1yr3: Difference between revisions

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-[[Image:1yr3.gif|left|200px]]
- {{Structure
+==Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene==
-|PDB= 1yr3 |SIZE=350|CAPTION= <scene name='initialview01'>1yr3</scene>, resolution 3.2&Aring;
+<StructureSection load='1yr3' size='340' side='right'caption='[[1yr3]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XAN:XANTHINE'>XAN</scene>
+<table><tr><td colspan='2'>[[1yr3]] 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=1YR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YR3 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
-|GENE= xapA, pndA ([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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XAN:XANTHINE'>XAN</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=1yr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yr3 OCA], [https://pdbe.org/1yr3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yr3 RCSB], [https://www.ebi.ac.uk/pdbsum/1yr3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yr3 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1yqq|1YQQ]], [[1yqu|1YQU]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yr3 OCA], [http://www.ebi.ac.uk/pdbsum/1yr3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yr3 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/XAPA_ECOLI XAPA_ECOLI] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate. This protein can degrade all purine nucleosides including xanthosine, inosine and guanosine, but cannot cleave adenosine, deoxyadenosine or hypoxanthine arabinoside. Has a preference for the neutral over the monoanionic form of xanthosine.<ref>PMID:7007808</ref> <ref>PMID:7007809</ref> <ref>PMID:3042752</ref> <ref>PMID:15808857</ref>
+== 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/yr/1yr3_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=1yr3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Purine nucleoside phosphorylases (PNPs, E. C. 2.4.2.1) use orthophosphate to cleave the N-glycosidic bond of beta-(deoxy)ribonucleosides to yield alpha-(deoxy)ribose 1-phosphate and the free purine base. Escherichia coli PNP-II, the product of the xapA gene, is similar to trimeric PNPs in sequence, but has been reported to migrate as a hexamer and to accept xanthosine with comparable efficiency to guanosine and inosine, the usual physiological substrates for trimeric PNPs. Here, we present a detailed biochemical characterization and the crystal structure of E.coli PNP-II. In three different crystal forms, PNP-II trimers dimerize, leading to a subunit arrangement that is qualitatively different from the "trimer of dimers" arrangement of conventional high molecular mass PNPs. Crystal structures are compatible with similar binding modes for guanine and xanthine, with a preference for the neutral over the monoanionic form of xanthine. A single amino acid exchange, tyrosine 191 to leucine, is sufficient to convert E.coli PNP-II into an enzyme with the specificity of conventional trimeric PNPs, but the reciprocal mutation in human PNP, valine 195 to tyrosine, does not elicit xanthosine phosphorylase activity in the human enzyme.
-'''Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene'''
+Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene.,Dandanell G, Szczepanowski RH, Kierdaszuk B, Shugar D, Bochtler M J Mol Biol. 2005 Apr 22;348(1):113-25. PMID:15808857<ref>PMID:15808857</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1yr3" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Purine nucleoside phosphorylases (PNPs, E. C. 2.4.2.1) use orthophosphate to cleave the N-glycosidic bond of beta-(deoxy)ribonucleosides to yield alpha-(deoxy)ribose 1-phosphate and the free purine base. Escherichia coli PNP-II, the product of the xapA gene, is similar to trimeric PNPs in sequence, but has been reported to migrate as a hexamer and to accept xanthosine with comparable efficiency to guanosine and inosine, the usual physiological substrates for trimeric PNPs. Here, we present a detailed biochemical characterization and the crystal structure of E.coli PNP-II. In three different crystal forms, PNP-II trimers dimerize, leading to a subunit arrangement that is qualitatively different from the "trimer of dimers" arrangement of conventional high molecular mass PNPs. Crystal structures are compatible with similar binding modes for guanine and xanthine, with a preference for the neutral over the monoanionic form of xanthine. A single amino acid exchange, tyrosine 191 to leucine, is sufficient to convert E.coli PNP-II into an enzyme with the specificity of conventional trimeric PNPs, but the reciprocal mutation in human PNP, valine 195 to tyrosine, does not elicit xanthosine phosphorylase activity in the human enzyme.
+*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-YR3 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=1YR3 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene., Dandanell G, Szczepanowski RH, Kierdaszuk B, Shugar D, Bochtler M, J Mol Biol. 2005 Apr 22;348(1):113-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15808857 15808857]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bochtler, M.]]
+[[Category: Bochtler M]]
-[[Category: Dandanell, G.]]
+[[Category: Dandanell G]]
-[[Category: Kierdaszuk, B.]]
+[[Category: Kierdaszuk B]]
-[[Category: Shugar, D.]]
+[[Category: Shugar D]]
-[[Category: Szczepanowski, R H.]]
+[[Category: Szczepanowski RH]]
-[[Category: purine nucleoside phosphorylase guanine xanthine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:18:45 2008''