7ljt - Revision history

OCA at 15:52, 18 October 2023

OCA — Wed, 18 Oct 2023 15:52:12 GMT

←Older revision		Revision as of 15:52, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='7ljt' size='340' side='right'caption='[[7ljt]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='7ljt' size='340' side='right'caption='[[7ljt]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ljt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pig Pig~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ljt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=Y3G:5-ethynylpyrimidine-2,4(1H,3H)-dione'>Y3G</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]] 1.98Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPYD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=Y3G:5-ethynylpyrimidine-2,4(1H,3H)-dione'>Y3G</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dihydropyrimidine_dehydrogenase_(NADP(+)) Dihydropyrimidine dehydrogenase (NADP(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.2 1.3.1.2] </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=7ljt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljt OCA], [https://pdbe.org/7ljt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljt RCSB], [https://www.ebi.ac.uk/pdbsum/7ljt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljt 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=7ljt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljt OCA], [https://pdbe.org/7ljt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljt RCSB], [https://www.ebi.ac.uk/pdbsum/7ljt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPYD_PIG DPYD_PIG]] Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine.<ref>PMID:9860876</ref> <ref>PMID:20831907</ref> <ref>PMID:11179210</ref>	+	[https://www.uniprot.org/uniprot/DPYD_PIG DPYD_PIG] Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine.<ref>PMID:9860876</ref> <ref>PMID:20831907</ref> <ref>PMID:11179210</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pig~~]]	+	[[Category: Sus scrofa]]
-	[[Category: Beaupre, B]]	+	[[Category: Beaupre B]]
-	[[Category: Butrin, A]]	+	[[Category: Butrin A]]
-	[[Category: Forouzesh, D]]	+	[[Category: Forouzesh D]]
-	[[Category: Liu, D]]	+	[[Category: Liu D]]
-	[[Category: Moran, G]]	+	[[Category: Moran G]]
-	[[Category: Wawrzak, Z]]	+	[[Category: Wawrzak Z]]
-	~~[[Category: 5-ethynyluracil]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Dihydropyrimidine dehydrogenase]]~~	+
-	~~[[Category: Dpd]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Inactivator]]~~	+
-	~~[[Category: Inhibitor~~]]	+

OCA at 05:34, 28 April 2021

OCA — Wed, 28 Apr 2021 05:34:24 GMT

←Older revision		Revision as of 05:34, 28 April 2021
Line 1:		Line 1:

	==Porcine Dihydropyrimidine Dehydrogenase (DPD) soaked with 5-Ethynyluracil (5EU), NADPH - 20 minutes==		==Porcine Dihydropyrimidine Dehydrogenase (DPD) soaked with 5-Ethynyluracil (5EU), NADPH - 20 minutes==
-	<StructureSection load='7ljt' size='340' side='right'caption='[[7ljt]]' scene=''>	+	<StructureSection load='7ljt' size='340' side='right'caption='[[7ljt]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ljt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJT FirstGlance]. <br>
-	</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=7ljt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljt OCA], [https://pdbe.org/7ljt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljt RCSB], [https://www.ebi.ac.uk/pdbsum/7ljt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljt ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=Y3G:5-ethynylpyrimidine-2,4(1H,3H)-dione'>Y3G</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DPYD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dihydropyrimidine_dehydrogenase_(NADP(+)) Dihydropyrimidine dehydrogenase (NADP(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.2 1.3.1.2] </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=7ljt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljt OCA], [https://pdbe.org/7ljt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljt RCSB], [https://www.ebi.ac.uk/pdbsum/7ljt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljt ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/DPYD_PIG DPYD_PIG]] Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine.<ref>PMID:9860876</ref> <ref>PMID:20831907</ref> <ref>PMID:11179210</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dihydropyrimidine dehydrogenase (DPD) is a complex enzyme that reduces the 5,6-vinylic bond of pyrimidines, uracil, and thymine. 5-Fluorouracil (5FU) is also a substrate for DPD and a common chemotherapeutic agent used to treat numerous cancers. The reduction of 5FU to 5-fluoro-5,6-dihydrouracil negates its toxicity and efficacy. Patients with high DPD activity levels typically have poor outcomes when treated with 5FU. DPD is thus a central mitigating factor in the treatment of a variety of cancers. 5-Ethynyluracil (5EU) covalently inactivates DPD by cross-linking with the active-site general acid cysteine in the pyrimidine binding site. This reaction is dependent on the simultaneous binding of 5EU and nicotinamide adenine dinucleotide phosphate (NADPH). This ternary complex induces DPD to become activated by taking up two electrons from the NADPH. The covalent inactivation of DPD by 5EU occurs concomitantly with this reductive activation with a rate constant of approximately 0.2 s(-1). This kinact value is correlated with the rate of reduction of one of the two flavin cofactors and the localization of a mobile loop in the pyrimidine active site that places the cysteine that serves as the general acid in catalysis proximal to the 5EU ethynyl group. Efficient cross-linking is reliant on enzyme activation, but this process appears to also have a conformational aspect in that nonreductive NADPH analogues can also induce a partial inactivation. Cross-linking then renders DPD inactive by severing the proton-coupled electron transfer mechanism that transmits electrons 56 A across the protein.
		+
		+	The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil.,Forouzesh DC, Beaupre BA, Butrin A, Wawrzak Z, Liu D, Moran GR Biochemistry. 2021 Mar 23. doi: 10.1021/acs.biochem.1c00096. PMID:33755421<ref>PMID:33755421</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ljt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Beaupre B]]	+	[[Category: Pig]]
-	[[Category: Butrin A]]	+	[[Category: Beaupre, B]]
-	[[Category: Forouzesh D]]	+	[[Category: Butrin, A]]
-	[[Category: Liu D]]	+	[[Category: Forouzesh, D]]
-	[[Category: Moran G]]	+	[[Category: Liu, D]]
-	[[Category: Wawrzak Z]]	+	[[Category: Moran, G]]
		+	[[Category: Wawrzak, Z]]
		+	[[Category: 5-ethynyluracil]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Dihydropyrimidine dehydrogenase]]
		+	[[Category: Dpd]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Inactivator]]
		+	[[Category: Inhibitor]]

