5haq - Revision history

OCA at 07:29, 9 August 2023

OCA — Wed, 09 Aug 2023 07:29:02 GMT

←Older revision		Revision as of 07:29, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='5haq' size='340' side='right'caption='[[5haq]], [[Resolution\|resolution]] 2.14Å' scene=''>		<StructureSection load='5haq' size='340' side='right'caption='[[5haq]], [[Resolution\|resolution]] 2.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5haq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus~~ pneumoniae~~" (schroeter 1886) flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HAQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HAQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5haq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HAQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CD:CADMIUM+ION'>CD</scene~~>, ~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 2.14Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~KCX~~:~~LYSINE~~+~~NZ-CARBOXYLIC+ACID~~'>~~KCX~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5hai\|5hai]]~~, ~~[[5hap\|5hap]], [[5har\|5har]]~~<~~/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=5haq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5haq OCA], [https://pdbe.org/5haq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5haq RCSB], [https://www.ebi.ac.uk/pdbsum/5haq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5haq ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">bla OXA~~-~~48, blaOXA-48, KPE71T_00045 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</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=5haq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5haq OCA], [~~http~~://pdbe.org/5haq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5haq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5haq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5haq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6XEC0_KLEPN Q6XEC0_KLEPN]
	<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: ~~Beta-lactamase~~]]	+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adamski~~, C J~~]]	+	[[Category: Adamski CJ]]
-	[[Category: Hu, L]]	+	[[Category: Hu L]]
-	[[Category: Mehta~~, S C~~]]	+	[[Category: Mehta SC]]
-	[[Category: Palzkill~~, T G~~]]	+	[[Category: Palzkill TG]]
-	[[Category: Prasad~~, B V.V~~]]	+	[[Category: Prasad BVV]]
-	[[Category: Sankaran, B]]	+	[[Category: Sankaran B]]
-	[[Category: Stojanoski, V]]	+	[[Category: Stojanoski V]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Serine beta-lactamase~~]]	+

OCA at 16:12, 11 December 2019

OCA — Wed, 11 Dec 2019 16:12:46 GMT

←Older revision		Revision as of 16:12, 11 December 2019
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	==OXa-48 beta-lactamase mutant - S70G==		==OXa-48 beta-lactamase mutant - S70G==
-	<StructureSection load='5haq' size='340' side='right' caption='[[5haq]], [[Resolution\|resolution]] 2.14Å' scene=''>	+	<StructureSection load='5haq' size='340' side='right'caption='[[5haq]], [[Resolution\|resolution]] 2.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5haq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HAQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5haq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HAQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hai\|5hai]], [[5hap\|5hap]], [[5har\|5har]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hai\|5hai]], [[5hap\|5hap]], [[5har\|5har]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla OXA-48, blaOXA-48, KPE71T_00045 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</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=5haq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5haq OCA], [http://pdbe.org/5haq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5haq RCSB], [http://www.ebi.ac.uk/pdbsum/5haq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5haq ProSAT]</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=5haq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5haq OCA], [http://pdbe.org/5haq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5haq RCSB], [http://www.ebi.ac.uk/pdbsum/5haq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5haq ProSAT]</span></td></tr>
Line 21:		Line 22:

	==See Also==		==See Also==
-	*[[Beta-lactamase\|Beta-lactamase]]	+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Adamski, C J]]		[[Category: Adamski, C J]]
	[[Category: Hu, L]]		[[Category: Hu, L]]

OCA at 06:56, 29 March 2017

OCA — Wed, 29 Mar 2017 06:56:11 GMT

←Older revision		Revision as of 06:56, 29 March 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5haq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5haq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase\|Beta-lactamase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:06, 10 September 2016

OCA — Sat, 10 Sep 2016 21:06:14 GMT

←Older revision		Revision as of 21:06, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5haq is ~~ON HOLD until Paper~~ Publication	+	==OXa-48 beta-lactamase mutant - S70G==
		+	<StructureSection load='5haq' size='340' side='right' caption='[[5haq]], [[Resolution\|resolution]] 2.14Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5haq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HAQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hai\|5hai]], [[5hap\|5hap]], [[5har\|5har]]</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=5haq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5haq OCA], [http://pdbe.org/5haq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5haq RCSB], [http://www.ebi.ac.uk/pdbsum/5haq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5haq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Serine beta-lactamases are bacterial enzymes that hydrolyze beta-lactam antibiotics. They utilize an active-site serine residue as a nucleophile, forming an acyl-enzyme intermediate during hydrolysis. In this study, thermal denaturation experiments as well as X-ray crystallography were performed to test the effect of substitution of the catalytic serine with glycine on protein stability in serine beta-lactamases. Six different enzymes comprising representatives from each of the three classes of serine beta-lactamases were examined, including TEM-1, CTX-M-14, and KPC-2 of class A, P99 of class C, and OXA-48 and OXA-163 of class D. For each enzyme, the wild type and a serine-to-glycine mutant were evaluated for stability. The glycine mutants all exhibited enhanced thermostability compared to that of the wild type. In contrast, alanine substitutions of the catalytic serine in TEM-1, OXA-48, and OXA-163 did not alter stability, suggesting removal of the Cbeta atom is key to the stability increase associated with the glycine mutants. The X-ray crystal structures of P99 S64G, OXA-48 S70G and S70A, and OXA-163 S70G suggest that removal of the side chain of the catalytic serine releases steric strain to improve enzyme stability. Additionally, analysis of the torsion angles at the nucleophile position indicates that the glycine mutants exhibit improved distance and angular parameters of the intrahelical hydrogen bond network compared to those of the wild-type enzymes, which is also consistent with increased stability. The increased stability of the mutants indicates that the enzyme pays a price in stability for the presence of a side chain at the catalytic serine position but that the cost is necessary in that removal of the serine drastically impairs function. These findings support the stability-function hypothesis, which states that active-site residues are optimized for substrate binding and catalysis but that the requirements for catalysis are often not consistent with the requirements for optimal stability.

