5kp4 - Revision history

OCA at 12:41, 6 March 2024

OCA — Wed, 06 Mar 2024 12:41:25 GMT

←Older revision		Revision as of 12:41, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]		[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The vibrational Stark effect (VSE) has been used to measure the electric field in the active site of ketosteroid isomerase (KSI). These measured fields correlate with DeltaG in a series of conventional mutants, yielding an estimate for the electrostatic contribution to catalysis (Fried et al. Science 2014, 346, 1510-1513). In this work we test this result with much more conservative variants in which individual Tyr residues in the active site are replaced by 3-chlorotyrosine via amber suppression. The electric fields sensed at the position of the carbonyl bond involved in charge displacement during catalysis were characterized using the VSE, where the field sensitivity has been calibrated by vibrational Stark spectroscopy, solvatochromism, and MD simulations. A linear relationship is observed between the electric field and DeltaG that interpolates between wild-type and more drastic conventional mutations, reinforcing the evaluation of the electrostatic contribution to catalysis in KSI. A simplified model and calculation are developed to estimate changes in the electric field accompanying changes in the extended hydrogen-bond network in the active site. The results are consistent with a model in which the O-H group of a key active site tyrosine functions by imposing a static electrostatic potential onto the carbonyl bond. The model suggests that the contribution to catalysis from the active site hydrogen bonds is of similar weight to the distal interactions from the rest of the protein. A similar linear correlation was also observed between the proton affinity of KSI's active site and the catalytic rate, suggesting a direct connection between the strength of the H-bond and the electric field it exerts.
-
-	A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase.,Wu Y, Boxer SG J Am Chem Soc. 2016 Sep 1. PMID:27545569<ref>PMID:27545569</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5kp4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]		*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:50, 27 September 2023

OCA — Wed, 27 Sep 2023 10:50:30 GMT

←Older revision		Revision as of 10:50, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5kp4' size='340' side='right'caption='[[5kp4]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='5kp4' size='340' side='right'caption='[[5kp4]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kp4]] is a 2 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=5KP4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KP4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kp4]] is a 2 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=5KP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KP4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VW:(8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-METHYL-17-OXIDANYL-2,6,7,8,9,10,11,12,14,15,16,17-DODECAHYDRO-1~{H}-CYCLOPENTA[A]PHENANTHREN-3-ONE'>6VW</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]] 1.706Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d81\|5d81]], [[5kp1\|5kp1]], [[5kp3\|5kp3]], [[5d82\|5d82]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6VW:(8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-METHYL-17-OXIDANYL-2,6,7,8,9,10,11,12,14,15,16,17-DODECAHYDRO-1~{H}-CYCLOPENTA[A]PHENANTHREN-3-ONE'>6VW</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kp4 OCA], [https://pdbe.org/5kp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kp4 RCSB], [https://www.ebi.ac.uk/pdbsum/5kp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kp4 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/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=5kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kp4 OCA], [~~http~~://pdbe.org/5kp4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kp4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kp4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kp4 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 ==
Line 26:		Line 26:
	__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: Wu, Y]]	+	[[Category: Wu Y]]
-	~~[[Category: Isomerase~~]]	+

OCA at 12:20, 25 December 2019

OCA — Wed, 25 Dec 2019 12:20:11 GMT

←Older revision		Revision as of 12:20, 25 December 2019
Line 1:		Line 1:

	==Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI) bound to 19-nortestosterone==		==Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI) bound to 19-nortestosterone==
-	<StructureSection load='5kp4' size='340' side='right' caption='[[5kp4]], [[Resolution\|resolution]] 1.71Å' scene=''>	+	<StructureSection load='5kp4' size='340' side='right'caption='[[5kp4]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kp4]] is a 2 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=5KP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KP4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kp4]] is a 2 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=5KP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KP4 FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5kp4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kp4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens putidus flugge 1886]]		[[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]]
	[[Category: Wu, Y]]		[[Category: Wu, Y]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 18:26, 15 November 2017

