5tpq - Revision history

OCA at 13:07, 4 October 2023

OCA — Wed, 04 Oct 2023 13:07:13 GMT

←Older revision		Revision as of 13:07, 4 October 2023
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	<StructureSection load='5tpq' size='340' side='right'caption='[[5tpq]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='5tpq' size='340' side='right'caption='[[5tpq]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tpq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TPQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tpq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TPQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.45Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[3tg0\|3tg0~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>phoA, b0383, JW0374 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83333 ECOLI])</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=5tpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpq OCA], [https://pdbe.org/5tpq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tpq RCSB], [https://www.ebi.ac.uk/pdbsum/5tpq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpq ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1]~~ </~~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=5tpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpq OCA], [~~http~~://pdbe.org/5tpq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tpq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tpq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PPB_ECOLI PPB_ECOLI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alkaline phosphatase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: AlSadhan, I]]	+	[[Category: AlSadhan I]]
-	[[Category: Doukov, T]]	+	[[Category: Doukov T]]
-	[[Category: Herschlag, D]]	+	[[Category: Herschlag D]]
-	[[Category: Lyubimov~~, A Y~~]]	+	[[Category: Lyubimov AY]]
-	[[Category: Sunden, F]]	+	[[Category: Sunden F]]
-	[[Category: Swan, J]]	+	[[Category: Swan J]]
-	~~[[Category: Bimetallo motif]]~~	+
-	~~[[Category: Catalytic promiscuity]]~~	+
-	~~[[Category: D101a/d153a/r166s/e322a/k328a]]~~	+
-	~~[[Category: Evolution]]~~	+
-	~~[[Category: Generalist enzyme]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:04, 1 January 2020

OCA — Wed, 01 Jan 2020 09:04:17 GMT

←Older revision		Revision as of 09:04, 1 January 2020
Line 1:		Line 1:

	==E. coli alkaline phosphatase D101A, D153A, R166S, E322A, K328A mutant==		==E. coli alkaline phosphatase D101A, D153A, R166S, E322A, K328A mutant==
-	<StructureSection load='5tpq' size='340' side='right' caption='[[5tpq]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='5tpq' size='340' side='right'caption='[[5tpq]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tpq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tpq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPQ FirstGlance]. <br>
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Alkaline phosphatase\|Alkaline phosphatase]]	+	*[[Alkaline phosphatase 3D structures\|Alkaline phosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	[[Category: Alkaline phosphatase]]		[[Category: Alkaline phosphatase]]
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: AlSadhan, I]]		[[Category: AlSadhan, I]]
	[[Category: Doukov, T]]		[[Category: Doukov, T]]

OCA at 06:31, 18 April 2018

OCA — Wed, 18 Apr 2018 06:31:14 GMT

←Older revision		Revision as of 06:31, 18 April 2018
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5tpq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5tpq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alkaline phosphatase\|Alkaline phosphatase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:32, 8 November 2017

OCA — Wed, 08 Nov 2017 07:32:57 GMT

←Older revision		Revision as of 07:32, 8 November 2017
Line 3:		Line 3:
	<StructureSection load='5tpq' size='340' side='right' caption='[[5tpq]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='5tpq' size='340' side='right' caption='[[5tpq]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tpq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tpq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tg0\|3tg0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tg0\|3tg0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phoA, b0383, JW0374 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </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=5tpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpq OCA], [http://pdbe.org/5tpq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tpq RCSB], [http://www.ebi.ac.uk/pdbsum/5tpq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpq 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=5tpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpq OCA], [http://pdbe.org/5tpq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tpq RCSB], [http://www.ebi.ac.uk/pdbsum/5tpq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Members of enzyme superfamilies specialize in different reactions but often exhibit catalytic promiscuity for one anothers reactions, consistent with catalytic promiscuity as an important driver in the evolution of new enzymes. Wanting to understand how catalytic promiscuity and other factors may influence evolution across a superfamily, we turned to the well-studied Alkaline Phosphatase (AP) superfamily, comparing three of its members-two evolutionarily distinct phosphatases and a phosphodiesterase. We mutated distinguishing active-site residues to generate enzymes that had a common Zn2+ bimetallo core, but little sequence similarity and different auxiliary domains. We then tested the catalytic capabilities of these pruned enzymes with a series of substrates. A substantial rate enhancement of ~1011-fold for both phosphate mono- and diester hydrolysis by each enzyme indicated that the Zn2+ bimetallo core is an effective mono/di-esterase generalist and that the bimetallo cores were not evolutionarily tuned to prefer their cognate reactions. In contrast, our pruned enzymes were ineffective sulfatases, and this limited promiscuity may have provided a driving force for founding the distinct one-metal-ion branch that contains all known AP superfamily sulfatases. Finally, our pruned enzymes exhibited 107-108 fold phosphotriesterase rate enhancements, despite absence of such enzymes within the AP superfamily. We speculate that the superfamily active site architecture involved in nucleophile positioning prevents accommodation of the additional triester substituent. Overall, we suggest that catalytic promiscuity and the ease or difficulty of remodeling and building onto existing protein scaffolds have greatly influenced the course of enzyme evolution and will provide lessons for engineering new enzymes.
		+
		+	Differential Catalytic Promiscuity of the Alkaline Phosphatase Superfamily Bimetallo Core Reveals Mechanistic Features Underlying Enzyme Evolution.,Sunden F, AlSadhan I, Lyubimov A, Doukov T, Swan J, Herschlag D J Biol Chem. 2017 Oct 25. pii: jbc.M117.788240. doi: 10.1074/jbc.M117.788240. PMID:29070681<ref>PMID:29070681</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5tpq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Alkaline phosphatase]]		[[Category: Alkaline phosphatase]]
		+	[[Category: Ecoli]]
	[[Category: AlSadhan, I]]		[[Category: AlSadhan, I]]
	[[Category: Doukov, T]]		[[Category: Doukov, T]]

OCA at 06:30, 1 November 2017

OCA — Wed, 01 Nov 2017 06:30:21 GMT

←Older revision		Revision as of 06:30, 1 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tpq is ~~ON HOLD until Paper Publication~~	+	==E. coli alkaline phosphatase D101A, D153A, R166S, E322A, K328A mutant==
-		+	<StructureSection load='5tpq' size='340' side='right' caption='[[5tpq]], [[Resolution\|resolution]] 2.45Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5tpq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPQ FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tg0\|3tg0]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </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=5tpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpq OCA], [http://pdbe.org/5tpq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tpq RCSB], [http://www.ebi.ac.uk/pdbsum/5tpq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpq ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alkaline phosphatase]]
		+	[[Category: AlSadhan, I]]
		+	[[Category: Doukov, T]]
		+	[[Category: Herschlag, D]]
		+	[[Category: Lyubimov, A Y]]
		+	[[Category: Sunden, F]]
		+	[[Category: Swan, J]]
		+	[[Category: Bimetallo motif]]
		+	[[Category: Catalytic promiscuity]]
		+	[[Category: D101a/d153a/r166s/e322a/k328a]]
		+	[[Category: Evolution]]
		+	[[Category: Generalist enzyme]]
		+	[[Category: Hydrolase]]

OCA at 17:43, 9 December 2016

OCA — Fri, 09 Dec 2016 17:43:53 GMT

←Older revision		Revision as of 17:43, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 26 Oct 2016 17:21:58 GMT

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

←Older revision

Revision as of 17:21, 26 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tpq is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Oct 2016 17:21:57 GMT

New page: '''Unreleased structure''' The entry 5tpq is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5tpq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]