5l92 - Revision history

OCA at 16:11, 4 October 2023

OCA — Wed, 04 Oct 2023 16:11:48 GMT

←Older revision		Revision as of 16:11, 4 October 2023
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	<StructureSection load='5l92' size='340' side='right'caption='[[5l92]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5l92' size='340' side='right'caption='[[5l92]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l92]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacmd Bacmd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L92 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5L92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l92]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Priestia_megaterium_DSM_319 Priestia megaterium DSM 319]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L92 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C0R:CORTICOSTERONE'>C0R</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</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]] 2.1Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BMD_3874 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=592022 BACMD])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C0R:CORTICOSTERONE'>C0R</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l92 OCA], [~~http~~://pdbe.org/5l92 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5l92 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5l92 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5l92 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=5l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l92 OCA], [https://pdbe.org/5l92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l92 RCSB], [https://www.ebi.ac.uk/pdbsum/5l92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l92 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D5DKI8_PRIM3 D5DKI8_PRIM3]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacmd]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Jozwik, I K~~]]	+	[[Category: Priestia megaterium DSM 319]]
-	[[Category: ~~Thunnissen, A M.W H~~]]	+	[[Category: Jozwik IK]]
-	[[Category: ~~Bacillus]]~~	+	[[Category: Thunnissen AMWH]]
-	~~[[Category: Bacterial protein]]~~	+
-	~~[[Category: Binding site]]~~	+
-	~~[[Category: Catalysis]]~~	+
-	~~[[Category: Corticosterone]]~~	+
-	~~[[Category: Cytochrome p-450 enzyme system]]~~	+
-	~~[[Category: Cytochrome p450]]~~	+
-	~~[[Category: Escherichia coli]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Hydroxylation]]~~	+
-	~~[[Category: Ligand]]~~	+
-	~~[[Category: Molecular structure]]~~	+
-	~~[[Category: Oxidation-reduction]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxygen]]~~	+
-	~~[[Category: Protein]]~~	+
-	~~[[Category: Protein structure]]~~	+
-	~~[[Category: Secondary]]~~	+
-	~~[[Category: Steroid]]~~	+
-	~~[[Category: Substrate specificity~~]]	+

OCA at 07:02, 5 August 2020

OCA — Wed, 05 Aug 2020 07:02:31 GMT

←Older revision		Revision as of 07:02, 5 August 2020
Line 1:		Line 1:

	==The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in complex with corticosterone==		==The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in complex with corticosterone==
-	<StructureSection load='5l92' size='340' side='right' caption='[[5l92]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5l92' size='340' side='right'caption='[[5l92]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l92]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L92 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5L92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l92]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacmd Bacmd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L92 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5L92 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0R:CORTICOSTERONE'>C0R</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C0R:CORTICOSTERONE'>C0R</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></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=5l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l92 OCA], [http://pdbe.org/5l92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l92 RCSB], [http://www.ebi.ac.uk/pdbsum/5l92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l92 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BMD_3874 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=592022 BACMD])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l92 OCA], [http://pdbe.org/5l92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l92 RCSB], [http://www.ebi.ac.uk/pdbsum/5l92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l92 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5l92" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5l92" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacmd]]
		+	[[Category: Large Structures]]
	[[Category: Jozwik, I K]]		[[Category: Jozwik, I K]]
	[[Category: Thunnissen, A M.W H]]		[[Category: Thunnissen, A M.W H]]

