6ol8 - Revision history

OCA at 07:12, 11 October 2023

OCA — Wed, 11 Oct 2023 07:12:48 GMT

←Older revision		Revision as of 07:12, 11 October 2023
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	<StructureSection load='6ol8' size='340' side='right'caption='[[6ol8]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6ol8' size='340' side='right'caption='[[6ol8]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ol8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OL8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6OL8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ol8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OL8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ZZ7:(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC+ACID'>ZZ7</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]] 2.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ogo\|6ogo]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ZZ7:(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC+ACID'>ZZ7</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaNDM-12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ol8 OCA], [https://pdbe.org/6ol8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ol8 RCSB], [https://www.ebi.ac.uk/pdbsum/6ol8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ol8 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=6ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ol8 OCA], [~~http~~://pdbe.org/6ol8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ol8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ol8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ol8 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A024FRL9_ECOLX A0A024FRL9_ECOLX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6ol8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ol8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Imiolczyk, B]]	+	[[Category: Imiolczyk B]]
-	[[Category: Jaskolski, M]]	+	[[Category: Jaskolski M]]
-	[[Category: Raczynska~~, J E]]~~	+	[[Category: Raczynska JE]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-antibiotic complex]]~~	+
-	~~[[Category: Metallo-beta-lactamase]]~~	+
-	~~[[Category: Ndm~~]]	+

OCA at 05:48, 13 May 2020

OCA — Wed, 13 May 2020 05:48:39 GMT

←Older revision		Revision as of 05:48, 13 May 2020
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	==Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin==		==Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin==
-	<StructureSection load='6ol8' size='340' side='right'caption='[[6ol8]]' scene=''>	+	<StructureSection load='6ol8' size='340' side='right'caption='[[6ol8]], [[Resolution\|resolution]] 2.10Å' 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=6OL8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OL8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ol8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OL8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OL8 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=6ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ol8 OCA], [http://pdbe.org/6ol8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ol8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ol8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ol8 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ZZ7:(2R,4S)-2-[(R)-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC+ACID'>ZZ7</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ogo\|6ogo]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaNDM-12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ol8 OCA], [http://pdbe.org/6ol8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ol8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ol8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ol8 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Two accessory loop regions that are present in numerous variants of New Delhi metallo-beta-lactamases (NDM) are important for the enzymatic activity. The first one is a flexible loop L3 that is located near the active site and is thought to play an important role in the catalytic process. The second region, Omega loop is located close to a structural element that coordinates two essential zinc ions. Both loops are not involved in any specific interactions with a substrate. Herein, we investigated how the length and hydrophobicity of loop L3 influence the enzymatic activity of NDMs, by analyzing mutants of NDM-1 with various deletions/point mutations within the L3 loop. We also investigated NDM variants with sequence variations/artificial deletions within the Omega loop. For all these variants we determined kinetic parameters for the hydrolysis of ampicillin, imipenem, and a chromogenic cephalosporin (CENTA). None of the mutations in the L3 loop completely abolished the enzymatic activity of NDM-1. Our results suggest that various elements of the loop play different roles in the hydrolysis of different substrates and the flexibility of the loop seems necessary to fulfill the requirements imposed by various substrates. Deletions within the Omega loop usually enhanced the enzymatic activity, particularly for the hydrolysis of ampicillin and imipenem. However, the exact role of the Omega loop in the catalytic reaction remains unclear. In our kinetic tests, the NDM enzymes were inhibited in the beta-lactamase reaction by the CENTA substrate. We also present the X-ray crystal structures of the NDM-1, NDM-9 and NDM-12 proteins.
		+
		+	Flexible loops of New Delhi metallo-beta-lactamase modulate its activity towards different substrates.,Raczynska JE, Imiolczyk B, Komorowska M, Sliwiak J, Czyrko-Horczak J, Brzezinski K, Jaskolski M Int J Biol Macromol. 2020 Apr 28;158:104-115. doi:, 10.1016/j.ijbiomac.2020.04.219. PMID:32353499<ref>PMID:32353499</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ol8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Imiolczyk B]]	+	[[Category: Imiolczyk, B]]
-	[[Category: Jaskolski M]]	+	[[Category: Jaskolski, M]]
-	[[Category: Raczynska JE]]	+	[[Category: Raczynska, J E]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-antibiotic complex]]
		+	[[Category: Metallo-beta-lactamase]]
		+	[[Category: Ndm]]

OCA at 05:41, 22 April 2020

OCA — Wed, 22 Apr 2020 05:41:25 GMT

←Older revision		Revision as of 05:41, 22 April 2020
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-	'''Unreleased structure'''

-	~~The entry 6ol8 is ON HOLD until Paper Publication~~	+	==Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin==
-		+	<StructureSection load='6ol8' size='340' side='right'caption='[[6ol8]]' scene=''>
-	~~Authors: Raczynska, J.E., Imiolczyk, B., Jaskolski, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OL8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OL8 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin	+	</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=6ol8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ol8 OCA], [http://pdbe.org/6ol8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ol8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ol8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ol8 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Imiolczyk, B]]	+	__TOC__
-	[[Category: Jaskolski, M]]	+	</StructureSection>
-	[[Category: Raczynska~~, J.E~~]]	+	[[Category: Large Structures]]
		+	[[Category: Imiolczyk B]]
		+	[[Category: Jaskolski M]]
		+	[[Category: Raczynska JE]]

OCA at 07:08, 1 May 2019

OCA — Wed, 01 May 2019 07:08:03 GMT

←Older revision		Revision as of 07:08, 1 May 2019
Line 3:		Line 3:
	The entry 6ol8 is ON HOLD until Paper Publication		The entry 6ol8 is ON HOLD until Paper Publication

-	Authors: Raczynska, J.E., Imiolczyk, B.I., Jaskolski, M.J.	+	Authors: Raczynska, J.E., Imiolczyk, B., Jaskolski, M.

	Description: Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin		Description: Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Jaskolski~~, ~~M.J~~]]	+	[[Category: Imiolczyk, B]]
-	[[Category: ~~Imiolczyk~~, ~~B.I~~]]	+	[[Category: Jaskolski, M]]
	[[Category: Raczynska, J.E]]		[[Category: Raczynska, J.E]]

OCA: Protected "6ol8" [edit=sysop:move=sysop]

OCA — Wed, 24 Apr 2019 05:02:10 GMT

Protected "6ol8" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:02, 24 April 2019

OCA: New page: '''Unreleased structure''' The entry 6ol8 is ON HOLD until Paper Publication Authors: Raczynska, J.E., Imiolczyk, B.I., Jaskolski, M.J. Description: Crystal structure of NDM-12 metallo...

OCA — Wed, 24 Apr 2019 05:02:08 GMT

New page: '''Unreleased structure''' The entry 6ol8 is ON HOLD until Paper Publication Authors: Raczynska, J.E., Imiolczyk, B.I., Jaskolski, M.J. Description: Crystal structure of NDM-12 metallo...

New page

'''Unreleased structure'''

The entry 6ol8 is ON HOLD until Paper Publication

Authors: Raczynska, J.E., Imiolczyk, B.I., Jaskolski, M.J.

Description: Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin
[[Category: Unreleased Structures]]
[[Category: Jaskolski, M.J]]
[[Category: Imiolczyk, B.I]]
[[Category: Raczynska, J.E]]