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1rxs

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(New page: 200px<br /><applet load="1rxs" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rxs, resolution 2.80&Aring;" /> '''E. coli uridine phos...)
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[[Image:1rxs.gif|left|200px]]<br /><applet load="1rxs" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rxs, resolution 2.80&Aring;" />
 
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'''E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex'''<br />
 
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==Overview==
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==E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex==
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Uridine phosphorylase (UP) is a key enzyme in the pyrimidine salvage, pathway that catalyses the reversible phosphorolysis of uridine to uracil, and ribose 1-phosphate. Inhibiting liver UP in humans raises blood uridine, levels and produces a protective effect ("uridine rescue") against the, toxicity of the chemotherapeutic agent 5-fluorouracil without reducing its, antitumour activity. We have investigated UP-substrate interactions by, determining the crystal structures of native Escherichia coli UP (two, forms), and complexes with 5-fluorouracil/ribose 1-phosphate, 2-deoxyuridine/phosphate and thymidine/phosphate. These hexameric, structures confirm the overall structural similarity of UP to E.coli, purine nucleoside phosphorylase (PNP) whereby, in the presence of, substrate, each displays a closed conformation resulting from a concerted, movement that closes the active site cleft. However, in contrast to PNP, where helix segmentation is the major conformational change between the, open and closed forms, in UP more extensive changes are observed. In, particular a swinging movement of a flap region consisting of residues, 224-234 seals the active site. This overall change in conformation results, in compression of the active site cleft. Gln166 and Arg168, part of an, inserted segment not seen in PNP, are key residues in the uracil binding, pocket and together with a tightly bound water molecule are seen to be, involved in the substrate specificity of UP. Enzyme activity shows a, twofold dependence on potassium ion concentration. The presence of a, potassium ion at the monomer/monomer interface induces some local, rearrangement, which results in dimer stabilisation. The conservation of, key residues and interactions with substrate in the phosphate and ribose, binding pockets suggest that ribooxocarbenium ion formation during, catalysis of UP may be similar to that proposed for E.coli PNP.
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<StructureSection load='1rxs' size='340' side='right'caption='[[1rxs]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rxs]] is a 30 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RXS FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [https://pdbe.org/1rxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [https://www.ebi.ac.uk/pdbsum/1rxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxs ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/UDP_ECOLI UDP_ECOLI] 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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/1rxs_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1rxs ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1RXS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with PO4, K, DUR and V7O as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RXS OCA].
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*[[Uridine phosphorylase 3D structures|Uridine phosphorylase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium., Caradoc-Davies TT, Cutfield SM, Lamont IL, Cutfield JF, J Mol Biol. 2004 Mar 19;337(2):337-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15003451 15003451]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Uridine phosphorylase]]
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[[Category: Caradoc-Davies TT]]
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[[Category: Caradoc-Davies, T.T.]]
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[[Category: Cutfield JF]]
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[[Category: Cutfield, J.F.]]
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[[Category: Cutfield SM]]
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[[Category: Cutfield, S.M.]]
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[[Category: Lamont IL]]
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[[Category: Lamont, I.L.]]
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[[Category: DUR]]
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[[Category: K]]
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[[Category: PO4]]
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[[Category: V7O]]
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[[Category: 2'-deoxyuridine]]
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[[Category: induced fit]]
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[[Category: pentosyltransferase]]
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[[Category: potassium]]
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[[Category: specificity]]
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[[Category: uridine phosphorylase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:56:24 2007''
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Current revision

E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex

PDB ID 1rxs

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