2y28 - Revision history

OCA at 14:01, 1 February 2024

OCA — Thu, 01 Feb 2024 14:01:48 GMT

←Older revision		Revision as of 14:01, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='2y28' size='340' side='right'caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2y28' size='340' side='right'caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacterium_freundii"_braak_1928 "bacterium~~ freundii~~" braak 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y28 FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j3g\|1j3g]]~~, ~~[[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28]~~ </~~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=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [https://pdbe.org/2y28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [https://www.ebi.ac.uk/pdbsum/2y28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y28 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=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [https://pdbe.org/2y28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [https://www.ebi.ac.uk/pdbsum/2y28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y28 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AMPD_CITFR AMPD_CITFR]] Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety.	+	[https://www.uniprot.org/uniprot/AMPD_CITFR AMPD_CITFR] Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ freundii ~~braak 1928~~]]	+	[[Category: Citrobacter freundii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N-acetylmuramoyl-L-alanine amidase]]~~	+	[[Category: Andre I]]
-	[[Category: Andre, I]]	+	[[Category: Barbe S]]
-	[[Category: Barbe, S]]	+	[[Category: Carrasco-Lopez C]]
-	[[Category: Carrasco-Lopez, C]]	+	[[Category: Hermoso JA]]
-	[[Category: Hermoso~~, J A~~]]	+	[[Category: Hesek D]]
-	[[Category: Hesek, D]]	+	[[Category: Lee M]]
-	[[Category: Lee, M]]	+	[[Category: Martinez-Ripoll M]]
-	[[Category: Martinez-Ripoll, M]]	+	[[Category: Mobashery S]]
-	[[Category: Mobashery, S]]	+	[[Category: Rojas-Altuve A]]
-	[[Category: Rojas-Altuve, A]]	+	[[Category: Silva-Martin N]]
-	[[Category: Silva-Martin, N]]	+	[[Category: Zhang W]]
-	[[Category: Zhang, W]]	+
-	~~[[Category: Activation mechanism]]~~	+
-	~~[[Category: Amidase_2 family]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidoglycan amidase~~]]	+

OCA at 12:21, 27 April 2022

OCA — Wed, 27 Apr 2022 12:21:37 GMT

OCA at 12:30, 22 July 2020

OCA — Wed, 22 Jul 2020 12:30:59 GMT

←Older revision		Revision as of 12:30, 22 July 2020
Line 1:		Line 1:

	==crystal structure of Se-Met AmpD derivative==		==crystal structure of Se-Met AmpD derivative==
-	<StructureSection load='2y28' size='340' side='right' caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2y28' size='340' side='right'caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Y28 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [http://pdbe.org/2y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [http://www.ebi.ac.uk/pdbsum/2y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2y28 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [http://pdbe.org/2y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [http://www.ebi.ac.uk/pdbsum/2y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2y28 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Bacterium freundii braak 1928]]		[[Category: Bacterium freundii braak 1928]]
		+	[[Category: Large Structures]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
	[[Category: Andre, I]]		[[Category: Andre, I]]

OCA at 09:29, 4 August 2016

OCA — Thu, 04 Aug 2016 09:29:17 GMT

←Older revision		Revision as of 09:29, 4 August 2016
Line 1:		Line 1:
		+
	==crystal structure of Se-Met AmpD derivative==		==crystal structure of Se-Met AmpD derivative==
	<StructureSection load='2y28' size='340' side='right' caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2y28' size='340' side='right' caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Citrobacter_freundii Citrobacter~~ freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y28 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [http://www.ebi.ac.uk/pdbsum/2y28 PDBsum]</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=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [http://pdbe.org/2y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [http://www.ebi.ac.uk/pdbsum/2y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2y28 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2y28" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Citrobacter~~ freundii]]	+	[[Category: Bacterium freundii braak 1928]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
	[[Category: Andre, I]]		[[Category: Andre, I]]

