1yoe

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[[Image:1yoe.gif|left|200px]]
 
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{{Structure
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==Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose==
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|PDB= 1yoe |SIZE=350|CAPTION= <scene name='initialview01'>1yoe</scene>, resolution 1.78&Aring;
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<StructureSection load='1yoe' size='340' side='right'caption='[[1yoe]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene>
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<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YOE FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </span>
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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]] 1.78&#8491;</td></tr>
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|GENE= ybeK/rihA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene></td></tr>
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|DOMAIN=
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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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [https://pdbe.org/1yoe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [https://www.ebi.ac.uk/pdbsum/1yoe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yoe ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1mas|1MAS]], [[2mas|2MAS]], [[1ezr|1EZR]], [[1q8f|1Q8F]], [[1hoz|1HOZ]], [[1kie|1KIE]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://www.ebi.ac.uk/pdbsum/1yoe PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/RIHA_ECOLI RIHA_ECOLI] Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively.
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== Evolutionary Conservation ==
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'''Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose'''
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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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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yo/1yoe_consurf.spt"</scriptWhenChecked>
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Enzymes with nucleoside hydrolase (NH) activity are crucial for salvaging nucleic acid components in purine auxotrophic protozoan parasites, but are also present in prokaryotes and higher eukaryotes. Here we analyze the distribution of genes encoding for putative NH proteins and characterize the yeiK gene product from Escherichia coli as a pyrimidine-specific NH. The crystal structure of YeiK to 1.7 A defines the structural basis for its substrate specificity and identifies residues involved in the catalytic mechanism that differ from both nonspecific and purine-specific NHs. Large differences in the tetrameric quaternary structure compared to nonspecific protozoan NHs are brought forth by minor differences in the interacting surfaces. The first structural and functional characterization of a nonparasitic, pyrimidine nucleoside-specific NH suggests a possible role for these enzymes in the metabolism of tRNA nucleosides. The high catalytic efficiency of YeiK toward 5-fluorouridine could be exploited for suicide gene therapy in cancer treatment.
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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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==About this Structure==
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</jmolCheckbox>
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1YOE 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=1YOE OCA].
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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=1yoe ConSurf].
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<div style="clear:both"></div>
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==Reference==
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__TOC__
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Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy., Giabbai B, Degano M, Structure. 2004 May;12(5):739-49. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15130467 15130467]
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Ribosylpyrimidine nucleosidase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Degano M]]
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[[Category: Degano, M.]]
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[[Category: Muzzolini L]]
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[[Category: Muzzolini, L.]]
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[[Category: Steyaert J]]
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[[Category: Steyaert, J.]]
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[[Category: Versees W]]
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[[Category: Versees, W.]]
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[[Category: bacterial nucleosidase]]
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[[Category: enzyme/product complex]]
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[[Category: pyrimidine nucleoside hydrolase]]
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[[Category: ribose]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:15:36 2008''
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Current revision

Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose

PDB ID 1yoe

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