5dre - Revision history

OCA at 21:56, 28 June 2023

OCA — Wed, 28 Jun 2023 21:56:20 GMT

←Older revision		Revision as of 21:56, 28 June 2023
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	<StructureSection load='5dre' size='340' side='right'caption='[[5dre]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5dre' size='340' side='right'caption='[[5dre]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dre]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_11996 Atcc 11996~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DRE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DRE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dre]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DRE FirstGlance]. <br>
-	</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~~=285 ATCC 11996])</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]] 2.151Å</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'>[https://proteopedia.org/fgij/fg.htm?mol=5dre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dre OCA], [https://pdbe.org/5dre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dre RCSB], [https://www.ebi.ac.uk/pdbsum/5dre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dre 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=5dre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dre OCA], [~~http~~://pdbe.org/5dre PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dre RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dre PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dre ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SDIS_COMTE SDIS_COMTE]
	<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: ~~Atcc 11996~~]]	+	[[Category: Comamonas testosteroni]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Steroid Delta-isomerase]]~~	+	[[Category: Herschlag D]]
-	[[Category: Herschlag, D]]	+	[[Category: Lamba V]]
-	[[Category: Lamba, V]]	+	[[Category: Yabukarski F]]
-	[[Category: Yabukarski, F]]	+
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 07:32, 27 November 2019

OCA — Wed, 27 Nov 2019 07:32:25 GMT

←Older revision		Revision as of 07:32, 27 November 2019
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	==Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI)==		==Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI)==
-	<StructureSection load='5dre' size='340' side='right' caption='[[5dre]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5dre' size='340' side='right'caption='[[5dre]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dre]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DRE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dre]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11996 Atcc 11996]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DRE FirstGlance]. <br>
-	</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>	+	</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=285 ATCC 11996])</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=5dre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dre OCA], [http://pdbe.org/5dre PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dre RCSB], [http://www.ebi.ac.uk/pdbsum/5dre PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dre 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=5dre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dre OCA], [http://pdbe.org/5dre PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dre RCSB], [http://www.ebi.ac.uk/pdbsum/5dre PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dre ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 11996]]
		+	[[Category: Large Structures]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]
	[[Category: Herschlag, D]]		[[Category: Herschlag, D]]

OCA at 10:29, 13 September 2017

OCA — Wed, 13 Sep 2017 10:29:30 GMT

←Older revision		Revision as of 10:29, 13 September 2017
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	</div>		</div>
	<div class="pdbe-citations 5dre" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dre" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:37, 27 July 2016

OCA — Wed, 27 Jul 2016 15:37:39 GMT

←Older revision		Revision as of 15:37, 27 July 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5dre is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI)==
		+	<StructureSection load='5dre' size='340' side='right' caption='[[5dre]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dre]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DRE FirstGlance]. <br>
		+	</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=5dre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dre OCA], [http://pdbe.org/5dre PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dre RCSB], [http://www.ebi.ac.uk/pdbsum/5dre PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dre ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proton transfer reactions are ubiquitous in enzymes and utilize active site residues as general acids and bases. Crystal structures and site-directed mutagenesis are routinely used to identify these residues, but assessment of their catalytic contribution remains a major challenge. In principle, effective molarity measurements, in which exogenous acids/bases rescue the reaction in mutants lacking these residues, can estimate these catalytic contributions. However, these exogenous moieties can be restricted in reactivity by steric hindrance or enhanced by binding interactions with nearby residues, thereby resulting in over- or underestimation of the catalytic contribution respectively. With these challenges in mind, we investigated the catalytic contribution of an aspartate general base in ketosteroid isomerase (KSI) by exogenous rescue. In addition to removing the general base, we systematically mutated nearby residues and probed each mutant with a series of carboxylate bases of similar pKa but varying size. Our results underscore the need for extensive and multi-faceted variation to assess and minimize steric and positioning effects and determine effective molarities that estimate catalytic contributions. We obtained consensus effective molarities of ~5 X 104 M for KSI from Comamonas testosteroni (tKSI) and ~103 M for KSI from Pseudomonas putida (pKSI). An X-ray crystal structure of a tKSI general base mutant showed no additional structural rearrangements and double-mutant cycles revealed similar contributions from an oxyanion hole mutation in the wild-type and base-rescued reactions, providing no indication of mutational effects extending beyond the general base site. Thus, the high effective molarities suggest a large catalytic contribution associated with the general base. A significant portion of this effect presumably arises from positioning of the base, but its large magnitude suggests the involvement of additional catalytic mechanisms as well.

-	~~Authors: Lamba~~, V., Yabukarski, F., ~~Herschlag~~, D.	+	Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase.,Lamba V, Yabukarski F, Pinney M, Herschlag D J Am Chem Soc. 2016 Jul 13. PMID:27410422<ref>PMID:27410422</ref>

-	~~Description: Crystal Structure~~ of ~~Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5dre" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Steroid Delta-isomerase]]
		+	[[Category: Herschlag, D]]
	[[Category: Lamba, V]]		[[Category: Lamba, V]]
	[[Category: Yabukarski, F]]		[[Category: Yabukarski, F]]
-	[[Category: ~~Herschlag, D~~]]	+	[[Category: Enzyme]]
		+	[[Category: Isomerase]]

OCA at 12:31, 7 October 2015

OCA — Wed, 07 Oct 2015 12:31:23 GMT

←Older revision		Revision as of 12:31, 7 October 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Lamba, V., Yabukarski, F., Herschlag, D.		Authors: Lamba, V., Yabukarski, F., Herschlag, D.

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

OCA — Wed, 30 Sep 2015 13:25:05 GMT

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

←Older revision

Revision as of 13:25, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dre is ON HOLD Authors: Lamba, V., Yabukarski, F., Herschlag, D. Description: Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from ...

OCA — Wed, 30 Sep 2015 13:25:04 GMT

New page: '''Unreleased structure''' The entry 5dre is ON HOLD Authors: Lamba, V., Yabukarski, F., Herschlag, D. Description: Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from ...

New page

'''Unreleased structure'''

The entry 5dre is ON HOLD

Authors: Lamba, V., Yabukarski, F., Herschlag, D.

Description: Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI)
[[Category: Unreleased Structures]]
[[Category: Lamba, V]]
[[Category: Yabukarski, F]]
[[Category: Herschlag, D]]