4ubs - Revision history

OCA at 09:01, 20 March 2024

2024-03-20T09:01:19Z

←Older revision		Revision as of 09:01, 20 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis_MA-4680_=_NBRC_14893 Streptomyces avermitilis MA-4680 = NBRC 14893]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UBS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis_MA-4680_=_NBRC_14893 Streptomyces avermitilis MA-4680 = NBRC 14893]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UBS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [https://pdbe.org/4ubs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [https://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs 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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [https://pdbe.org/4ubs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [https://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CYP28_STRAW CYP28_STRAW] Catalyzes the conversion of 1-deoxypentalenic acid to pentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:21081950</ref>		[https://www.uniprot.org/uniprot/CYP28_STRAW CYP28_STRAW] Catalyzes the conversion of 1-deoxypentalenic acid to pentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:21081950</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Diclofenac is a nonsteroidal anti-inflammatory drug. It undergoes hydroxylation by mammalian cytochrome P450 enzymes at 4'- and/or 5'-positions. A bacterial P450 enzyme, CYP105D7 from Streptomyces avermitilis, has been shown to catalyze hydroxylation of 1-deoxypentalenic acid and an isoflavone daidzein. Here, we demonstrated that CYP105D7 also catalyzes hydroxylation of diclofenac at the C4'-position. A spectroscopic analysis showed that CYP105D7 binds diclofenac in a slightly cooperative manner with an affinity of 65 muM and a Hill coefficient of 1.16. The crystal structure of CYP105D7 in complex with diclofenac was determined at 2.2 A resolution. The distal pocket of CYP105D7 contains two diclofenac molecules, illustrating drug recognition with a double-ligand-binding mode. The C3' and C4' atoms of the dichlorophenyl ring of one diclofenac molecule are positioned near the heme iron, suggesting that it is positioned appropriately for aromatic hydroxylation to yield the 4'-hydroxylated product. However, recognition of diclofenac by CYP105D7 was completely different from that of rabbit CYP2C5, which binds one diclofenac molecule with a cluster of water molecules. The distal pocket of CYP105D7 contains four arginine residues, forming a wall of the substrate-binding pocket, and the arginine residues are conserved in bacterial P450s in the CYP105 family.
-
-	Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase.,Xu LH, Ikeda H, Liu L, Arakawa T, Wakagi T, Shoun H, Fushinobu S Appl Microbiol Biotechnol. 2014 Oct 24. PMID:25341403<ref>PMID:25341403</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4ubs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:13, 22 March 2023

2023-03-22T08:13:53Z

←Older revision		Revision as of 08:13, 22 March 2023
Line 3:		Line 3:
	<StructureSection load='4ubs' size='340' side='right'caption='[[4ubs]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4ubs' size='340' side='right'caption='[[4ubs]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Straw Straw~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4UBS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis_MA-4680_=_NBRC_14893 Streptomyces avermitilis MA-4680 = NBRC 14893]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UBS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cyp105d7, cyp28, SAV_7469 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227882 STRAW])</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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [https://pdbe.org/4ubs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [https://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs 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/Pentalenic_acid_synthase Pentalenic acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.15.11 1.14.15.11] </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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [~~http~~://pdbe.org/4ubs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CYP28_STRAW CYP28_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to pentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:21081950</ref>	+	[https://www.uniprot.org/uniprot/CYP28_STRAW CYP28_STRAW] Catalyzes the conversion of 1-deoxypentalenic acid to pentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:21081950</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pentalenic acid synthase]]~~	+	[[Category: Streptomyces avermitilis MA-4680 = NBRC 14893]]
-	~~[[Category: Straw~~]]	+	[[Category: Arakawa T]]
-	[[Category: Arakawa, T]]	+	[[Category: Fushinobu S]]
-	[[Category: Fushinobu, S]]	+	[[Category: Ikeda H]]
-	[[Category: Ikeda, H]]	+	[[Category: Shoun H]]
-	[[Category: Shoun, H]]	+	[[Category: Wakagi T]]
-	[[Category: Wakagi, T]]	+	[[Category: Xu LH]]
-	[[Category: Xu~~, L H]]~~	+
-	~~[[Category: Cytochrome p450]]~~	+
-	~~[[Category: Diclofenac]]~~	+
-	~~[[Category: Hydroxylation]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:25, 21 May 2019

2019-05-21T09:25:29Z

←Older revision		Revision as of 09:25, 21 May 2019
Line 1:		Line 1:

	==The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac==		==The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac==
-	<StructureSection load='4ubs' size='340' side='right' caption='[[4ubs]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4ubs' size='340' side='right'caption='[[4ubs]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UBS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Straw Straw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UBS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cyp105d7, cyp28, SAV_7469 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227882 STRAW])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenic_acid_synthase Pentalenic acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.15.11 1.14.15.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenic_acid_synthase Pentalenic acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.15.11 1.14.15.11] </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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [http://pdbe.org/4ubs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [http://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs 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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [http://pdbe.org/4ubs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [http://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pentalenic acid synthase]]		[[Category: Pentalenic acid synthase]]
		+	[[Category: Straw]]
	[[Category: Arakawa, T]]		[[Category: Arakawa, T]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]

OCA at 01:22, 19 January 2017

2017-01-19T01:22:01Z

←Older revision		Revision as of 01:22, 19 January 2017
Line 1:		Line 1:
		+
	==The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac==		==The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac==
	<StructureSection load='4ubs' size='340' side='right' caption='[[4ubs]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4ubs' size='340' side='right' caption='[[4ubs]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenic_acid_synthase Pentalenic acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.15.11 1.14.15.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenic_acid_synthase Pentalenic acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.15.11 1.14.15.11] </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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [http://www.ebi.ac.uk/pdbsum/4ubs 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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [http://pdbe.org/4ubs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [http://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4ubs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:30, 25 December 2014