OCA at 07:51, 25 December 2014

OCA — Thu, 25 Dec 2014 07:51:44 GMT

←Older revision		Revision as of 07:51, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='2y28' size='340' side='right' caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2y28' size='340' side='right' caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. <br>	+	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y28 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.~~2 2~~.7.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [http://www.ebi.ac.uk/pdbsum/2y28 PDBsum]</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=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [http://www.ebi.ac.uk/pdbsum/2y28 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMPD_CITFR AMPD_CITFR]] Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism.,Carrasco-Lopez C, Rojas-Altuve A, Zhang W, Hesek D, Lee M, Barbe S, Andre I, Ferrer P, Silva-Martin N, Castro GR, Martinez-Ripoll M, Mobashery S, Hermoso JA J Biol Chem. 2011 Sep 9;286(36):31714-22. Epub 2011 Jul 20. PMID:21775432<ref>PMID:21775432</ref>		Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism.,Carrasco-Lopez C, Rojas-Altuve A, Zhang W, Hesek D, Lee M, Barbe S, Andre I, Ferrer P, Silva-Martin N, Castro GR, Martinez-Ripoll M, Mobashery S, Hermoso JA J Biol Chem. 2011 Sep 9;286(36):31714-22. Epub 2011 Jul 20. PMID:21775432<ref>PMID:21775432</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 23:		Line 25:
	[[Category: Citrobacter freundii]]		[[Category: Citrobacter freundii]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
-	[[Category: Andre, I.]]	+	[[Category: Andre, I]]
-	[[Category: Barbe, S.]]	+	[[Category: Barbe, S]]
-	[[Category: Carrasco-Lopez, C.]]	+	[[Category: Carrasco-Lopez, C]]
-	[[Category: Hermoso, J A.]]	+	[[Category: Hermoso, J A]]
-	[[Category: Hesek, D.]]	+	[[Category: Hesek, D]]
-	[[Category: Lee, M.]]	+	[[Category: Lee, M]]
-	[[Category: Martinez-Ripoll, M.]]	+	[[Category: Martinez-Ripoll, M]]
-	[[Category: Mobashery, S.]]	+	[[Category: Mobashery, S]]
-	[[Category: Rojas-Altuve, A.]]	+	[[Category: Rojas-Altuve, A]]
-	[[Category: Silva-Martin, N.]]	+	[[Category: Silva-Martin, N]]
-	[[Category: Zhang, W.]]	+	[[Category: Zhang, W]]
	[[Category: Activation mechanism]]		[[Category: Activation mechanism]]
	[[Category: Amidase_2 family]]		[[Category: Amidase_2 family]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Peptidoglycan amidase]]		[[Category: Peptidoglycan amidase]]

OCA at 07:49, 14 May 2014

OCA — Wed, 14 May 2014 07:49:05 GMT

←Older revision		Revision as of 07:49, 14 May 2014
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-	[[~~Image:~~2y28.~~png~~\|~~left~~\|~~200px~~]]	+	==crystal structure of Se-Met AmpD derivative==
		+	<StructureSection load='2y28' size='340' side='right' caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [http://www.ebi.ac.uk/pdbsum/2y28 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	AmpD is a cytoplasmic peptidoglycan (PG) amidase involved in bacterial cell-wall recycling and in induction of beta-lactamase, a key enzyme of beta-lactam antibiotic resistance. AmpD belongs to the amidase_2 family that includes zinc-dependent amidases and the peptidoglycan-recognition proteins (PGRPs), highly conserved pattern-recognition molecules of the immune system. Crystal structures of Citrobacter freundii AmpD were solved in this study for the apoenzyme, for the holoenzyme at two different pH values, and for the complex with the reaction products, providing insights into the PG recognition and the catalytic process. These structures are significantly different compared with the previously reported NMR structure for the same protein. The NMR structure does not possess an accessible active site and shows the protein in what is proposed herein as an inactive "closed" conformation. The transition of the protein from this inactive conformation to the active "open" conformation, as seen in the x-ray structures, was studied by targeted molecular dynamics simulations, which revealed large conformational rearrangements (as much as 17 A) in four specific regions representing one-third of the entire protein. It is proposed that the large conformational change that would take the inactive NMR structure to the active x-ray structure represents an unprecedented mechanism for activation of AmpD. Analysis is presented to argue that this activation mechanism might be representative of a regulatory process for other intracellular members of the bacterial amidase_2 family of enzymes.

