6u3k - Revision history

OCA at 07:43, 11 October 2023

2023-10-11T07:43:36Z

←Older revision		Revision as of 07:43, 11 October 2023
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	<StructureSection load='6u3k' size='340' side='right'caption='[[6u3k]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6u3k' size='340' side='right'caption='[[6u3k]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u3k]] 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=6U3K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6U3K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u3k]] 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=6U3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U3K 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=PQS:4-(pyridin-2-yl)benzoic+acid'>PQS</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]] 1.8Å</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=PQS:4-(pyridin-2-yl)benzoic+acid'>PQS</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=6u3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3k OCA], [~~http~~://pdbe.org/6u3k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u3k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u3k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3k 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=6u3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3k OCA], [https://pdbe.org/6u3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u3k RCSB], [https://www.ebi.ac.uk/pdbsum/6u3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3k 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 ==
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	</div>		</div>
	<div class="pdbe-citations 6u3k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6u3k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</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: 4-pyridin-2-ylbenzoic acid]]~~	+
-	~~[[Category: Cytochrome p450]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:33, 26 February 2020

2020-02-26T10:33:22Z

←Older revision		Revision as of 10:33, 26 February 2020
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	<StructureSection load='6u3k' size='340' side='right'caption='[[6u3k]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6u3k' size='340' side='right'caption='[[6u3k]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u3k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U3K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u3k]] 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=6U3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U3K 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=PQS:4-(pyridin-2-yl)benzoic+acid'>PQS</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=PQS:4-(pyridin-2-yl)benzoic+acid'>PQS</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=6u3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3k OCA], [http://pdbe.org/6u3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3k RCSB], [http://www.ebi.ac.uk/pdbsum/6u3k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3k 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=6u3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3k OCA], [http://pdbe.org/6u3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3k RCSB], [http://www.ebi.ac.uk/pdbsum/6u3k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3k ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cytochrome P450 superfamily of heme monooxygenases catalyzes important chemical reactions across nature. The changes in the optical spectra of these enzymes, induced by the addition of substrates or inhibitors, are critical for assessing how these molecules bind to the P450, enhancing or inhibiting the catalytic cycle. Here we use the bacterial CYP199A4 enzyme (Uniprot entry Q2IUO2 ), from Rhodopseudomonas palustris HaA2, and a range of substituted benzoic acids to investigate different binding modes. 4-Methoxybenzoic acid elicits an archetypal type I spectral response due to a >/=95% switch from the low- to high-spin state with concomitant dissociation of the sixth aqua ligand. 4-(Pyridin-3-yl)- and 4-(pyridin-2-yl)benzoic acid induced different type II ultraviolet-visible (UV-vis) spectral responses in CYP199A4. The former induced a greater red shift in the Soret wavelength (424 nm vs 422 nm) along with a larger overall absorbance change and other differences in the alpha-, beta-, and delta-bands. There were also variations in the ferrous UV-vis spectra of these two substrate-bound forms with a spectrum indicative of Fe-N bond formation with 4-(pyridin-3-yl)benzoic acid. The crystal structures of CYP199A4, with the pyridinyl compounds bound, revealed that while the nitrogen of 4-(pyridin-3-yl)benzoic acid is coordinated to the heme, with 4-(pyridin-2-yl)benzoic acid an aqua ligand remains. Continuous wave and pulse electron paramagnetic resonance data in frozen solution revealed that the substrates are bound in the active site in a form consistent with the crystal structures. The redox potential of each CYP199A4-substrate combination was measured, allowing correlation among binding modes, spectroscopic properties, and the observed biochemical activity.
		+
		+	Biophysical Techniques for Distinguishing Ligand Binding Modes in Cytochrome P450 Monooxygenases.,Podgorski MN, Harbort JS, Coleman T, Stok JE, Yorke JA, Wong LL, Bruning JB, Bernhardt PV, De Voss JJ, Harmer JR, Bell SG Biochemistry. 2020 Feb 24. doi: 10.1021/acs.biochem.0c00027. PMID:32058707<ref>PMID:32058707</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6u3k" 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 06:41, 19 February 2020

2020-02-19T06:41:31Z

←Older revision		Revision as of 06:41, 19 February 2020
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-	'''Unreleased structure'''

-	The ~~entry~~ 6u3k ~~is ON HOLD until Paper Publication~~	+	==The crystal structure of 4-(pyridin-2-yl)benzoate-bound CYP199A4==
-		+	<StructureSection load='6u3k' size='340' side='right'caption='[[6u3k]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~: ~~Podgorski, M~~.N.~~, Bruning, J~~.B.~~, Bell, S~~.G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6u3k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U3K FirstGlance]. <br>
-	~~Description~~: ~~The crystal structure of~~ 4-(pyridin-2-yl)~~benzoate~~-~~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=PQS:4-(pyridin-2-yl)benzoic+acid'>PQS</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=6u3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3k OCA], [http://pdbe.org/6u3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3k RCSB], [http://www.ebi.ac.uk/pdbsum/6u3k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3k ProSAT]</span></td></tr>
-	[[Category: ~~Bruning~~, ~~J.B~~]]	+	</table>
-	[[Category: ~~Bell~~, ~~S.G~~]]	+	__TOC__
-	[[Category: Podgorski, M.N]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bell, S G]]
		+	[[Category: Bruning, J B]]
		+	[[Category: Podgorski, M N]]
		+	[[Category: 4-pyridin-2-ylbenzoic acid]]
		+	[[Category: Cytochrome p450]]
		+	[[Category: Oxidoreductase]]

OCA at 08:09, 2 October 2019

2019-10-02T08:09:10Z

←Older revision		Revision as of 08:09, 2 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u3k is ON HOLD	+	The entry 6u3k 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.
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	Description: The crystal structure of 4-(pyridin-2-yl)benzoate-bound CYP199A4		Description: The crystal structure of 4-(pyridin-2-yl)benzoate-bound CYP199A4
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Bruning, J.B]]
	[[Category: Bell, S.G]]		[[Category: Bell, S.G]]
	[[Category: Podgorski, M.N]]		[[Category: Podgorski, M.N]]
-	[[Category: Bruning, J.B]]

OCA: Protected "6u3k" [edit=sysop:move=sysop]

2019-08-28T14:06:44Z

Protected "6u3k" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:06, 28 August 2019

OCA: New page: '''Unreleased structure''' The entry 6u3k is ON HOLD Authors: Podgorski, M.N., Bruning, J.B., Bell, S.G. Description: The crystal structure of 4-(pyridin-2-yl)benzoate-bound CYP199A4 [...

2019-08-28T14:06:42Z

New page: '''Unreleased structure''' The entry 6u3k is ON HOLD Authors: Podgorski, M.N., Bruning, J.B., Bell, S.G. Description: The crystal structure of 4-(pyridin-2-yl)benzoate-bound CYP199A4 [...

New page

'''Unreleased structure'''

The entry 6u3k is ON HOLD

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

Description: The crystal structure of 4-(pyridin-2-yl)benzoate-bound CYP199A4
[[Category: Unreleased Structures]]
[[Category: Bell, S.G]]
[[Category: Podgorski, M.N]]
[[Category: Bruning, J.B]]