.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Muramoyltetrapeptide_carboxypeptidase Muramoyltetrapeptide carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.13 3.4.17.13] </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=5z01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z01 OCA], [http://pdbe.org/5z01 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z01 RCSB], [http://www.ebi.ac.uk/pdbsum/5z01 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z01 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=5z01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z01 OCA], [http://pdbe.org/5z01 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z01 RCSB], [http://www.ebi.ac.uk/pdbsum/5z01 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z01 ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Muramoyltetrapeptide carboxypeptidase]]		[[Category: Muramoyltetrapeptide carboxypeptidase]]
	[[Category: Meyer, K]]		[[Category: Meyer, K]]

OCA at 05:30, 25 April 2018

OCA — Wed, 25 Apr 2018 05:30:10 GMT

←Older revision		Revision as of 05:30, 25 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z01 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Native Escherichia coli L,D-carboxypeptidase A (LdcA)==
		+	<StructureSection load='5z01' size='340' side='right' caption='[[5z01]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z01]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z01 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Muramoyltetrapeptide_carboxypeptidase Muramoyltetrapeptide carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.13 3.4.17.13] </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=5z01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z01 OCA], [http://pdbe.org/5z01 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z01 RCSB], [http://www.ebi.ac.uk/pdbsum/5z01 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z01 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LDCA_ECOLI LDCA_ECOLI]] Releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso-Dap-D-Ala. To a lesser extent, can also cleave D-Ala from murein derivatives containing the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide, GlcNAc-MurNAc-tetrapeptide, and GlcNAc-anhMurNAc-tetrapeptide. Does not act on murein sacculi or cross-linked muropeptides. The tripeptides produced by the LcdA reaction can then be reused as peptidoglycan building blocks; LcdA is thereby involved in murein recycling. Is also essential for viability during stationary phase.<ref>PMID:10428950</ref> <ref>PMID:18535144</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial peptidoglycan is constructed by cross-linking sugar chains carrying pentapeptide building blocks with two d-alanine residues at the C-terminus. Incorporation into the polymer and subsequent breakdown of peptidoglycan releases a tetrapeptide with a single d-alanine residue. Removal of this residue is necessary for the tripeptide to receive a new D-Ala-D-Ala dipeptide in the synthetic pathway, but proteases are generally unable to work with substrates having residues of unusual chirality close to the scissile bond. Processing of the tetrapeptide is carried out by a dedicated ld-carboxypeptidase, which is of interest as a novel drug target. We describe the high resolution crystal structure of the enzyme from E. coli, and demonstrate the dimeric structure is highly conserved.

-	~~Authors: Meyer~~, K., Tame, J.R.H.	+	The crystal structure and oligomeric form of Escherichia colil,d-carboxypeptidase A.,Meyer K, Addy C, Akashi S, Roper DI, Tame JRH Biochem Biophys Res Commun. 2018 May 15;499(3):594-599. doi:, 10.1016/j.bbrc.2018.03.195. Epub 2018 Apr 5. PMID:29601819<ref>PMID:29601819</ref>

-	~~Description: Native Escherichia coli L~~,~~D-carboxypeptidase A (LdcA)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Tame, J.R.H~~]]	+	<div class="pdbe-citations 5z01" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Muramoyltetrapeptide carboxypeptidase]]
	[[Category: Meyer, K]]		[[Category: Meyer, K]]
		+	[[Category: Tame, J R.H]]
		+	[[Category: Cell-wall]]
		+	[[Category: Hydrolase]]
		+	[[Category: Peptidoglycan]]
		+	[[Category: Recycling]]

OCA at 05:30, 17 January 2018

OCA — Wed, 17 Jan 2018 05:30:39 GMT

←Older revision		Revision as of 05:30, 17 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z01 is ON HOLD	+	The entry 5z01 is ON HOLD until Paper Publication

	Authors: Meyer, K., Tame, J.R.H.		Authors: Meyer, K., Tame, J.R.H.

OCA: Protected "5z01" [edit=sysop:move=sysop]

OCA — Wed, 27 Dec 2017 07:12:46 GMT

Protected "5z01" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:12, 27 December 2017

OCA: New page: '''Unreleased structure''' The entry 5z01 is ON HOLD Authors: Meyer, K., Tame, J.R.H. Description: Native Escherichia coli L,D-carboxypeptidase A (LdcA) [[Category: Unreleased Structur...

OCA — Wed, 27 Dec 2017 07:12:45 GMT

New page: '''Unreleased structure''' The entry 5z01 is ON HOLD Authors: Meyer, K., Tame, J.R.H. Description: Native Escherichia coli L,D-carboxypeptidase A (LdcA) [[Category: Unreleased Structur...

New page

'''Unreleased structure'''

The entry 5z01 is ON HOLD

Authors: Meyer, K., Tame, J.R.H.

Description: Native Escherichia coli L,D-carboxypeptidase A (LdcA)
[[Category: Unreleased Structures]]
[[Category: Tame, J.R.H]]
[[Category: Meyer, K]]