5d81 - Revision history

OCA at 10:25, 21 June 2023

OCA — Wed, 21 Jun 2023 10:25:04 GMT

←Older revision		Revision as of 10:25, 21 June 2023
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	<StructureSection load='5d81' size='340' side='right'caption='[[5d81]], [[Resolution\|resolution]] 1.39Å' scene=''>		<StructureSection load='5d81' size='340' side='right'caption='[[5d81]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d81]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D81 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D81 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d81]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D81 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><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=3CT:3-CHLORO-L-TYROSINE'>3CT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene>~~</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=5d81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d81 OCA], [https://pdbe.org/5d81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d81 RCSB], [https://www.ebi.ac.uk/pdbsum/5d81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d81 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d82\|5d82]]~~, ~~[[5d83\|5d83]]~~<~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">ksi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" 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/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </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=5d81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d81 OCA], [~~http~~://pdbe.org/5d81 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d81 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d81 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d81 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]
	<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 fluorescens putidus flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Steroid Delta-isomerase~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: Boxer~~, S G~~]]	+	[[Category: Boxer SG]]
-	[[Category: Fried~~, S D~~]]	+	[[Category: Fried SD]]
-	[[Category: Wu, Y]]	+	[[Category: Wu Y]]
-	~~[[Category: Isomerase~~]]	+

OCA at 11:19, 25 December 2019

OCA — Wed, 25 Dec 2019 11:19:33 GMT

←Older revision		Revision as of 11:19, 25 December 2019
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		+
	==Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI); D40N, Y57(Cl-Y)==		==Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI); D40N, Y57(Cl-Y)==
-	<StructureSection load='5d81' size='340' side='right' caption='[[5d81]], [[Resolution\|resolution]] 1.39Å' scene=''>	+	<StructureSection load='5d81' size='340' side='right'caption='[[5d81]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d81]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D81 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d81]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D81 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d82\|5d82]], [[5d83\|5d83]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d82\|5d82]], [[5d83\|5d83]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" 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/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </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=5d81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d81 OCA], [http://pdbe.org/5d81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d81 RCSB], [http://www.ebi.ac.uk/pdbsum/5d81 PDBsum]</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=5d81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d81 OCA], [http://pdbe.org/5d81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d81 RCSB], [http://www.ebi.ac.uk/pdbsum/5d81 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d81 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5d81" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5d81" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens putidus flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]
	[[Category: Boxer, S G]]		[[Category: Boxer, S G]]

OCA at 16:12, 2 December 2015

OCA — Wed, 02 Dec 2015 16:12:45 GMT

←Older revision		Revision as of 16:12, 2 December 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI); D40N, Y57(Cl-Y)==
		+	<StructureSection load='5d81' size='340' side='right' caption='[[5d81]], [[Resolution\|resolution]] 1.39Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5d81]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D81 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d82\|5d82]], [[5d83\|5d83]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </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=5d81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d81 OCA], [http://pdbe.org/5d81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d81 RCSB], [http://www.ebi.ac.uk/pdbsum/5d81 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Extended hydrogen bond networks are a common structural motif of enzymes. A recent analysis proposed quantum delocalization of protons as a feature present in the hydrogen bond network spanning a triad of tyrosines (Y16, Y32, and Y57) in the active site of ketosteroid isomerase (KSI), contributing to its unusual acidity and large isotope shift. In this study, we utilized amber suppression to substitute each tyrosine residue with 3-chlorotyrosine to test the delocalization model and the proton affinity balance in the triad. X-ray crystal structures of each variant demonstrated that the structure, notably the O-O distances within the triad, was unaffected by 3-chlorotyrosine substitutions. The changes in the cluster's acidity and the acidity's isotope dependence in these variants were assessed via UV-vis spectroscopy and the proton sharing pattern among individual residues with 13C nuclear magnetic resonance. Our data show pKa detuning at each triad residue alters the proton delocalization behavior in the H-bond network. The extra stabilization energy necessary for the unusual acidity mainly comes from the strong interactions between Y57 and Y16. This is further enabled by Y32, which maintains the right geometry and matched proton affinity in the triad. This study provides a rich picture of the energetics of the hydrogen bond network in enzymes for further model refinement.

-	~~The entry 5d81 is ON HOLD until Paper Publication~~	+	Dissecting Proton Delocalization in an Enzyme's Hydrogen Bond Network with Unnatural Amino Acids.,Wu Y, Fried SD, Boxer SG Biochemistry. 2015 Nov 25. PMID:26571340<ref>PMID:26571340</ref>

-	~~Authors: Wu~~, Y.~~, Fried,~~ S.~~D., Boxer, S.G~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI)~~; ~~D40N, Y57(Cl~~-Y)	+	<div class="pdbe-citations 5d81" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: Fried, S.D]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Steroid Delta-isomerase]]
		+	[[Category: Boxer, S G]]
		+	[[Category: Fried, S D]]
	[[Category: Wu, Y]]		[[Category: Wu, Y]]
-	[[Category: ~~Boxer, S.G~~]]	+	[[Category: Isomerase]]

OCA: Protected "5d81" [edit=sysop:move=sysop]

OCA — Wed, 26 Aug 2015 12:31:38 GMT

Protected "5d81" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:31, 26 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d81 is ON HOLD until Paper Publication Authors: Wu, Y., Fried, S.D., Boxer, S.G. Description: Crystal Structure of Ketosteroid Isomerase from Pseu...

OCA — Wed, 26 Aug 2015 12:31:37 GMT

New page: '''Unreleased structure''' The entry 5d81 is ON HOLD until Paper Publication Authors: Wu, Y., Fried, S.D., Boxer, S.G. Description: Crystal Structure of Ketosteroid Isomerase from Pseu...

New page

'''Unreleased structure'''

The entry 5d81 is ON HOLD until Paper Publication

Authors: Wu, Y., Fried, S.D., Boxer, S.G.

Description: Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI); D40N, Y57(Cl-Y)
[[Category: Unreleased Structures]]
[[Category: Fried, S.D]]
[[Category: Wu, Y]]
[[Category: Boxer, S.G]]