5x5g - Revision history

OCA at 07:54, 22 November 2023

OCA — Wed, 22 Nov 2023 07:54:10 GMT

←Older revision		Revision as of 07:54, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5x5g' size='340' side='right'caption='[[5x5g]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5x5g' size='340' side='right'caption='[[5x5g]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5g]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus~~ marcescens~~" (bizio 1823) trevisan in de toni and trevisan 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X5G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X5G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</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]] 2Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5x5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5g OCA], [~~http~~://pdbe.org/5x5g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x5g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x5g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5g 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=5x5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5g OCA], [https://pdbe.org/5x5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x5g RCSB], [https://www.ebi.ac.uk/pdbsum/5x5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5g ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0B6VPP7_SERMA A0A0B6VPP7_SERMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Arakawa, Y~~]]	+	[[Category: Serratia marcescens]]
-	[[Category: ~~Jin, W~~]]	+	[[Category: Arakawa Y]]
-	[[Category: ~~Wachino, J~~]]	+	[[Category: Jin W]]
-	[[Category: ~~Extended-spectrum beta-lactamase]]~~	+	[[Category: Wachino J]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:26, 7 October 2020

OCA — Wed, 07 Oct 2020 07:26:42 GMT

←Older revision		Revision as of 07:26, 7 October 2020
Line 1:		Line 1:

	==Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with OP0595==		==Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with OP0595==
-	<StructureSection load='5x5g' size='340' side='right' caption='[[5x5g]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5x5g' size='340' side='right'caption='[[5x5g]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X5G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X5G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</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'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5x5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5g OCA], [http://pdbe.org/5x5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5g RCSB], [http://www.ebi.ac.uk/pdbsum/5x5g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5g 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=5x5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5g OCA], [http://pdbe.org/5x5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5g RCSB], [http://www.ebi.ac.uk/pdbsum/5x5g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5g ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The development of effective inhibitors that block extended-spectrum beta-lactamases (ESBLs) and restore the action of beta-lactams represents an effective strategy against ESBL-producing Enterobacteriaceae We evaluated the inhibitory effects of the diazabicyclooctanes avibactam and OP0595 against TLA-3, an ESBL that we identified previously. Avibactam and OP0595 inhibited TLA-3 with apparent inhibitor constants (Kiapp) of 1.71 +/- 0.10 and 1.49 +/- 0.05 muM, respectively, and could restore susceptibility to cephalosporins in the TLA-3-producing Escherichia coli strain. The value of the second-order acylation rate constant (k2/K, where k2 is the acylation rate constant and K is the equilibrium constant) of avibactam [(3.25 +/- 0.03) x 10(3) M(-1) . s(-1)] was closer to that of class C and D beta-lactamases (k2/K, <10(4) M(-1) . s(-1)) than that of class A beta-lactamases (k2/K, >10(4) M(-1) . s(-1)). In addition, we determined the structure of TLA-3 and that of TLA-3 complexed with avibactam or OP0595 at resolutions of 1.6, 1.6, and 2.0 A, respectively. TLA-3 contains an inverted Omega loop and an extended loop between the beta5 and beta6 strands (insertion after Ser237), which appear only in PER-type class A beta-lactamases. These structures might favor the accommodation of cephalosporins harboring bulky R1 side chains. TLA-3 presented a high catalytic efficiency (kcat/Km ) against cephalosporins, including cephalothin, cefuroxime, and cefotaxime. Avibactam and OP0595 bound covalently to TLA-3 via the Ser70 residue and made contacts with residues Ser130, Thr235, and Ser237, which are conserved in ESBLs. Additionally, the sulfate group of the inhibitors formed polar contacts with amino acid residues in a positively charged pocket of TLA-3. Our findings provide a structural template for designing improved diazabicyclooctane-based inhibitors that are effective against ESBL-producing Enterobacteriaceae.
		+
		+	Structural Insights into the TLA-3 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam and OP0595.,Jin W, Wachino JI, Yamaguchi Y, Kimura K, Kumar A, Yamada M, Morinaka A, Sakamaki Y, Yonezawa M, Kurosaki H, Arakawa Y Antimicrob Agents Chemother. 2017 Sep 22;61(10). pii: AAC.00501-17. doi:, 10.1128/AAC.00501-17. Print 2017 Oct. PMID:28739781<ref>PMID:28739781</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x5g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Arakawa, Y]]		[[Category: Arakawa, Y]]
	[[Category: Jin, W]]		[[Category: Jin, W]]

OCA at 10:11, 10 September 2017

OCA — Sun, 10 Sep 2017 10:11:17 GMT

←Older revision		Revision as of 10:11, 10 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x5g is ~~ON HOLD until Feb 15 2019~~	+	==Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with OP0595==
-		+	<StructureSection load='5x5g' size='340' side='right' caption='[[5x5g]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Wachino~~, J., ~~Jin~~, W., ~~Arakawa~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x5g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5G FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of TLA-3 extended-spectrum beta~~-lactamase ~~in a complex with OP0595~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5x5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5g OCA], [http://pdbe.org/5x5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5g RCSB], [http://www.ebi.ac.uk/pdbsum/5x5g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5g ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Arakawa, Y]]
		+	[[Category: Jin, W]]
	[[Category: Wachino, J]]		[[Category: Wachino, J]]
-	[[Category: ~~Jin, W~~]]	+	[[Category: Extended-spectrum beta-lactamase]]
-	[[Category: ~~Arakawa, Y~~]]	+	[[Category: Hydrolase]]

OCA: Protected "5x5g" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:46:27 GMT

Protected "5x5g" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:46, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x5g is ON HOLD until Feb 15 2019 Authors: Wachino, J., Jin, W., Arakawa, Y. Description: Crystal structure of TLA-3 extended-spectrum beta-lactama...

OCA — Thu, 09 Mar 2017 15:46:26 GMT

New page: '''Unreleased structure''' The entry 5x5g is ON HOLD until Feb 15 2019 Authors: Wachino, J., Jin, W., Arakawa, Y. Description: Crystal structure of TLA-3 extended-spectrum beta-lactama...

New page

'''Unreleased structure'''

The entry 5x5g is ON HOLD until Feb 15 2019

Authors: Wachino, J., Jin, W., Arakawa, Y.

Description: Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with OP0595
[[Category: Unreleased Structures]]
[[Category: Wachino, J]]
[[Category: Jin, W]]
[[Category: Arakawa, Y]]