6ll9 - Revision history

OCA at 11:03, 22 November 2023

2023-11-22T11:03:21Z

←Older revision		Revision as of 11:03, 22 November 2023
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	==Crystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila==		==Crystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila==
-	<StructureSection load='6ll9' size='340' side='right'caption='[[6ll9]]' scene=''>	+	<StructureSection load='6ll9' size='340' side='right'caption='[[6ll9]], [[Resolution\|resolution]] 2.70Å' 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=6LL9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LL9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ll9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeromonas_hydrophila Aeromonas hydrophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LL9 FirstGlance]. <br>
-	</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=6ll9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ll9 OCA], [~~http~~://pdbe.org/6ll9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ll9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ll9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ll9 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]] 2.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</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=6ll9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ll9 OCA], [https://pdbe.org/6ll9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ll9 RCSB], [https://www.ebi.ac.uk/pdbsum/6ll9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ll9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DDL_AERHH DDL_AERHH] Cell wall formation.[HAMAP-Rule:MF_00047]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aeromonas hydrophila, a pathogenic bacterium, is harmful to humans, domestic animals, and fishes and, moreover, of public health concern due to the emergence of multiple drug-resistant strains. The cell wall has been discovered as a novel and efficient drug target against bacteria, and d-alanine-d-alanine ligase (Ddl) is considered as an essential enzyme in bacterial cell wall biosynthesis. Herein, we studied the A. hydrophila HBNUAh01 Ddl (AhDdl) enzyme activity and kinetics and determined the crystal structure of AhDdl/d-Ala complex at 2.7 A resolution. An enzymatic assay showed that AhDdl exhibited higher affinity to ATP (Km: 54.1 +/- 9.1 muM) compared to d-alanine (Km: 1.01 +/- 0.19 mM). The kinetic studies indicated a competitive inhibition of AhDdl by d-cycloserine (DCS), with an inhibition constant (Ki) of 120 muM and the 50% inhibitory concentrations (IC50) value of 0.5 mM. Meanwhile, structural analysis indicated that the AhDdl/d-Ala complex structure adopted a semi-closed conformation form, and the active site was extremely conserved. Noteworthy is that the substrate d-Ala occupied the second d-Ala position, not the first d-Ala position. These results provided more insights for understanding the details of the catalytic mechanism and resources for the development of novel drugs against the diseases caused by A. hydrophila.
		+
		+	Insights into the Inhibition of Aeromonas hydrophila d-Alanine-d-Alanine Ligase by Integration of Kinetics and Structural Analysis.,Zhang Y, Gong S, Wang X, Muhammad M, Li Y, Meng S, Li Q, Liu D, Zhang H J Agric Food Chem. 2020 Jul 15;68(28):7509-7519. doi: 10.1021/acs.jafc.0c00682., Epub 2020 Jul 1. PMID:32609505<ref>PMID:32609505</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ll9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[D-alanine-D-alanine ligase 3D structures\|D-alanine-D-alanine ligase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aeromonas hydrophila]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Zhang H]]		[[Category: Zhang H]]

OCA at 11:21, 29 July 2020

2020-07-29T11:21:58Z

←Older revision		Revision as of 11:21, 29 July 2020
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-	'''Unreleased structure'''

-	~~The entry 6ll9 is ON HOLD until Paper Publication~~	+	==Crystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila==
-		+	<StructureSection load='6ll9' size='340' side='right'caption='[[6ll9]]' scene=''>
-	~~Authors: Zhang, H.D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LL9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LL9 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila	+	</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=6ll9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ll9 OCA], [http://pdbe.org/6ll9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ll9 RCSB], [http://www.ebi.ac.uk/pdbsum/6ll9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ll9 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Zhang, H.D]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Zhang H]]

OCA at 13:30, 22 January 2020

2020-01-22T13:30:59Z

←Older revision		Revision as of 13:30, 22 January 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ll9 is ON HOLD	+	The entry 6ll9 is ON HOLD until Paper Publication

	Authors: Zhang, H.D.		Authors: Zhang, H.D.

OCA: Protected "6ll9" [edit=sysop:move=sysop]

2020-01-01T06:36:26Z

Protected "6ll9" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:36, 1 January 2020

OCA: New page: '''Unreleased structure''' The entry 6ll9 is ON HOLD Authors: Zhang, H.D. Description: Crystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila [[Category: Unreleased ...

2020-01-01T06:36:24Z

New page: '''Unreleased structure''' The entry 6ll9 is ON HOLD Authors: Zhang, H.D. Description: Crystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 6ll9 is ON HOLD

Authors: Zhang, H.D.

Description: Crystal structure of D-alanine-D-alanine ligase from Aeromonas hydrophila
[[Category: Unreleased Structures]]
[[Category: Zhang, H.D]]