OCA at 06:53, 7 April 2021

OCA — Wed, 07 Apr 2021 06:53:18 GMT

←Older revision		Revision as of 06:53, 7 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7ljt is ON HOLD until Paper Publication~~	+	==Porcine Dihydropyrimidine Dehydrogenase (DPD) soaked with 5-Ethynyluracil (5EU), NADPH - 20 minutes==
-		+	<StructureSection load='7ljt' size='340' side='right'caption='[[7ljt]]' scene=''>
-	~~Authors: Butrin, A., Forouzesh, D., Beaupre, B., Wawrzak, Z., Liu, D., Moran, G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJT FirstGlance]. <br>
-	~~Description:~~ Porcine Dihydropyrimidine Dehydrogenase (DPD) soaked with 5-Ethynyluracil (5EU), NADPH -20 minutes	+	</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=7ljt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ljt OCA], [https://pdbe.org/7ljt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ljt RCSB], [https://www.ebi.ac.uk/pdbsum/7ljt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ljt ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Wawrzak, Z~~]]	+	__TOC__
-	[[Category: ~~Forouzesh, D~~]]	+	</StructureSection>
-	[[Category: ~~Liu,~~ D]]	+	[[Category: Large Structures]]
-	[[Category: ~~Moran, G~~]]	+	[[Category: Beaupre B]]
-	[[Category: ~~Beaupre, B~~]]	+	[[Category: Butrin A]]
-	[[Category: ~~Butrin, A~~]]	+	[[Category: Forouzesh D]]
		+	[[Category: Liu D]]
		+	[[Category: Moran G]]
		+	[[Category: Wawrzak Z]]

OCA at 14:39, 10 March 2021

OCA — Wed, 10 Mar 2021 14:39:36 GMT

←Older revision		Revision as of 14:39, 10 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ljt is ON HOLD	+	The entry 7ljt is ON HOLD until Paper Publication

	Authors: Butrin, A., Forouzesh, D., Beaupre, B., Wawrzak, Z., Liu, D., Moran, G.		Authors: Butrin, A., Forouzesh, D., Beaupre, B., Wawrzak, Z., Liu, D., Moran, G.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Wawrzak, Z]]		[[Category: Wawrzak, Z]]
		+	[[Category: Forouzesh, D]]
	[[Category: Liu, D]]		[[Category: Liu, D]]
	[[Category: Moran, G]]		[[Category: Moran, G]]
	[[Category: Beaupre, B]]		[[Category: Beaupre, B]]
	[[Category: Butrin, A]]		[[Category: Butrin, A]]
-	[[Category: Forouzesh, D]]

OCA: Protected "7ljt" [edit=sysop:move=sysop]

OCA — Wed, 10 Feb 2021 09:18:09 GMT

Protected "7ljt" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:18, 10 February 2021

OCA: New page: '''Unreleased structure''' The entry 7ljt is ON HOLD Authors: Butrin, A., Forouzesh, D., Beaupre, B., Wawrzak, Z., Liu, D., Moran, G. Description: Porcine Dihydropyrimidine Dehydrogena...

OCA — Wed, 10 Feb 2021 09:18:08 GMT

New page: '''Unreleased structure''' The entry 7ljt is ON HOLD Authors: Butrin, A., Forouzesh, D., Beaupre, B., Wawrzak, Z., Liu, D., Moran, G. Description: Porcine Dihydropyrimidine Dehydrogena...

New page

'''Unreleased structure'''

The entry 7ljt is ON HOLD

Authors: Butrin, A., Forouzesh, D., Beaupre, B., Wawrzak, Z., Liu, D., Moran, G.

Description: Porcine Dihydropyrimidine Dehydrogenase (DPD) soaked with 5-Ethynyluracil (5EU), NADPH -20 minutes
[[Category: Unreleased Structures]]
[[Category: Wawrzak, Z]]
[[Category: Liu, D]]
[[Category: Moran, G]]
[[Category: Beaupre, B]]
[[Category: Butrin, A]]
[[Category: Forouzesh, D]]