-	~~Authors: Stojanoski~~, V., Adamski~~, C.J.~~, Hu, L., Mehta~~, S.C.~~, Sankaran, B., Prasad, B.V.V., ~~Palzkill, T.G~~.	+	Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine beta-Lactamases by Relieving Steric Strain.,Stojanoski V, Adamski CJ, Hu L, Mehta SC, Sankaran B, Zwart P, Prasad BV, Palzkill T Biochemistry. 2016 May 3;55(17):2479-90. doi: 10.1021/acs.biochem.6b00056. Epub, 2016 Apr 22. PMID:27073009<ref>PMID:27073009</ref>

-	~~Description: OXa-48 beta-lactamase mutant -S70G~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Mehta~~, S.~~C]]~~	+	<div class="pdbe-citations 5haq" style="background-color:#fffaf0;"></div>
-	~~[[Category~~: ~~Stojanoski, V]]~~	+	== References ==
-	[[Category: ~~Sankaran, B~~]]	+	<references/>
-	[[Category: Adamski, C.J]]	+	__TOC__
-	~~[[Category: Palzkill, T.G~~]]	+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Adamski, C J]]
	[[Category: Hu, L]]		[[Category: Hu, L]]
-	[[Category: Prasad, B.V.V]]	+	[[Category: Mehta, S C]]
		+	[[Category: Palzkill, T G]]
		+	[[Category: Prasad, B V.V]]
		+	[[Category: Sankaran, B]]
		+	[[Category: Stojanoski, V]]
		+	[[Category: Hydrolase]]
		+	[[Category: Serine beta-lactamase]]

OCA at 12:23, 2 March 2016

OCA — Wed, 02 Mar 2016 12:23:54 GMT

←Older revision		Revision as of 12:23, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5haq is ON HOLD	+	The entry 5haq is ON HOLD until Paper Publication

	Authors: Stojanoski, V., Adamski, C.J., Hu, L., Mehta, S.C., Sankaran, B., Prasad, B.V.V., Palzkill, T.G.		Authors: Stojanoski, V., Adamski, C.J., Hu, L., Mehta, S.C., Sankaran, B., Prasad, B.V.V., Palzkill, T.G.

OCA at 18:44, 13 January 2016

OCA — Wed, 13 Jan 2016 18:44:13 GMT

←Older revision		Revision as of 18:44, 13 January 2016
Line 3:		Line 3:
	The entry 5haq is ON HOLD		The entry 5haq is ON HOLD

-	Authors: Stojanoski, V., Adamski, C.J., Hu, L., Mehta, S.C., Sankaran, B., Prasad B.V.V., ~~and~~ Palzkill T.G.	+	Authors: Stojanoski, V., Adamski, C.J., Hu, L., Mehta, S.C., Sankaran, B., Prasad, B.V.V., Palzkill, T.G.

	Description: OXa-48 beta-lactamase mutant -S70G		Description: OXa-48 beta-lactamase mutant -S70G
Line 10:		Line 10:
	[[Category: Stojanoski, V]]		[[Category: Stojanoski, V]]
	[[Category: Sankaran, B]]		[[Category: Sankaran, B]]
-	[[Category: Prasad B.V.V]]
	[[Category: Adamski, C.J]]		[[Category: Adamski, C.J]]
-	[[Category: ~~And~~ Palzkill T.G]]	+	[[Category: Palzkill, T.G]]
	[[Category: Hu, L]]		[[Category: Hu, L]]
		+	[[Category: Prasad, B.V.V]]

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

OCA — Thu, 07 Jan 2016 10:25:15 GMT

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

←Older revision

Revision as of 10:25, 7 January 2016

OCA: New page: '''Unreleased structure''' The entry 5haq is ON HOLD Authors: Stojanoski, V., Adamski, C.J., Hu, L., Mehta, S.C., Sankaran, B., Prasad B.V.V., and Palzkill T.G. Description: OXa-48 bet...

OCA — Thu, 07 Jan 2016 10:25:13 GMT

New page: '''Unreleased structure''' The entry 5haq is ON HOLD Authors: Stojanoski, V., Adamski, C.J., Hu, L., Mehta, S.C., Sankaran, B., Prasad B.V.V., and Palzkill T.G. Description: OXa-48 bet...

New page

'''Unreleased structure'''

The entry 5haq is ON HOLD

Authors: Stojanoski, V., Adamski, C.J., Hu, L., Mehta, S.C., Sankaran, B., Prasad B.V.V., and Palzkill T.G.

Description: OXa-48 beta-lactamase mutant -S70G
[[Category: Unreleased Structures]]
[[Category: Mehta, S.C]]
[[Category: Stojanoski, V]]
[[Category: Sankaran, B]]
[[Category: Prasad B.V.V]]
[[Category: Adamski, C.J]]
[[Category: And Palzkill T.G]]
[[Category: Hu, L]]