OCA at 10:07, 19 October 2016

OCA — Wed, 19 Oct 2016 10:07:15 GMT

←Older revision		Revision as of 10:07, 19 October 2016
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	<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=5l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l92 OCA], [http://pdbe.org/5l92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l92 RCSB], [http://www.ebi.ac.uk/pdbsum/5l92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l92 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=5l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l92 OCA], [http://pdbe.org/5l92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l92 RCSB], [http://www.ebi.ac.uk/pdbsum/5l92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l92 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cytochrome P450 monooxygenases (P450s) are attractive enzymes for the pharmaceutical industry, in particular, for applications in steroidal drug synthesis. Here, we report a comprehensive functional and structural characterization of CYP109E1, a novel steroid-converting cytochrome P450 enzyme identified from the genome of Bacillus megaterium DSM319. In vitro and whole-cell in vivo turnover experiments, combined with binding assays, revealed that CYP109E1 is able to hydroxylate testosterone at position 16beta. Related steroids with bulky substituents at carbon C17, like corticosterone, bind to the enzyme without being converted. High-resolution X-ray structures were solved of a steroid-free form of CYP109E1 and of complexes with testosterone and corticosterone. The structural analysis revealed a highly dynamic active site at the distal side of the heme, which is wide open in the absence of steroids, can bind four ordered corticosterone molecules simultaneously, and undergoes substantial narrowing upon binding of single steroid molecules. In the crystal structures, the single bound steroids adopt unproductive binding modes coordinating the heme-iron with their C3-keto oxygen. Molecular dynamics (MD) simulations suggest that the steroids may also bind in ~180 degrees reversed orientations with the C16 carbon and C17-substituents pointing toward the heme, leading to productive binding of testosterone explaining the observed regio- and stereoselectivity. The X-ray structures and MD simulations further identify several residues with important roles in steroid binding and conversion, which could be confirmed by site-directed mutagenesis. Taken together, our results provide unique insights into the CYP109E1 activity, substrate specificity, and regio/stereoselectivity. DATABASE: The atomic coordinates and structure factors have been deposited in the Protein Data Bank with accession codes 5L90 (steroid-free CYP109E1), 5L91 (CYP109E1-COR4), 5L94 (CYP109E1-TES), and 5L92 (CYP109E1-COR). ENZYMES: Cytochrome P450 monooxygenase CYP109E1, EC 1.14.14.1, UniProt ID: D5DKI8, Adrenodoxin reductase EC 1.18.1.6.
		+
		+	Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium.,Jozwik IK, Kiss FM, Gricman L, Abdulmughni A, Brill E, Zapp J, Pleiss J, Bernhardt R, Thunnissen AW FEBS J. 2016 Sep 30. doi: 10.1111/febs.13911. PMID:27686671<ref>PMID:27686671</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5l92" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:36, 5 October 2016

OCA — Wed, 05 Oct 2016 21:36:08 GMT

←Older revision		Revision as of 21:36, 5 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5l92 is ~~ON HOLD~~	+	==The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in complex with corticosterone==
-		+	<StructureSection load='5l92' size='340' side='right' caption='[[5l92]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~: ~~Jozwik~~, I.K., ~~Thunnissen~~, A.M.W.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5l92]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L92 FirstGlance]. <br>
-	~~Description~~: ~~The 2~~.~~1 A crystal structure of CYP109E1 from Bacillus megaterium in complex with corticosterone~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0R:CORTICOSTERONE'>C0R</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l92 OCA], [http://pdbe.org/5l92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l92 RCSB], [http://www.ebi.ac.uk/pdbsum/5l92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l92 ProSAT]</span></td></tr>
-	[[Category: Thunnissen, A.M.W.H]]	+	</table>
-	[[Category: ~~Jozwik, I.K~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Jozwik, I K]]
		+	[[Category: Thunnissen, A M.W H]]
		+	[[Category: Bacillus]]
		+	[[Category: Bacterial protein]]
		+	[[Category: Binding site]]
		+	[[Category: Catalysis]]
		+	[[Category: Corticosterone]]
		+	[[Category: Cytochrome p-450 enzyme system]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Heme]]
		+	[[Category: Hydroxylation]]
		+	[[Category: Ligand]]
		+	[[Category: Molecular structure]]
		+	[[Category: Oxidation-reduction]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxygen]]
		+	[[Category: Protein]]
		+	[[Category: Protein structure]]
		+	[[Category: Secondary]]
		+	[[Category: Steroid]]
		+	[[Category: Substrate specificity]]

OCA: Protected "5l92" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 14:04:10 GMT

Protected "5l92" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:04, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5l92 is ON HOLD Authors: Jozwik, I.K., Thunnissen, A.M.W.H. Description: The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in comple...

OCA — Mon, 20 Jun 2016 14:04:09 GMT

New page: '''Unreleased structure''' The entry 5l92 is ON HOLD Authors: Jozwik, I.K., Thunnissen, A.M.W.H. Description: The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in comple...

New page

'''Unreleased structure'''

The entry 5l92 is ON HOLD

Authors: Jozwik, I.K., Thunnissen, A.M.W.H.

Description: The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in complex with corticosterone
[[Category: Unreleased Structures]]
[[Category: Thunnissen, A.M.W.H]]
[[Category: Jozwik, I.K]]