1u1d: Difference between revisions

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-[[Image:1u1d.gif|left|200px]]
- {{Structure
+==Structure of e. coli uridine phosphorylase complexed to 5-(phenylthio)acyclouridine (ptau)==
-|PDB= 1u1d |SIZE=350|CAPTION= <scene name='initialview01'>1u1d</scene>, resolution 2.001&Aring;
+<StructureSection load='1u1d' size='340' side='right'caption='[[1u1d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=181:1-((2-HYDROXYETHOXY)METHYL)-5-(PHENYLTHIO)PYRIMIDINE-2,4(1H,3H)-DIONE'>181</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
+<table><tr><td colspan='2'>[[1u1d]] is a 6 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=1U1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U1D FirstGlance]. <br>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.001&#8491;</td></tr>
-|GENE= UDP, B3831 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=181:1-((2-HYDROXYETHOXY)METHYL)-5-(PHENYLTHIO)PYRIMIDINE-2,4(1H,3H)-DIONE'>181</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1d OCA], [https://pdbe.org/1u1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u1d RCSB], [https://www.ebi.ac.uk/pdbsum/1u1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u1d ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1tgw|1TGW]], [[1tgy|1TGY]], [[1tgv|1TGV]], [[1u1c|1U1C]], [[1u1e|1U1E]], [[1u1f|1U1F]], [[1u1g|1U1G]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1d OCA], [http://www.ebi.ac.uk/pdbsum/1u1d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1u1d RCSB]</span>
+== Function ==
-}}
+[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.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u1/1u1d_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1u1d ConSurf].
+<div style="clear:both"></div>
-'''Structure of e. coli uridine phosphorylase complexed to 5-(phenylthio)acyclouridine (ptau)'''
+==See Also==
+*[[Uridine phosphorylase 3D structures|Uridine phosphorylase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Uridine phosphorylase (UP) catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate and is a key enzyme in the pyrimidine-salvage pathway. Escherichia coli UP is structurally homologous to E. coli purine nucleoside phosphorylase and other members of the type I family of nucleoside phosphorylases. The structures of 5-benzylacyclouridine, 5-phenylthioacyclouridine, 5-phenylselenenylacyclouridine, 5-m-benzyloxybenzyl acyclouridine and 5-m-benzyloxybenzyl barbituric acid acyclonucleoside bound to the active site of E. coli UP have been determined, with resolutions ranging from 1.95 to 2.3 A. For all five complexes the acyclo sugar moiety binds to the active site in a conformation that mimics the ribose ring of the natural substrates. Surprisingly, the terminal hydroxyl group occupies the position of the nonessential 5'-hydroxyl substituent of the substrate rather than the 3'-hydroxyl group, which is normally required for catalytic activity. Until recently, inhibitors of UP were designed with limited structural knowledge of the active-site residues. These structures explain the basis of inhibition for this series of acyclouridine analogs and suggest possible additional avenues for future drug-design efforts. Furthermore, the studies can be extended to design inhibitors of human UP, for which no X-ray structure is available.
-==About this Structure==
-U1D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1D OCA].
-==Reference==
-Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines., Bu W, Settembre EC, el Kouni MH, Ealick SE, Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):863-72. Epub 2005, Jun 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15983408 15983408]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Uridine phosphorylase]]
+[[Category: Bu W]]
-[[Category: Bu, W.]]
+[[Category: Ealick SE]]
-[[Category: Ealick, S E.]]
+[[Category: Settembre EC]]
-[[Category: Settembre, E C.]]
-[[Category: 5-(phenylthio)acyclouridine]]
-[[Category: ptau]]
-[[Category: pyrimidine nucleoside phosphorylase]]
-[[Category: uridine salvage]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:04:01 2008''