6pqd - Revision history

OCA at 07:33, 11 October 2023

OCA — Wed, 11 Oct 2023 07:33:47 GMT

←Older revision		Revision as of 07:33, 11 October 2023
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	<StructureSection load='6pqd' size='340' side='right'caption='[[6pqd]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='6pqd' size='340' side='right'caption='[[6pqd]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pqd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhop2 Rhop2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PQD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pqd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_HaA2 Rhodopseudomonas palustris HaA2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PQD 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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OVP:3-(methylsulfanyl)benzoic+acid'>OVP</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]] 1.89Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPB_3613 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316058 RHOP2])~~</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OVP:3-(methylsulfanyl)benzoic+acid'>OVP</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=6pqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqd OCA], [~~http~~://pdbe.org/6pqd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pqd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pqd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqd 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=6pqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqd OCA], [https://pdbe.org/6pqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pqd RCSB], [https://www.ebi.ac.uk/pdbsum/6pqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2IU02_RHOP2 Q2IU02_RHOP2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6pqd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6pqd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Rhop2~~]]	+	[[Category: Rhodopseudomonas palustris HaA2]]
-	[[Category: Bell~~, S G~~]]	+	[[Category: Bell SG]]
-	[[Category: Bruning~~, J B~~]]	+	[[Category: Bruning JB]]
-	[[Category: Podgorski~~, M N]]~~	+	[[Category: Podgorski MN]]
-	~~[[Category: 3-methylthiobenzoic acid]]~~	+
-	~~[[Category: Cytochrome p450]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:47, 4 December 2019

OCA — Wed, 04 Dec 2019 10:47:48 GMT

←Older revision		Revision as of 10:47, 4 December 2019
Line 3:		Line 3:
	<StructureSection load='6pqd' size='340' side='right'caption='[[6pqd]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='6pqd' size='340' side='right'caption='[[6pqd]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pqd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PQD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pqd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhop2 Rhop2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PQD 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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OVP:3-(methylsulfanyl)benzoic+acid'>OVP</scene></td></tr>		</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OVP:3-(methylsulfanyl)benzoic+acid'>OVP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RPB_3613 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316058 RHOP2])</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=6pqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqd OCA], [http://pdbe.org/6pqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pqd RCSB], [http://www.ebi.ac.uk/pdbsum/6pqd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqd 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=6pqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqd OCA], [http://pdbe.org/6pqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pqd RCSB], [http://www.ebi.ac.uk/pdbsum/6pqd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqd ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cytochrome P450 metalloenzyme (CYP) CYP199A4 from Rhodopseudomonas palustris HaA2 catalyzes the highly efficient oxidation of para-substituted benzoic acids. Here we determined crystal structures of CYP199A4, and the binding and turnover parameters, with different meta-substituted benzoic acids in order to establish which criteria are important for efficient catalysis. When compared to the para isomers, the meta-substituted benzoic acids were less efficiently oxidized. For example, 3-formylbenzoic acid was oxidized with lower activity than the equivalent para isomer and 3-methoxybenzoic acid did not undergo O-demethylation by CYP199A4. The structural data highlighted that the meta-substituted benzoic acids bound in the enzyme active site in a modified position with incomplete loss of the distal water ligand of the heme moiety. However, for both sets of isomers the meta- or para-substituent pointed towards, and was in close proximity, to the heme iron. The absence of oxidation activity with 3-methoxybenzoic acid was assigned to the observation that the CH bonds of this molecule point away from the heme iron. In contrast, in the para isomer they are in an ideal location for abstraction. These findings were confirmed by using the bulkier 3-ethoxybenzoic acid as a substrate which removed the water ligand and reoriented the meta-substituent so that the methylene hydrogens pointed towards the heme, enabling more efficient oxidation. Overall we show relatively small changes in substrate structure and position in the active site can have a dramatic effect on the activity.
		+
		+	Investigation of the requirements for efficient and selective cytochrome P450 monooxygenase catalysis across different reactions.,Podgorski MN, Coleman T, Chao RR, De Voss JJ, Bruning JB, Bell SG J Inorg Biochem. 2019 Nov 13;203:110913. doi: 10.1016/j.jinorgbio.2019.110913. PMID:31759265<ref>PMID:31759265</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pqd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Rhop2]]
	[[Category: Bell, S G]]		[[Category: Bell, S G]]
	[[Category: Bruning, J B]]		[[Category: Bruning, J B]]

OCA at 06:52, 27 November 2019

OCA — Wed, 27 Nov 2019 06:52:55 GMT

←Older revision		Revision as of 06:52, 27 November 2019
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-	'''Unreleased structure'''

-	The ~~entry~~ 6pqd is ~~ON HOLD until Paper Publication~~	+	==The crystal structure of 3-methylthiobenzoate-bound CYP199A4==
-		+	<StructureSection load='6pqd' size='340' side='right'caption='[[6pqd]], [[Resolution\|resolution]] 1.89Å' scene=''>
-	~~Authors~~: ~~Podgorski~~, M.N., ~~Bruning~~, J.B., ~~Bell~~, S.G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6pqd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PQD FirstGlance]. <br>
-	~~Description: The crystal structure of 3-methylthiobenzoate-bound CYP199A4~~	+	</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OVP:3-(methylsulfanyl)benzoic+acid'>OVP</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=6pqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pqd OCA], [http://pdbe.org/6pqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pqd RCSB], [http://www.ebi.ac.uk/pdbsum/6pqd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pqd ProSAT]</span></td></tr>
-	[[Category: Bell, S.G]]	+	</table>
-	[[Category: Podgorski, M.N]]	+	__TOC__
-	[[Category: ~~Bruning, J.B~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bell, S G]]
		+	[[Category: Bruning, J B]]
		+	[[Category: Podgorski, M N]]
		+	[[Category: 3-methylthiobenzoic acid]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: Oxidoreductase]]

OCA at 13:44, 28 August 2019

OCA — Wed, 28 Aug 2019 13:44:41 GMT

←Older revision		Revision as of 13:44, 28 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pqd is ON HOLD	+	The entry 6pqd is ON HOLD until Paper Publication

	Authors: Podgorski, M.N., Bruning, J.B., Bell, S.G.		Authors: Podgorski, M.N., Bruning, J.B., Bell, S.G.

OCA: Protected "6pqd" [edit=sysop:move=sysop]

OCA — Wed, 17 Jul 2019 09:06:57 GMT

Protected "6pqd" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:06, 17 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pqd is ON HOLD Authors: Podgorski, M.N., Bruning, J.B., Bell, S.G. Description: The crystal structure of 3-methylthiobenzoate-bound CYP199A4 [[Cat...

OCA — Wed, 17 Jul 2019 09:06:56 GMT

New page: '''Unreleased structure''' The entry 6pqd is ON HOLD Authors: Podgorski, M.N., Bruning, J.B., Bell, S.G. Description: The crystal structure of 3-methylthiobenzoate-bound CYP199A4 [[Cat...

New page

'''Unreleased structure'''

The entry 6pqd is ON HOLD

Authors: Podgorski, M.N., Bruning, J.B., Bell, S.G.

Description: The crystal structure of 3-methylthiobenzoate-bound CYP199A4
[[Category: Unreleased Structures]]
[[Category: Bell, S.G]]
[[Category: Podgorski, M.N]]
[[Category: Bruning, J.B]]