6k5h: Difference between revisions

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<StructureSection load='6k5h' size='340' side='right'caption='[[6k5h]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='6k5h' size='340' side='right'caption='[[6k5h]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6k5h]] 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=6K5H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K5H FirstGlance]. <br>
<table><tr><td colspan='2'>[[6k5h]] 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=6K5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K5H FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=URA:URACIL'>URA</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]] 2.503&#8491;</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=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=URA:URACIL'>URA</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=6k5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5h OCA], [https://pdbe.org/6k5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k5h RCSB], [https://www.ebi.ac.uk/pdbsum/6k5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5h 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=6k5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5h OCA], [http://pdbe.org/6k5h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k5h RCSB], [http://www.ebi.ac.uk/pdbsum/6k5h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5h ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A410UCT3_PHYCP A0A410UCT3_PHYCP]
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6k5h" 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>
[[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: R1p]]
[[Category: Transferase]]

Latest revision as of 13:41, 27 March 2024

Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.Structural and catalytic analysis of two diverse uridine phosphorylases in the oomycete Phytophthora capsici.

Structural highlights

6k5h is a 4 chain structure with sequence from Phytophthora capsici LT1534. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.503Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A410UCT3_PHYCP

See Also

6k5h, resolution 2.50Å

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OCA
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