-	<!--	+	Crystal Structures of Bacterial Peptidoglycan Amidase AmpD and an Unprecedented Activation Mechanism.,Carrasco-Lopez C, Rojas-Altuve A, Zhang W, Hesek D, Lee M, Barbe S, Andre I, Ferrer P, Silva-Martin N, Castro GR, Martinez-Ripoll M, Mobashery S, Hermoso JA J Biol Chem. 2011 Sep 9;286(36):31714-22. Epub 2011 Jul 20. PMID:21775432<ref>PMID:21775432</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2y28"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_2y28\| PDB=2y28 \| SCENE= }}~~	+

-	~~===crystal structure~~ of ~~Se-Met AmpD derivative===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21775432}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21775432 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21775432}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2y28]] is a 3 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021775432<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Citrobacter freundii]]		[[Category: Citrobacter freundii]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]

OCA at 06:09, 28 December 2011

OCA — Wed, 28 Dec 2011 06:09:08 GMT

←Older revision		Revision as of 06:09, 28 December 2011
Line 9:		Line 9:
	{{STRUCTURE_2y28\| PDB=2y28 \| SCENE= }}		{{STRUCTURE_2y28\| PDB=2y28 \| SCENE= }}

-	===~~CRYSTAL STRUCTURE OF SE~~-~~MET AMPD DERIVATIVE~~===	+	===crystal structure of Se-Met AmpD derivative===

OCA at 05:42, 14 September 2011

OCA — Wed, 14 Sep 2011 05:42:45 GMT

←Older revision		Revision as of 05:42, 14 September 2011
Line 11:		Line 11:
	===CRYSTAL STRUCTURE OF SE-MET AMPD DERIVATIVE===		===CRYSTAL STRUCTURE OF SE-MET AMPD DERIVATIVE===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21775432}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21775432 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21775432}}

	==About this Structure==		==About this Structure==
	[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA].		[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021775432</ref><references group="xtra"/>
	[[Category: Citrobacter freundii]]		[[Category: Citrobacter freundii]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]

OCA at 06:10, 27 July 2011

OCA — Wed, 27 Jul 2011 06:10:44 GMT

←Older revision		Revision as of 06:10, 27 July 2011
Line 1:		Line 1:
-	[[Image:2y28.~~jpg~~\|left\|200px]]	+	[[Image:2y28.png\|left\|200px]]

	<!--		<!--

OCA at 06:48, 20 July 2011

OCA — Wed, 20 Jul 2011 06:48:52 GMT

←Older revision		Revision as of 06:48, 20 July 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:2y28.jpg\|left\|200px]]

-	The ~~entry 2y28~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2y28", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_2y28\| PDB=2y28 \| SCENE= }}

-	~~Authors: Carrasco~~-~~Lopez, C., Rojas-Altuve, A., Zhang, W., Hesek, D., Lee, M., Barbe, S., Andre, I., Silva-Martin, N., Martinez-Ripoll, M., Mobashery, S., Hermoso, J.A.~~	+	===CRYSTAL STRUCTURE OF SE-MET AMPD DERIVATIVE===

-	~~Description: crystal~~ structure ~~of Se~~-~~Met AmpD derivative~~	+
		+	==About this Structure==
		+	[[2y28]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA].
		+	[[Category: Citrobacter freundii]]
		+	[[Category: N-acetylmuramoyl-L-alanine amidase]]
		+	[[Category: Andre, I.]]
		+	[[Category: Barbe, S.]]
		+	[[Category: Carrasco-Lopez, C.]]
		+	[[Category: Hermoso, J A.]]
		+	[[Category: Hesek, D.]]
		+	[[Category: Lee, M.]]
		+	[[Category: Martinez-Ripoll, M.]]
		+	[[Category: Mobashery, S.]]
		+	[[Category: Rojas-Altuve, A.]]
		+	[[Category: Silva-Martin, N.]]
		+	[[Category: Zhang, W.]]
		+	[[Category: Activation mechanism]]
		+	[[Category: Amidase_2 family]]
		+	[[Category: Hydrolase]]
		+	[[Category: Peptidoglycan amidase]]

←Older revision		Revision as of 12:21, 27 April 2022
Line 3:		Line 3:
	<StructureSection load='2y28' size='340' side='right'caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2y28' size='340' side='right'caption='[[2y28]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2y28]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y28 FirstGlance]. <br>
	</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>		</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j3g\|1j3g]], [[2y2e\|2y2e]], [[2y2c\|2y2c]], [[2y2d\|2y2d]], [[2y2b\|2y2b]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [~~http~~://pdbe.org/2y28 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2y28 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2y28 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=2y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y28 OCA], [https://pdbe.org/2y28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y28 RCSB], [https://www.ebi.ac.uk/pdbsum/2y28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y28 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AMPD_CITFR AMPD_CITFR]] Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety.	+	[[https://www.uniprot.org/uniprot/AMPD_CITFR AMPD_CITFR]] Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==