2014-12-25T08:30:29Z

←Older revision		Revision as of 08:30, 25 December 2014
Line 7:		Line 7:
	<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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [http://www.ebi.ac.uk/pdbsum/4ubs 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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [http://www.ebi.ac.uk/pdbsum/4ubs PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CYP28_STRAW CYP28_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to pentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:21081950</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Pentalenic acid synthase]]		[[Category: Pentalenic acid synthase]]
-	[[Category: Arakawa, T.]]	+	[[Category: Arakawa, T]]
-	[[Category: Fushinobu, S.]]	+	[[Category: Fushinobu, S]]
-	[[Category: Ikeda, H.]]	+	[[Category: Ikeda, H]]
-	[[Category: Shoun, H.]]	+	[[Category: Shoun, H]]
-	[[Category: Wakagi, T.]]	+	[[Category: Wakagi, T]]
-	[[Category: Xu, L H.]]	+	[[Category: Xu, L H]]
	[[Category: Cytochrome p450]]		[[Category: Cytochrome p450]]
	[[Category: Diclofenac]]		[[Category: Diclofenac]]
	[[Category: Hydroxylation]]		[[Category: Hydroxylation]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 08:48, 5 November 2014

2014-11-05T08:48:13Z

←Older revision		Revision as of 08:48, 5 November 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac==
		+	<StructureSection load='4ubs' size='340' side='right' caption='[[4ubs]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UBS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenic_acid_synthase Pentalenic acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.15.11 1.14.15.11] </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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [http://www.ebi.ac.uk/pdbsum/4ubs PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Diclofenac is a nonsteroidal anti-inflammatory drug. It undergoes hydroxylation by mammalian cytochrome P450 enzymes at 4'- and/or 5'-positions. A bacterial P450 enzyme, CYP105D7 from Streptomyces avermitilis, has been shown to catalyze hydroxylation of 1-deoxypentalenic acid and an isoflavone daidzein. Here, we demonstrated that CYP105D7 also catalyzes hydroxylation of diclofenac at the C4'-position. A spectroscopic analysis showed that CYP105D7 binds diclofenac in a slightly cooperative manner with an affinity of 65 muM and a Hill coefficient of 1.16. The crystal structure of CYP105D7 in complex with diclofenac was determined at 2.2 A resolution. The distal pocket of CYP105D7 contains two diclofenac molecules, illustrating drug recognition with a double-ligand-binding mode. The C3' and C4' atoms of the dichlorophenyl ring of one diclofenac molecule are positioned near the heme iron, suggesting that it is positioned appropriately for aromatic hydroxylation to yield the 4'-hydroxylated product. However, recognition of diclofenac by CYP105D7 was completely different from that of rabbit CYP2C5, which binds one diclofenac molecule with a cluster of water molecules. The distal pocket of CYP105D7 contains four arginine residues, forming a wall of the substrate-binding pocket, and the arginine residues are conserved in bacterial P450s in the CYP105 family.

-	~~The entry 4ubs is ON HOLD~~	+	Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase.,Xu LH, Ikeda H, Liu L, Arakawa T, Wakagi T, Shoun H, Fushinobu S Appl Microbiol Biotechnol. 2014 Oct 24. PMID:25341403<ref>PMID:25341403</ref>

-	~~Authors: Xu~~, L.H.~~, Ikeda, H~~., Arakawa, T., ~~Wakagi, T~~., Shoun, H., ~~Fushinobu~~, S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with~~ Diclofenac	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pentalenic acid synthase]]
		+	[[Category: Arakawa, T.]]
		+	[[Category: Fushinobu, S.]]
		+	[[Category: Ikeda, H.]]
		+	[[Category: Shoun, H.]]
		+	[[Category: Wakagi, T.]]
		+	[[Category: Xu, L H.]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: Diclofenac]]
		+	[[Category: Hydroxylation]]
		+	[[Category: Oxidoreductase]]

OCA at 07:21, 27 August 2014

2014-08-27T07:21:12Z

←Older revision		Revision as of 07:21, 27 August 2014
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	The entry 4ubs is ON HOLD		The entry 4ubs is ON HOLD

-	Authors: Xu,L.H., Ikeda,H., Arakawa,T., Wakagi,T., Shoun,H., Fushinobu,S.	+	Authors: Xu, L.H., Ikeda, H., Arakawa, T., Wakagi, T., Shoun, H., Fushinobu, S.

	Description: The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac		Description: The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac

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

2014-08-20T15:09:15Z

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

←Older revision

Revision as of 15:09, 20 August 2014

OCA: New page: '''Unreleased structure''' The entry 4ubs is ON HOLD Authors: Xu,L.H., Ikeda,H., Arakawa,T., Wakagi,T., Shoun,H., Fushinobu,S. Description: The crystal structure of cytochrome P450 105...

2014-08-20T15:09:13Z

New page: '''Unreleased structure''' The entry 4ubs is ON HOLD Authors: Xu,L.H., Ikeda,H., Arakawa,T., Wakagi,T., Shoun,H., Fushinobu,S. Description: The crystal structure of cytochrome P450 105...

New page

'''Unreleased structure'''

The entry 4ubs is ON HOLD

Authors: Xu,L.H., Ikeda,H., Arakawa,T., Wakagi,T., Shoun,H., Fushinobu,S.

Description: The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac