1opy - Revision history

OCA at 08:02, 14 February 2024

2024-02-14T08:02:20Z

← Older revision		Revision as of 08:02, 14 February 2024
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	<StructureSection load='1opy' size='340' side='right'caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1opy' size='340' side='right'caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1opy]] is a 1 chain structure with sequence from [https://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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OPY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1opy]] 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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OPY FirstGlance]. <br>
	</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>~~[https://en.wikipedia.org/wiki/Steroid_Delta~~-~~isomerase Steroid Delta-isomerase]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.~~1 5.~~3.3.1] </span>~~</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]] 1.9Å</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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [https://pdbe.org/1opy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [https://www.ebi.ac.uk/pdbsum/1opy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1opy ProSAT]</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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [https://pdbe.org/1opy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [https://www.ebi.ac.uk/pdbsum/1opy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1opy ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1opy ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1opy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Bacterial Delta5-3-ketosteroid isomerase (KSI) catalyzes a stereospecific isomerization of steroid substrates at an extremely fast rate, overcoming a large disparity of pKa values between a catalytic residue and its target. The crystal structures of KSI from Pseudomonas putida and of the enzyme in complex with equilenin, an analogue of the reaction intermediate, have been determined at 1.9 and 2.5 A resolution, respectively. The structures reveal that the side chains of Tyr14 and Asp99 (a newly identified catalytic residue) form hydrogen bonds directly with the oxyanion of the bound inhibitor in a completely apolar milieu of the active site. No water molecule is found at the active site, and the access of bulk solvent is blocked by a layer of apolar residues. Asp99 is surrounded by six apolar residues, and consequently, its pKa appears to be elevated as high as 9.5 to be consistent with early studies. No interaction was found between the bound inhibitor and the residue 101 (phenylalanine in Pseudomonas testosteroni and methionine in P. putida KSI) which was suggested to contribute significantly to the rate enhancement based on mutational analysis. This observation excludes the residue 101 as a potential catalytic residue and requires that the rate enhancement should be explained solely by Tyr14 and Asp99. Kinetic analyses of Y14F and D99L mutant enzymes demonstrate that Tyr14 contributes much more significantly to the rate enhancement than Asp99. Previous studies and the structural analysis strongly suggest that the low-barrier hydrogen bond of Tyr14 (>7.1 kcal/mol), along with a moderate strength hydrogen bond of Asp99 ( approximately 4 kcal/mol), accounts for the required energy of 11 kcal/mol for the transition-state stabilization.

	High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue.,Kim SW, Cha SS, Cho HS, Kim JS, Ha NC, Cho MJ, Joo S, Kim KK, Choi KY, Oh BH Biochemistry. 1997 Nov 18;36(46):14030-6. PMID:9369474<ref>PMID:9369474</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 1opy" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]		*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Bacillus fluorescens putidus flugge 1886]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Steroid Delta-isomerase~~]]		[[Category: Pseudomonas putida]]
	[[Category: Cha, S S]]		[[Category: Cha S-S]]
	[[Category: Cho, H S]]		[[Category: Cho H-S]]
	[[Category: Cho, M J]]		[[Category: Cho M-J]]
	[[Category: Choi, K Y]]		[[Category: Choi K-Y]]
	[[Category: Ha, N C]]		[[Category: Ha N-C]]
	[[Category: Kim, J S]]		[[Category: Kim J-S]]
	[[Category: Kim, S W]]		[[Category: Kim S-W]]
	[[Category: Oh, B H]]		[[Category: Oh B-H]]
	~~[[Category: High resolution]]~~
	~~[[Category: Isomerase]]~~
	~~[[Category: Ksi]]~~
	~~[[Category: Low-barrier hydrogen bond]]~~
	~~[[Category: Pseudomonas putida biotype b~~]]

OCA at 09:19, 8 September 2021

2021-09-08T09:19:46Z

← Older revision		Revision as of 09:19, 8 September 2021
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	<StructureSection load='1opy' size='340' side='right'caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1opy' size='340' side='right'caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1opy]] 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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1OPY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1opy]] is a 1 chain structure with sequence from [https://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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OPY 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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [https://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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [~~http~~://pdbe.org/1opy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1opy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1opy ProSAT]</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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [https://pdbe.org/1opy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [https://www.ebi.ac.uk/pdbsum/1opy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1opy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 18:21, 20 November 2019

