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| | <StructureSection load='4r2x' size='340' side='right'caption='[[4r2x]], [[Resolution|resolution]] 0.93Å' scene=''> | | <StructureSection load='4r2x' size='340' side='right'caption='[[4r2x]], [[Resolution|resolution]] 0.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4r2x]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4hen 4hen]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R2X FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4r2x]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4hen 4hen]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R2X FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4r2w|4r2w]]</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=4r2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r2x OCA], [https://pdbe.org/4r2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r2x RCSB], [https://www.ebi.ac.uk/pdbsum/4r2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r2x ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">udp, so_4133 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</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=4r2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r2x OCA], [http://pdbe.org/4r2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r2x RCSB], [http://www.ebi.ac.uk/pdbsum/4r2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r2x ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8E9X9_SHEON Q8E9X9_SHEON] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Uridine phosphorylase|Uridine phosphorylase]] | + | *[[Uridine phosphorylase 3D structures|Uridine phosphorylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Sheon]] | + | [[Category: Shewanella oneidensis MR-1]] |
| - | [[Category: Uridine phosphorylase]]
| + | [[Category: Manuvera VA]] |
| - | [[Category: Manuvera, V A]] | + | [[Category: Mordkovich NN]] |
| - | [[Category: Mordkovich, N N]] | + | [[Category: Polyakov KM]] |
| - | [[Category: Polyakov, K M]] | + | [[Category: Popov VO]] |
| - | [[Category: Popov, V O]] | + | [[Category: Safonova TN]] |
| - | [[Category: Safonova, T N]] | + | [[Category: Veiko VP]] |
| - | [[Category: Veiko, V P]] | + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
Q8E9X9_SHEON
Publication Abstract from PubMed
Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Expression of UP from Shewanella oneidensis MR-1 (SoUP) was performed in Escherichia coli. The high-resolution X-ray structure of SoUP was solved in the free form and in complex with uridine. A crystal of SoUP in the free form was grown under microgravity and diffracted to ultrahigh resolution. Both forms of SoUP contained sulfate instead of phosphate in the active site owing to the presence of ammonium sulfate in the crystallization solution. The latter can be considered as a good mimic of phosphate. In the complex, uridine adopts a high-syn conformation with a nearly planar ribose ring and is present only in one subunit of the hexamer. A comparison of the structures of SoUP in the free form and in complex with the natural substrate uridine showed that the subunits of the hexamer are not identical, with the active sites having either an open or a closed conformation. In the monomers with the closed conformation, the active sites in which uridine is absent contain a glycerol molecule mimicking the ribose moiety of uridine.
High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine.,Safonova TN, Mikhailov SN, Veiko VP, Mordkovich NN, Manuvera VA, Alekseev CS, Kovalchuk MV, Popov VO, Polyakov KM Acta Crystallogr D Biol Crystallogr. 2014 Dec 1;70(Pt 12):3310-9. doi:, 10.1107/S1399004714024079. Epub 2014 Nov 28. PMID:25478848[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Safonova TN, Mikhailov SN, Veiko VP, Mordkovich NN, Manuvera VA, Alekseev CS, Kovalchuk MV, Popov VO, Polyakov KM. High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine. Acta Crystallogr D Biol Crystallogr. 2014 Dec 1;70(Pt 12):3310-9. doi:, 10.1107/S1399004714024079. Epub 2014 Nov 28. PMID:25478848 doi:http://dx.doi.org/10.1107/S1399004714024079
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