OCA — Wed, 15 Nov 2017 18:26:26 GMT

←Older revision		Revision as of 18:26, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5kp4' size='340' side='right' caption='[[5kp4]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='5kp4' size='340' side='right' caption='[[5kp4]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kp4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KP4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kp4]] is a 2 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=5KP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KP4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VW:(8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-METHYL-17-OXIDANYL-2,6,7,8,9,10,11,12,14,15,16,17-DODECAHYDRO-1~{H}-CYCLOPENTA[A]PHENANTHREN-3-ONE'>6VW</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VW:(8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-METHYL-17-OXIDANYL-2,6,7,8,9,10,11,12,14,15,16,17-DODECAHYDRO-1~{H}-CYCLOPENTA[A]PHENANTHREN-3-ONE'>6VW</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d81\|5d81]], [[5kp1\|5kp1]], [[5kp3\|5kp3]], [[5d82\|5d82]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d81\|5d81]], [[5kp1\|5kp1]], [[5kp3\|5kp3]], [[5d82\|5d82]]</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=5kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kp4 OCA], [http://pdbe.org/5kp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kp4 RCSB], [http://www.ebi.ac.uk/pdbsum/5kp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kp4 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=5kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kp4 OCA], [http://pdbe.org/5kp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kp4 RCSB], [http://www.ebi.ac.uk/pdbsum/5kp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kp4 ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]
	[[Category: Boxer, S G]]		[[Category: Boxer, S G]]
	[[Category: Wu, Y]]		[[Category: Wu, Y]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 21:12, 10 September 2016

OCA — Sat, 10 Sep 2016 21:12:17 GMT

←Older revision		Revision as of 21:12, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kp4 is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI) bound to 19-nortestosterone==
		+	<StructureSection load='5kp4' size='340' side='right' caption='[[5kp4]], [[Resolution\|resolution]] 1.71Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kp4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KP4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VW:(8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-METHYL-17-OXIDANYL-2,6,7,8,9,10,11,12,14,15,16,17-DODECAHYDRO-1~{H}-CYCLOPENTA[A]PHENANTHREN-3-ONE'>6VW</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d81\|5d81]], [[5kp1\|5kp1]], [[5kp3\|5kp3]], [[5d82\|5d82]]</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=5kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kp4 OCA], [http://pdbe.org/5kp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kp4 RCSB], [http://www.ebi.ac.uk/pdbsum/5kp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kp4 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The vibrational Stark effect (VSE) has been used to measure the electric field in the active site of ketosteroid isomerase (KSI). These measured fields correlate with DeltaG in a series of conventional mutants, yielding an estimate for the electrostatic contribution to catalysis (Fried et al. Science 2014, 346, 1510-1513). In this work we test this result with much more conservative variants in which individual Tyr residues in the active site are replaced by 3-chlorotyrosine via amber suppression. The electric fields sensed at the position of the carbonyl bond involved in charge displacement during catalysis were characterized using the VSE, where the field sensitivity has been calibrated by vibrational Stark spectroscopy, solvatochromism, and MD simulations. A linear relationship is observed between the electric field and DeltaG that interpolates between wild-type and more drastic conventional mutations, reinforcing the evaluation of the electrostatic contribution to catalysis in KSI. A simplified model and calculation are developed to estimate changes in the electric field accompanying changes in the extended hydrogen-bond network in the active site. The results are consistent with a model in which the O-H group of a key active site tyrosine functions by imposing a static electrostatic potential onto the carbonyl bond. The model suggests that the contribution to catalysis from the active site hydrogen bonds is of similar weight to the distal interactions from the rest of the protein. A similar linear correlation was also observed between the proton affinity of KSI's active site and the catalytic rate, suggesting a direct connection between the strength of the H-bond and the electric field it exerts.

-	~~Authors~~:	+	A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase.,Wu Y, Boxer SG J Am Chem Soc. 2016 Sep 1. PMID:27545569<ref>PMID:27545569</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5kp4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Steroid Delta-isomerase]]
		+	[[Category: Boxer, S G]]
		+	[[Category: Wu, Y]]
		+	[[Category: Isomerase]]

OCA at 13:12, 27 July 2016

OCA — Wed, 27 Jul 2016 13:12:36 GMT

←Older revision		Revision as of 13:12, 27 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kp4 is ON HOLD	+	The entry 5kp4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5kp4" [edit=sysop:move=sysop]

OCA — Thu, 14 Jul 2016 09:31:45 GMT

Protected "5kp4" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:31, 14 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kp4 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 14 Jul 2016 09:31:44 GMT

New page: '''Unreleased structure''' The entry 5kp4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5kp4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]