2019-11-20T18:21:31Z

← Older revision		Revision as of 18:21, 20 November 2019
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	==KSI==		==KSI==
	<StructureSection load='1opy' size='340' side='right' caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1opy' size='340' side='right'caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1opy]] 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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1opy]] 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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1opy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1opy" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
	== References ==		== References ==
	<references/>		<references/>
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	</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: Cha, S S]]		[[Category: Cha, S S]]

OCA at 07:33, 15 February 2018

2018-02-15T07:33:57Z

← Older revision		Revision as of 07:33, 15 February 2018
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	==KSI==		==KSI==
	<StructureSection load='1opy' size='340' side='right' caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1opy' size='340' side='right' caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	<table><tr><td colspan='2'>[[1opy]] 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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1opy]] 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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY 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='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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [http://pdbe.org/1opy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [http://www.ebi.ac.uk/pdbsum/1opy 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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [http://pdbe.org/1opy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [http://www.ebi.ac.uk/pdbsum/1opy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1opy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/op/1opy_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/op/1opy_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1opy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 1opy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1opy" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:30, 11 September 2015

2015-09-11T17:30:07Z

← Older revision		Revision as of 17:30, 11 September 2015
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	<StructureSection load='1opy' size='340' side='right' caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1opy' size='340' side='right' caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1opy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_putida Pseudomonas putida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1opy]] 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=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY 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='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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [http://www.ebi.ac.uk/pdbsum/1opy 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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [http://pdbe.org/1opy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [http://www.ebi.ac.uk/pdbsum/1opy PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 1opy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Pseudomonas putida~~]]		[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]
	[[Category: Cha, S S]]		[[Category: Cha, S S]]

OCA at 07:52, 6 January 2015

2015-01-06T07:52:23Z

← Older revision		Revision as of 07:52, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1opy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1opy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY FirstGlance]. <br>
	</td></tr><tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [http://www.ebi.ac.uk/pdbsum/1opy 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=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [http://www.ebi.ac.uk/pdbsum/1opy PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]
	[[Category: Cha, S S.]]		[[Category: Cha, S S]]
	[[Category: Cho, H S.]]		[[Category: Cho, H S]]
	[[Category: Cho, M J.]]		[[Category: Cho, M J]]
	[[Category: Choi, K Y.]]		[[Category: Choi, K Y]]
	[[Category: Ha, N C.]]		[[Category: Ha, N C]]
	[[Category: Kim, J S.]]		[[Category: Kim, J S]]
	[[Category: Kim, S W.]]		[[Category: Kim, S W]]
	[[Category: Oh, B H.]]		[[Category: Oh, B H]]
	[[Category: High resolution]]		[[Category: High resolution]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 14:30, 29 September 2014

2014-09-29T14:30:37Z

← Older revision		Revision as of 14:30, 29 September 2014
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	~~{{STRUCTURE_1opy~~\| ~~PDB~~=1opy \| ~~SCENE~~= }}		==KSI==
	===~~KSI~~===		<StructureSection load='1opy' size='340' side='right' caption='[[1opy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	~~{{ABSTRACT_PUBMED_9369474}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[1opy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OPY FirstGlance]. <br>
			</td></tr><tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1opy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1opy RCSB], [http://www.ebi.ac.uk/pdbsum/1opy PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/op/1opy_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Bacterial Delta5-3-ketosteroid isomerase (KSI) catalyzes a stereospecific isomerization of steroid substrates at an extremely fast rate, overcoming a large disparity of pKa values between a catalytic residue and its target. The crystal structures of KSI from Pseudomonas putida and of the enzyme in complex with equilenin, an analogue of the reaction intermediate, have been determined at 1.9 and 2.5 A resolution, respectively. The structures reveal that the side chains of Tyr14 and Asp99 (a newly identified catalytic residue) form hydrogen bonds directly with the oxyanion of the bound inhibitor in a completely apolar milieu of the active site. No water molecule is found at the active site, and the access of bulk solvent is blocked by a layer of apolar residues. Asp99 is surrounded by six apolar residues, and consequently, its pKa appears to be elevated as high as 9.5 to be consistent with early studies. No interaction was found between the bound inhibitor and the residue 101 (phenylalanine in Pseudomonas testosteroni and methionine in P. putida KSI) which was suggested to contribute significantly to the rate enhancement based on mutational analysis. This observation excludes the residue 101 as a potential catalytic residue and requires that the rate enhancement should be explained solely by Tyr14 and Asp99. Kinetic analyses of Y14F and D99L mutant enzymes demonstrate that Tyr14 contributes much more significantly to the rate enhancement than Asp99. Previous studies and the structural analysis strongly suggest that the low-barrier hydrogen bond of Tyr14 (>7.1 kcal/mol), along with a moderate strength hydrogen bond of Asp99 ( approximately 4 kcal/mol), accounts for the required energy of 11 kcal/mol for the transition-state stabilization.

	~~==About this Structure==~~		High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue.,Kim SW, Cha SS, Cho HS, Kim JS, Ha NC, Cho MJ, Joo S, Kim KK, Choi KY, Oh BH Biochemistry. 1997 Nov 18;36(46):14030-6. PMID:9369474<ref>PMID:9369474</ref>
	~~[[1opy]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_putida Pseudomonas putida]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1OPY OCA].~~
			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	==See Also==		==See Also==
	*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]		*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:009369474<~~/~~ref~~><~~ref group="xtra">PMID:011917145</ref><references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]

OCA at 09:48, 11 March 2013

2013-03-11T09:48:28Z

← Older revision		Revision as of 09:48, 11 March 2013
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	~~[[Image:1opy.png\|left\|200px]]~~

	{{STRUCTURE_1opy\| PDB=1opy \| SCENE= }}		{{STRUCTURE_1opy\| PDB=1opy \| SCENE= }}

	===KSI===		===KSI===

	{{ABSTRACT_PUBMED_9369474}}		{{ABSTRACT_PUBMED_9369474}}

	==About this Structure==		==About this Structure==
	[[1opy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPY OCA].		[[1opy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPY OCA].

			==See Also==
			*[[Ketosteroid Isomerase\|Ketosteroid Isomerase]]

	==Reference==		==Reference==

OCA: Protected "1opy" [edit=sysop:move=sysop]

2012-12-12T21:56:59Z

Protected "1opy" [edit=sysop:move=sysop]

← Older revision	Revision as of 21:56, 12 December 2012
(No difference)

OCA at 21:56, 12 December 2012

2012-12-12T21:56:53Z

← Older revision		Revision as of 21:56, 12 December 2012
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	~~{{Seed}}~~
	[[Image:1opy.png\|left\|200px]]		[[Image:1opy.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1opy", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_1opy\| PDB=1opy \| SCENE= }}		{{STRUCTURE_1opy\| PDB=1opy \| SCENE= }}

	===KSI===		===KSI===

			{{ABSTRACT_PUBMED_9369474}}
	~~<!--~~
	~~The line below this paragraph,~~ {{~~ABSTRACT_PUBMED_9103200}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 9103200 is the PubMed ID number.~~
	~~-->~~
	~~{{ABSTRACT_PUBMED_9103200~~}}

	==About this Structure==		==About this Structure==
	~~1OPY~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPY OCA].		[[1opy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPY OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~9103200~~</ref><references group="xtra"/>		<ref group="xtra">PMID:009369474</ref><ref group="xtra">PMID:011917145</ref><references group="xtra"/>
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
	[[Category: Steroid Delta-isomerase]]		[[Category: Steroid Delta-isomerase]]
Line 39:		Line 27:
	[[Category: Low-barrier hydrogen bond]]		[[Category: Low-barrier hydrogen bond]]
	[[Category: Pseudomonas putida biotype b]]		[[Category: Pseudomonas putida biotype b]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:46:44 2009''~~