6k8p - Revision history

OCA at 10:28, 22 November 2023

OCA — Wed, 22 Nov 2023 10:28:03 GMT

←Older revision		Revision as of 10:28, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6k8p' size='340' side='right'caption='[[6k8p]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='6k8p' size='340' side='right'caption='[[6k8p]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k8p]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Phytophthora_capsici_lt1534~~ Phytophthora capsici ~~lt1534~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K8P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6K8P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k8p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phytophthora_capsici_LT1534 Phytophthora capsici LT1534]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K8P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</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]] 1.965Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">up ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=763924 Phytophthora capsici LT1534])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=6k8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8p OCA], [https://pdbe.org/6k8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k8p RCSB], [https://www.ebi.ac.uk/pdbsum/6k8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8p ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6k8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8p OCA], [~~http~~://pdbe.org/6k8p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k8p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k8p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8p ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A410UCT3_PHYCP A0A410UCT3_PHYCP]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Phytophthora capsici ~~lt1534]]~~	+	[[Category: Phytophthora capsici LT1534]]
-	~~[[Category: Uridine phosphorylase~~]]	+	[[Category: Yang CC]]
-	[[Category: Yang~~, C C~~]]	+	[[Category: Zhang XG]]
-	[[Category: Zhang~~, X G]]~~	+
-	~~[[Category: Phytophthora capsici]]~~	+
-	~~[[Category: Thymidine]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:32, 17 June 2020

OCA — Wed, 17 Jun 2020 10:32:56 GMT

←Older revision		Revision as of 10:32, 17 June 2020
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8p OCA], [http://pdbe.org/6k8p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k8p RCSB], [http://www.ebi.ac.uk/pdbsum/6k8p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8p ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8p OCA], [http://pdbe.org/6k8p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k8p RCSB], [http://www.ebi.ac.uk/pdbsum/6k8p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Uridine phosphorylase (UP) is a key enzyme of pyrimidine salvage pathways that enables the recycling of endogenous or exogenous-supplied pyrimidines and plays an important intracellular metabolic role. Here, we biochemically and structurally characterized two evolutionarily divergent uridine phosphorylases, PcUP1 and PcUP2 from the oomycete pathogen Phytophthora capsici. Our analysis of other oomycete genomes revealed that both uridine phosphorylases are present in Phytophthora and Pythium genomes, but only UP2 is seen in Saprolegnia spp. which are basal members of the oomycetes. Moreover, uridine phosphorylases are not found in obligate oomycete pathogens such as Hyaloperonospora arabidopsidis and Albugo spp. PcUP1 and PcUP2 are upregulated 300 and 500 fold respectively, within 90 min after infection of pepper leaves. The crystal structures of PcUP1 in ligand-free and in complex with uracil/ribose-1-phosphate, 2'-deoxyuridine/phosphate and thymidine/phosphate were analyzed. Crystal structure of this uridine phosphorylase showed strict conservation of key residues in the binding pocket. Structure analysis of PcUP1 with bound ligands, and site-directed mutagenesis of key residues provide additional support for the "push-pull" model of catalysis. Our study highlights the importance of pyrimidine salvage during the earliest stages of infection.
		+
		+	Structural and catalytic analysis of two diverse uridine phosphorylases in Phytophthora capsici.,Yang C, Li J, Huang Z, Zhang X, Gao X, Zhu C, Morris PF, Zhang X Sci Rep. 2020 Jun 3;10(1):9051. doi: 10.1038/s41598-020-65935-9. PMID:32493959<ref>PMID:32493959</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k8p" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]		*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:12, 27 May 2020

OCA — Wed, 27 May 2020 07:12:15 GMT

←Older revision		Revision as of 07:12, 27 May 2020
Line 3:		Line 3:
	<StructureSection load='6k8p' size='340' side='right'caption='[[6k8p]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='6k8p' size='340' side='right'caption='[[6k8p]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k8p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K8P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K8P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k8p]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Phytophthora_capsici_lt1534 Phytophthora capsici lt1534]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K8P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K8P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">up ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=763924 Phytophthora capsici LT1534])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=6k8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8p OCA], [http://pdbe.org/6k8p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k8p RCSB], [http://www.ebi.ac.uk/pdbsum/6k8p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8p ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8p OCA], [http://pdbe.org/6k8p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k8p RCSB], [http://www.ebi.ac.uk/pdbsum/6k8p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8p ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Phytophthora capsici lt1534]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
	[[Category: Yang, C C]]		[[Category: Yang, C C]]

OCA at 11:00, 13 November 2019

OCA — Wed, 13 Nov 2019 11:00:25 GMT

←Older revision		Revision as of 11:00, 13 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6k8p is ON HOLD~~	+	==Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.==
-		+	<StructureSection load='6k8p' size='340' side='right'caption='[[6k8p]], [[Resolution\|resolution]] 1.96Å' scene=''>
-	~~Authors: Yang, C.C., Zhang, X.G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6k8p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K8P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K8P FirstGlance]. <br>
-	~~Description:~~ Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </span></td></tr>
-	[[Category: Yang, C.C]]	+	<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=6k8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8p OCA], [http://pdbe.org/6k8p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k8p RCSB], [http://www.ebi.ac.uk/pdbsum/6k8p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8p ProSAT]</span></td></tr>
-	[[Category: Zhang, X.G]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Uridine phosphorylase]]
		+	[[Category: Yang, C C]]
		+	[[Category: Zhang, X G]]
		+	[[Category: Phytophthora capsici]]
		+	[[Category: Thymidine]]
		+	[[Category: Transferase]]

OCA: Protected "6k8p" [edit=sysop:move=sysop]

OCA — Wed, 19 Jun 2019 04:07:25 GMT

Protected "6k8p" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:07, 19 June 2019

OCA: New page: '''Unreleased structure''' The entry 6k8p is ON HOLD Authors: Yang, C.C., Zhang, X.G. Description: Structural and catalytic analysis of two diverse uridine phosphorylases in the oomyce...

OCA — Wed, 19 Jun 2019 04:07:23 GMT

New page: '''Unreleased structure''' The entry 6k8p is ON HOLD Authors: Yang, C.C., Zhang, X.G. Description: Structural and catalytic analysis of two diverse uridine phosphorylases in the oomyce...

New page

'''Unreleased structure'''

The entry 6k8p is ON HOLD

Authors: Yang, C.C., Zhang, X.G.

Description: Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.
[[Category: Unreleased Structures]]
[[Category: Yang, C.C]]
[[Category: Zhang, X.G]]