5t6q - Revision history

OCA at 12:55, 4 October 2023

OCA — Wed, 04 Oct 2023 12:55:42 GMT

←Older revision		Revision as of 12:55, 4 October 2023
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	<StructureSection load='5t6q' size='340' side='right'caption='[[5t6q]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5t6q' size='340' side='right'caption='[[5t6q]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t6q]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~European_rabbit European rabbit~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T6Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t6q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T6Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene~~>, ~~<scene name='pdbligand=OCT:N-OCTANE'>OCT</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]] 2.701Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CYP4B1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9986 European rabbit])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Unspecific_monooxygenase Unspecific monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.1 1.14.14.1]~~ </~~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=5t6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6q OCA], [https://pdbe.org/5t6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t6q RCSB], [https://www.ebi.ac.uk/pdbsum/5t6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6q 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=5t6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6q OCA], [~~http~~://pdbe.org/5t6q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t6q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t6q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6q ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CP4B1_RABIT CP4B1_RABIT]] Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.	+	[https://www.uniprot.org/uniprot/CP4B1_RABIT CP4B1_RABIT] Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: European rabbit]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Unspecific monooxygenase~~]]	+	[[Category: Oryctolagus cuniculus]]
-	[[Category: Hsu, M]]	+	[[Category: Hsu M]]
-	[[Category: Johnson~~, E F]]~~	+	[[Category: Johnson EF]]
-	~~[[Category: Cyp4b1]]~~	+
-	~~[[Category: Cytochrome p450]]~~	+
-	~~[[Category: Fatty acid omega-hydroxylase]]~~	+
-	~~[[Category: Octane]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 12:29, 25 December 2019

OCA — Wed, 25 Dec 2019 12:29:01 GMT

←Older revision		Revision as of 12:29, 25 December 2019
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	==Structure of cytochrome P450 4B1 (CYP4B1) complexed with octane: An n-Alkane and fatty acid omega-hydroxylase with a covalently bound heme==		==Structure of cytochrome P450 4B1 (CYP4B1) complexed with octane: An n-Alkane and fatty acid omega-hydroxylase with a covalently bound heme==
-	<StructureSection load='5t6q' size='340' side='right' caption='[[5t6q]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5t6q' size='340' side='right'caption='[[5t6q]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5t6q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[5t6q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6Q FirstGlance]. <br>
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Cytochrome P450\|Cytochrome P450]]	+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: European rabbit]]		[[Category: European rabbit]]
		+	[[Category: Large Structures]]
	[[Category: Unspecific monooxygenase]]		[[Category: Unspecific monooxygenase]]
	[[Category: Hsu, M]]		[[Category: Hsu, M]]

OCA at 07:04, 28 March 2018

OCA — Wed, 28 Mar 2018 07:04:09 GMT

←Older revision		Revision as of 07:04, 28 March 2018
Line 3:		Line 3:
	<StructureSection load='5t6q' size='340' side='right' caption='[[5t6q]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5t6q' size='340' side='right' caption='[[5t6q]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t6q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t6q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYP4B1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unspecific_monooxygenase Unspecific monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.1 1.14.14.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unspecific_monooxygenase Unspecific monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.1 1.14.14.1] </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=5t6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6q OCA], [http://pdbe.org/5t6q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6q RCSB], [http://www.ebi.ac.uk/pdbsum/5t6q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6q 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=5t6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6q OCA], [http://pdbe.org/5t6q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6q RCSB], [http://www.ebi.ac.uk/pdbsum/5t6q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6q ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: European rabbit]]
	[[Category: Unspecific monooxygenase]]		[[Category: Unspecific monooxygenase]]
	[[Category: Hsu, M]]		[[Category: Hsu, M]]

OCA at 05:00, 12 April 2017

OCA — Wed, 12 Apr 2017 05:00:54 GMT

←Older revision		Revision as of 05:00, 12 April 2017
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	</div>		</div>
	<div class="pdbe-citations 5t6q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5t6q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450\|Cytochrome P450]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:26, 9 March 2017

