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==X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution==
==X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution==
<StructureSection load='4e1v' size='340' side='right' caption='[[4e1v]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
<StructureSection load='4e1v' size='340' side='right'caption='[[4e1v]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4e1v]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium_str._lt2 Salmonella enterica subsp. enterica serovar typhimurium str. lt2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3nsr 3nsr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E1V FirstGlance]. <br>
<table><tr><td colspan='2'>[[4e1v]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3nsr 3nsr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E1V FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</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]] 2.15&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">STM3968, STMD1.21, udp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</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=4e1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e1v OCA], [https://pdbe.org/4e1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e1v RCSB], [https://www.ebi.ac.uk/pdbsum/4e1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e1v 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=4e1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e1v RCSB], [http://www.ebi.ac.uk/pdbsum/4e1v PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/UDP_SALTY UDP_SALTY]] Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis (By similarity).  
[https://www.uniprot.org/uniprot/UDP_SALTY UDP_SALTY] Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Uridine phosphorylase (UPh), which is a key enzyme in the reutilization pathway of pyrimidine nucleoside metabolism, is a validated target for the treatment of infectious diseases and cancer. A detailed analysis of the interactions of UPh with the therapeutic ligand 5-fluorouracil (5-FUra) is important for the rational design of pharmacological inhibitors of these enzymes in prokaryotes and eukaryotes. Expanding on the preliminary analysis of the spatial organization of the active centre of UPh from the pathogenic bacterium Salmonella typhimurium (StUPh) in complex with 5-FUra [Lashkov et al. (2009), Acta Cryst. F65, 601-603], the X-ray structure of the StUPh-5-FUra complex was analysed at atomic resolution and an in silico model of the complex formed by the drug with UPh from Vibrio cholerae (VchUPh) was generated. These results should be considered in the design of selective inhibitors of UPhs from various species.
 
X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae.,Lashkov AA, Sotnichenko SE, Prokofiev II, Gabdulkhakov AG, Agapov II, Shtil AA, Betzel C, Mironov AS, Mikhailov AM Acta Crystallogr D Biol Crystallogr. 2012 Aug;68(Pt 8):968-74. Epub 2012 Jul 17. PMID:22868762<ref>PMID:22868762</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Uridine phosphorylase|Uridine phosphorylase]]
*[[Uridine phosphorylase|Uridine phosphorylase]]
== References ==
*[[Uridine phosphorylase 3D structures|Uridine phosphorylase 3D structures]]
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Salmonella enterica subsp. enterica serovar typhimurium str. lt2]]
[[Category: Large Structures]]
[[Category: Uridine phosphorylase]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
[[Category: Gabdoulkhakov, A G]]
[[Category: Gabdoulkhakov AG]]
[[Category: Lashkov, A A]]
[[Category: Lashkov AA]]
[[Category: Mikhailov, A M]]
[[Category: Mikhailov AM]]
[[Category: Prokofev, I I]]
[[Category: Prokofev II]]
[[Category: Sotnichenko, S E]]
[[Category: Sotnichenko SE]]
[[Category: Drug metabolism]]
[[Category: Rossmann fold]]
[[Category: Transferase]]

Latest revision as of 17:50, 14 March 2024

X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A ResolutionX-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution

Structural highlights

4e1v is a 9 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2. This structure supersedes the now removed PDB entry 3nsr. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.15Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UDP_SALTY Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis (By similarity).

See Also

4e1v, resolution 2.15Å

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