5gzw - Revision history

OCA at 11:47, 2 August 2023

OCA — Wed, 02 Aug 2023 11:47:26 GMT

←Older revision		Revision as of 11:47, 2 August 2023
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	<StructureSection load='5gzw' size='340' side='right'caption='[[5gzw]], [[Resolution\|resolution]] 1.49Å' scene=''>		<StructureSection load='5gzw' size='340' side='right'caption='[[5gzw]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gzw]] is a 2 chain structure with sequence from [https://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=5GZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gzw]] 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=5GZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GZW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.489Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ampC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6]~~ </~~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=5gzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzw OCA], [https://pdbe.org/5gzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gzw RCSB], [https://www.ebi.ac.uk/pdbsum/5gzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzw 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=5gzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzw OCA], [https://pdbe.org/5gzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gzw RCSB], [https://www.ebi.ac.uk/pdbsum/5gzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A076YIY5_ECOLX A0A076YIY5_ECOLX] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.[ARBA:ARBA00003808]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: Beta-lactamase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: An~~, Y J~~]]	+	[[Category: An YJ]]
-	[[Category: Cha~~, S S]]~~	+	[[Category: Cha SS]]
-	~~[[Category: Ampc]]~~	+
-	~~[[Category: Class c]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:38, 31 March 2021

OCA — Wed, 31 Mar 2021 10:38:53 GMT

←Older revision		Revision as of 10:38, 31 March 2021
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-	==Crystal structure of AmpC BER==	+	==Crystal structure of AmpC BER adenylylated by acetyl-AMP==
-	<StructureSection load='5gzw' size='340' side='right'caption='[[5gzw]]' scene=''>	+	<StructureSection load='5gzw' size='340' side='right'caption='[[5gzw]], [[Resolution\|resolution]] 1.49Å' 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=5GZW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gzw]] is a 2 chain structure with sequence from [https://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=5GZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GZW 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=5gzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzw OCA], [~~http~~://pdbe.org/5gzw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gzw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gzw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzw 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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=5gzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzw OCA], [https://pdbe.org/5gzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gzw RCSB], [https://www.ebi.ac.uk/pdbsum/5gzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzw ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Objectives: : Investigation into the adenylylation of the nucleophilic serine in AmpC BER and CMY-10 extended-spectrum class C beta-lactamases. Methods: : The formation and the stability of the adenylate adduct were examined by X-ray crystallography and MS. Inhibition assays for kinetic parameters were performed by monitoring the hydrolytic activity of AmpC BER and CMY-10 using nitrocefin as a reporter substrate. The effect of adenosine 5'-(P-acetyl)monophosphate (acAMP) on the MIC of ceftazidime was tested with four Gram-negative clinical isolates. Results: : The crystal structures and MS analyses confirmed the acAMP-mediated adenylylation of the nucleophilic serine in AmpC BER and CMY-10. acAMP inhibited AmpC BER and CMY-10 through the adenylylation of the nucleophilic serine, which could be modelled as a two-step mechanism. The initial non-covalent binding of acAMP to the active site is followed by the covalent attachment of its AMP moiety to the nucleophilic serine. The inhibition efficiencies ( k inact / K I ) of acAMP against AmpC BER and CMY-10 were determined to be 320 and 140 M -1 s -1 , respectively. The combination of ceftazidime and acAMP reduced the MIC of ceftazidime against the tested bacteria. Conclusions: : Our structural and kinetic studies revealed the detailed mechanism of adenylylation of the nucleophilic serine and may serve as a starting point for the design of novel class C beta-lactamase inhibitors on the basis of the nucleotide scaffold.
		+
		+	Structural and mechanistic insights into the inhibition of class C beta-lactamases through the adenylylation of the nucleophilic serine.,Kim MK, An YJ, Na JH, Seol JH, Ryu JY, Lee JW, Kang LW, Chung KM, Lee JH, Moon JH, Lee JS, Cha SS J Antimicrob Chemother. 2017 Mar 1;72(3):735-743. doi: 10.1093/jac/dkw491. PMID:27999057<ref>PMID:27999057</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5gzw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]		*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: An YJ]]	+	[[Category: An, Y J]]
-	[[Category: Cha SS]]	+	[[Category: Cha, S S]]
		+	[[Category: Ampc]]
		+	[[Category: Class c]]
		+	[[Category: Hydrolase]]

OCA at 06:47, 20 May 2020

OCA — Wed, 20 May 2020 06:47:39 GMT

←Older revision		Revision as of 06:47, 20 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gzw is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of AmpC BER==
		+	<StructureSection load='5gzw' size='340' side='right'caption='[[5gzw]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GZW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GZW 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=5gzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzw OCA], [http://pdbe.org/5gzw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gzw RCSB], [http://www.ebi.ac.uk/pdbsum/5gzw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzw ProSAT]</span></td></tr>
		+	</table>

-	~~Authors: An, Y.J., Cha, S.S.~~	+	==See Also==
-		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
-	~~Description: Crystal structure of AmpC BER~~	+	__TOC__
-	[[Category: ~~Unreleased~~ Structures]]	+	</StructureSection>
-	[[Category: ~~Cha, S.S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~An, Y.J~~]]	+	[[Category: An YJ]]
		+	[[Category: Cha SS]]

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

OCA — Wed, 19 Oct 2016 11:58:37 GMT

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

←Older revision

Revision as of 11:58, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5gzw is ON HOLD until Paper Publication Authors: An, Y.J., Cha, S.S. Description: Crystal structure of AmpC BER Category: Unreleased Structures...

OCA — Wed, 19 Oct 2016 11:58:36 GMT

New page: '''Unreleased structure''' The entry 5gzw is ON HOLD until Paper Publication Authors: An, Y.J., Cha, S.S. Description: Crystal structure of AmpC BER Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 5gzw is ON HOLD until Paper Publication

Authors: An, Y.J., Cha, S.S.

Description: Crystal structure of AmpC BER
[[Category: Unreleased Structures]]
[[Category: Cha, S.S]]
[[Category: An, Y.J]]