OCA — Thu, 09 Mar 2017 08:26:43 GMT

←Older revision		Revision as of 08:26, 9 March 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5t6q is ~~ON HOLD until Paper~~ Publication	+	==Structure of cytochrome P450 4B1 (CYP4B1) complexed with octane: An n-Alkane and fatty acid omega-hydroxylase with a covalently bound heme==
		+	<StructureSection load='5t6q' size='340' side='right' caption='[[5t6q]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5t6q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T6Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unspecific_monooxygenase Unspecific monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.1 1.14.14.1] </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=5t6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t6q OCA], [http://pdbe.org/5t6q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t6q RCSB], [http://www.ebi.ac.uk/pdbsum/5t6q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t6q ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CP4B1_RABIT CP4B1_RABIT]] Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	P450 family 4 fatty acid omega-hydroxylases preferentially oxygenate primary C-H bonds over adjacent, energetically favored secondary C-H bonds, but the mechanism explaining this intriguing preference is unclear. To this end, the structure of rabbit P450 4B1 complexed with its substrate octane was determined by X-ray crystallography to define features of the active site that contribute to a preference for omega-hydroxylation. The structure indicated that octane is bound in a narrow active site cavity that limits access of the secondary C-H bond to the reactive intermediate. A highly conserved sequence motif on helix I contributes to positioning the terminal carbon of octane for omega-hydroxylation. Glu-310 of this motif auto-catalytically forms an ester bond with the heme 5-methyl, and the immobilized E310 contributes to substrate positioning. The preference for omega-hydroxylation was decreased in a E310A mutant having a shorter side-chain, but overall rates of metabolism were retained. E310D and E310Q substitutions having longer side-chains exhibit lower overall rates, likely due to higher conformational entropy for these residues, but they retained high preferences for octane omega-hydroxylation. Sequence comparisons indicated that active-site residues constraining octane for omega-hydroxylation are conserved in family 4 P450s. Moreover, the heme 7-propionate is positioned in the active site and provides additional restraints on substrate binding. In conclusion, P450 4B1 exhibits structural adaptations for omega-hydroxylation that include changes in the conformation of the heme and changes in a highly conserved helix I motif that is associated with selective oxygenation of un-activated primary C-H bonds.

-	~~Authors:~~ Hsu, M., ~~Johnson~~, E.F.	+	The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monoxygenase Complexed with Octane Discloses Several Structural Adaptations for omega-Hydroxylation.,Hsu MH, Baer BR, Rettie AE, Johnson EF J Biol Chem. 2017 Feb 6. pii: jbc.M117.775494. doi: 10.1074/jbc.M117.775494. PMID:28167536<ref>PMID:28167536</ref>

-	~~Description: Structure~~ of ~~cytochrome P450 4B1 (CYP4B1) complexed with octane: An n~~-~~Alkane and fatty acid omega~~-~~hydroxylase with a covalently bound heme~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5t6q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Unspecific monooxygenase]]
	[[Category: Hsu, M]]		[[Category: Hsu, M]]
-	[[Category: Johnson, E.F]]	+	[[Category: Johnson, E F]]
		+	[[Category: Cyp4b1]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: Fatty acid omega-hydroxylase]]
		+	[[Category: Octane]]
		+	[[Category: Oxidoreductase]]

OCA at 15:27, 19 October 2016

OCA — Wed, 19 Oct 2016 15:27:57 GMT

←Older revision		Revision as of 15:27, 19 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5t6q is ON HOLD	+	The entry 5t6q is ON HOLD until Paper Publication

	Authors: Hsu, M., Johnson, E.F.		Authors: Hsu, M., Johnson, E.F.

OCA: Protected "5t6q" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 15:48:21 GMT

Protected "5t6q" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:48, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t6q is ON HOLD Authors: Hsu, M., Johnson, E.F. Description: Structure of cytochrome P450 4B1 (CYP4B1) complexed with octane: An n-Alkane and fatty...

OCA — Fri, 09 Sep 2016 15:48:19 GMT

New page: '''Unreleased structure''' The entry 5t6q is ON HOLD Authors: Hsu, M., Johnson, E.F. Description: Structure of cytochrome P450 4B1 (CYP4B1) complexed with octane: An n-Alkane and fatty...

New page

'''Unreleased structure'''

The entry 5t6q is ON HOLD

Authors: Hsu, M., Johnson, E.F.

Description: Structure of cytochrome P450 4B1 (CYP4B1) complexed with octane: An n-Alkane and fatty acid omega-hydroxylase with a covalently bound heme
[[Category: Unreleased Structures]]
[[Category: Hsu, M]]
[[Category: Johnson, E.F]]