4c3x - Revision history

OCA at 11:08, 9 May 2024

2024-05-09T11:08:30Z

←Older revision		Revision as of 11:08, 9 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C3X FirstGlance]. <br>		<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C3X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</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=4c3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c3x OCA], [https://pdbe.org/4c3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c3x RCSB], [https://www.ebi.ac.uk/pdbsum/4c3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c3x 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=4c3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c3x OCA], [https://pdbe.org/4c3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c3x RCSB], [https://www.ebi.ac.uk/pdbsum/4c3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c3x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q9RA02_RHOER Q9RA02_RHOER]]	+	[https://www.uniprot.org/uniprot/Q9RA02_RHOER Q9RA02_RHOER]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	3-Ketosteroid Delta1-dehydrogenases are FAD-dependent enzymes that catalyze the 1,2-desaturation of 3-ketosteroid substrates to initiate degradation of the steroid nucleus. Here we report the 2.0 A resolution crystal structure of the 56 kDa enzyme from Rhodococcus erythropolis SQ1 (Delta1-KSTD1). The enzyme contains two domains, an FAD-binding domain and a catalytic domain, between which the active site is situated as evidenced by the 2.3 A resolution structure of Delta1-KSTD1 in complex with the reaction product 1,4-androstadiene-3,17-dione. The active site contains four key residues, Tyr-119, Tyr-318, Tyr-487, and Gly-491. Modeling of the substrate 4-androstene-3,17-dione at the position of the product revealed its interactions with these residues and the FAD. The C1 and C2 atoms of the substrate are at reaction distance to the N5 atom of the isoalloxazine ring of FAD and the hydroxyl group of Tyr-318, respectively, while the C3 carbonyl group is at hydrogen bonding distance from the hydroxyl group of Tyr-487 and the backbone amide of Gly-491. Site-directed mutagenesis of the tyrosines to phenylalanines confirmed their importance for catalysis. The structural features and the kinetic properties of the mutants suggest a catalytic mechanism, in which Tyr-487 and Gly-491 work in tandem to promote keto-enol tautomerisation and increase the acidity of the substrate's C2 hydrogen atoms. With assistance of Tyr-119, the general base Tyr-318 abstracts the axial beta-hydrogen from C2 as a proton, while the FAD accepts the axial alpha-hydrogen from the substrate's C1 atom as a hydride ion.
		+
		+	Crystal structure and site-directed mutagenesis of 3-ketosteroid Delta1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism.,Rohman A, van Oosterwijk N, Thunnissen AM, Dijkstra BW J Biol Chem. 2013 Oct 28. PMID:24165124<ref>PMID:24165124</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4c3x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:24, 7 September 2022

2022-09-07T17:24:58Z

←Older revision		Revision as of 17:24, 7 September 2022
Line 3:		Line 3:
	<StructureSection load='4c3x' size='340' side='right'caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4c3x' size='340' side='right'caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium~~ erythropolis~~" gray and thornton 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4C3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C3X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NA:~~SODIUM+ION~~'>NA</scene>, <scene name='pdbligand=~~PG4~~:~~TETRAETHYLENE+GLYCOL~~'>~~PG4~~</scene>, <scene name='pdbligand=~~SUC~~:~~SUCROSE~~'>~~SUC~~</scene><~~/td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat">[[4c3y\|4c3y]]</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=4c3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c3x OCA], [https://pdbe.org/4c3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c3x RCSB], [https://www.ebi.ac.uk/pdbsum/4c3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c3x 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/3-oxosteroid_1-dehydrogenase 3-oxosteroid 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.4 1.3.99.4]~~ </~~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=4c3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c3x OCA], [~~http~~://pdbe.org/4c3x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4c3x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4c3x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4c3x ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/Q9RA02_RHOER Q9RA02_RHOER]]
-	3-Ketosteroid Delta1-dehydrogenases are FAD-dependent enzymes that catalyze the 1,2-desaturation of 3-ketosteroid substrates to initiate degradation of the steroid nucleus. Here we report the 2.0 A resolution crystal structure of the 56 kDa enzyme from Rhodococcus erythropolis SQ1 (Delta1-KSTD1). The enzyme contains two domains, an FAD-binding domain and a catalytic domain, between which the active site is situated as evidenced by the 2.3 A resolution structure of Delta1-KSTD1 in complex with the reaction product 1,4-androstadiene-3,17-dione. The active site contains four key residues, Tyr-119, Tyr-318, Tyr-487, and Gly-491. Modeling of the substrate 4-androstene-3,17-dione at the position of the product revealed its interactions with these residues and the FAD. The C1 and C2 atoms of the substrate are at reaction distance to the N5 atom of the isoalloxazine ring of FAD and the hydroxyl group of Tyr-318, respectively, while the C3 carbonyl group is at hydrogen bonding distance from the hydroxyl group of Tyr-487 and the backbone amide of Gly-491. Site-directed mutagenesis of the tyrosines to phenylalanines confirmed their importance for catalysis. The structural features and the kinetic properties of the mutants suggest a catalytic mechanism, in which Tyr-487 and Gly-491 work in tandem to promote keto-enol tautomerisation and increase the acidity of the substrate's C2 hydrogen atoms. With assistance of Tyr-119, the general base Tyr-318 abstracts the axial beta-hydrogen from C2 as a proton, while the FAD accepts the axial alpha-hydrogen from the substrate's C1 atom as a hydride ion.	+
-		+
-	Crystal structure and site-directed mutagenesis of 3-ketosteroid Delta1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism.,Rohman A, van Oosterwijk N, Thunnissen AM, Dijkstra BW J Biol Chem. 2013 Oct 28. PMID:~~24165124<ref>PMID:24165124<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 4c3x" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium erythropolis gray and thornton 1928]]
-	[[Category: 3-oxosteroid 1-dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dijkstra, B W~~]]	+	[[Category: Rhodococcus erythropolis]]
-	[[Category: ~~Oosterwijk, N van~~]]	+	[[Category: Dijkstra BW]]
-	[[Category: Rohman, A]]	+	[[Category: Rohman A]]
-	[[Category: Thunnissen~~, A M.W H~~]]	+	[[Category: Thunnissen AMWH]]
-	[[Category: ~~Flavoprotein]]~~	+	[[Category: Van Oosterwijk N]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 12:46, 10 May 2019

2019-05-10T12:46:42Z

←Older revision		Revision as of 12:46, 10 May 2019
Line 1:		Line 1:

	==Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1==		==Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1==
-	<StructureSection load='4c3x' size='340' side='right' caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4c3x' size='340' side='right'caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C3X FirstGlance]. <br>		<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C3X FirstGlance]. <br>
Line 24:		Line 24:
	[[Category: Mycobacterium erythropolis gray and thornton 1928]]		[[Category: Mycobacterium erythropolis gray and thornton 1928]]
	[[Category: 3-oxosteroid 1-dehydrogenase]]		[[Category: 3-oxosteroid 1-dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Dijkstra, B W]]		[[Category: Dijkstra, B W]]
	[[Category: Oosterwijk, N van]]		[[Category: Oosterwijk, N van]]

OCA at 08:07, 6 March 2019

2019-03-06T08:07:56Z

←Older revision		Revision as of 08:07, 6 March 2019
Line 1:		Line 1:

	==Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1==		==Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1==
-	<StructureSection load='4c3x' size='340' side='right' caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4c3x' size='340' side='right' caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C3X FirstGlance]. <br>		<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C3X FirstGlance]. <br>

OCA at 15:48, 5 August 2016

2016-08-05T15:48:07Z

←Older revision		Revision as of 15:48, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1==		==Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1==
	<StructureSection load='4c3x' size='340' side='right' caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4c3x' size='340' side='right' caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c3y\|4c3y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c3y\|4c3y]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-oxosteroid_1-dehydrogenase 3-oxosteroid 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.4 1.3.99.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-oxosteroid_1-dehydrogenase 3-oxosteroid 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.4 1.3.99.4] </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=4c3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4c3x RCSB], [http://www.ebi.ac.uk/pdbsum/4c3x 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=4c3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c3x OCA], [http://pdbe.org/4c3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4c3x RCSB], [http://www.ebi.ac.uk/pdbsum/4c3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4c3x ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4c3x" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:22, 21 December 2014

2014-12-21T16:22:54Z

←Older revision		Revision as of 16:22, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4c3x\| PDB=4c3x \| SCENE= }}~~	+	==Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1==
-	===Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1===	+	<StructureSection load='4c3x' size='340' side='right' caption='[[4c3x]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24165124}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4c3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C3X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4c3y\|4c3y]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-oxosteroid_1-dehydrogenase 3-oxosteroid 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.4 1.3.99.4] </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=4c3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4c3x RCSB], [http://www.ebi.ac.uk/pdbsum/4c3x PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	3-Ketosteroid Delta1-dehydrogenases are FAD-dependent enzymes that catalyze the 1,2-desaturation of 3-ketosteroid substrates to initiate degradation of the steroid nucleus. Here we report the 2.0 A resolution crystal structure of the 56 kDa enzyme from Rhodococcus erythropolis SQ1 (Delta1-KSTD1). The enzyme contains two domains, an FAD-binding domain and a catalytic domain, between which the active site is situated as evidenced by the 2.3 A resolution structure of Delta1-KSTD1 in complex with the reaction product 1,4-androstadiene-3,17-dione. The active site contains four key residues, Tyr-119, Tyr-318, Tyr-487, and Gly-491. Modeling of the substrate 4-androstene-3,17-dione at the position of the product revealed its interactions with these residues and the FAD. The C1 and C2 atoms of the substrate are at reaction distance to the N5 atom of the isoalloxazine ring of FAD and the hydroxyl group of Tyr-318, respectively, while the C3 carbonyl group is at hydrogen bonding distance from the hydroxyl group of Tyr-487 and the backbone amide of Gly-491. Site-directed mutagenesis of the tyrosines to phenylalanines confirmed their importance for catalysis. The structural features and the kinetic properties of the mutants suggest a catalytic mechanism, in which Tyr-487 and Gly-491 work in tandem to promote keto-enol tautomerisation and increase the acidity of the substrate's C2 hydrogen atoms. With assistance of Tyr-119, the general base Tyr-318 abstracts the axial beta-hydrogen from C2 as a proton, while the FAD accepts the axial alpha-hydrogen from the substrate's C1 atom as a hydride ion.

-	~~==About this Structure==~~	+	Crystal structure and site-directed mutagenesis of 3-ketosteroid Delta1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism.,Rohman A, van Oosterwijk N, Thunnissen AM, Dijkstra BW J Biol Chem. 2013 Oct 28. PMID:24165124<ref>PMID:24165124</ref>
-	~~[[4c3x]] is a 8 chain~~ structure ~~with sequence~~ from ~~[http://en~~.~~wikipedia~~.~~org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024165124</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium erythropolis gray and thornton 1928]]		[[Category: Mycobacterium erythropolis gray and thornton 1928]]
	[[Category: 3-oxosteroid 1-dehydrogenase]]		[[Category: 3-oxosteroid 1-dehydrogenase]]
-	[[Category: Dijkstra, B W.]]	+	[[Category: Dijkstra, B W]]
-	[[Category: Oosterwijk, N van.]]	+	[[Category: Oosterwijk, N van]]
-	[[Category: Rohman, A.]]	+	[[Category: Rohman, A]]
-	[[Category: Thunnissen, A M.W H.]]	+	[[Category: Thunnissen, A M.W H]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

OCA at 08:46, 25 December 2013

2013-12-25T08:46:38Z

←Older revision		Revision as of 08:46, 25 December 2013
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[4c3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodococcus_erythropolis Rhodococcus~~ erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA].	+	[[4c3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024165124</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024165124</ref><references group="xtra"/><references/>
		+	[[Category: Mycobacterium erythropolis gray and thornton 1928]]
	[[Category: 3-oxosteroid 1-dehydrogenase]]		[[Category: 3-oxosteroid 1-dehydrogenase]]
-	[[Category: Rhodococcus erythropolis]]
	[[Category: Dijkstra, B W.]]		[[Category: Dijkstra, B W.]]
	[[Category: Oosterwijk, N van.]]		[[Category: Oosterwijk, N van.]]

OCA at 07:38, 6 November 2013

2013-11-06T07:38:19Z

←Older revision		Revision as of 07:38, 6 November 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4c3x\| PDB=4c3x \| SCENE= }}
		+	===Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1===
		+	{{ABSTRACT_PUBMED_24165124}}

-	~~The entry~~ 4c3x is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4c3x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C3X OCA].

-	~~Authors~~: ~~Rohman~~, A.~~, van~~ Oosterwijk, N., Thunnissen, A.M.W.H.~~, Dijkstra, B.W.~~	+	==Reference==
-		+	<ref group="xtra">PMID:024165124</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1~~	+	[[Category: 3-oxosteroid 1-dehydrogenase]]
		+	[[Category: Rhodococcus erythropolis]]
		+	[[Category: Dijkstra, B W.]]
		+	[[Category: Oosterwijk, N van.]]
		+	[[Category: Rohman, A.]]
		+	[[Category: Thunnissen, A M.W H.]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

OCA at 07:07, 16 October 2013

2013-10-16T07:07:58Z

←Older revision		Revision as of 07:07, 16 October 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4c3x is ON HOLD	+	The entry 4c3x is ON HOLD until Paper Publication

	Authors: Rohman, A., van Oosterwijk, N., Thunnissen, A.M.W.H., Dijkstra, B.W.		Authors: Rohman, A., van Oosterwijk, N., Thunnissen, A.M.W.H., Dijkstra, B.W.

	Description: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1		Description: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1

OCA: Protected "4c3x" [edit=sysop:move=sysop]

2013-09-04T09:32:14Z

Protected "4c3x" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:32, 4 September 2013