1yr3: Difference between revisions
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<StructureSection load='1yr3' size='340' side='right'caption='[[1yr3]], [[Resolution|resolution]] 3.20Å' scene=''> | <StructureSection load='1yr3' size='340' side='right'caption='[[1yr3]], [[Resolution|resolution]] 3.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1yr3]] is a 6 chain structure with sequence from [ | <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> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2Å</td></tr> | ||
<tr id=' | <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> | ||
<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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == 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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bochtler | [[Category: Bochtler M]] | ||
[[Category: Dandanell | [[Category: Dandanell G]] | ||
[[Category: Kierdaszuk | [[Category: Kierdaszuk B]] | ||
[[Category: Shugar | [[Category: Shugar D]] | ||
[[Category: Szczepanowski | [[Category: Szczepanowski RH]] | ||
Latest revision as of 10:00, 23 August 2023
Escherichia coli purine nucleoside phosphorylase II, the product of the xapA geneEscherichia coli purine nucleoside phosphorylase II, the product of the xapA gene
Structural highlights
FunctionXAPA_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.[1] [2] [3] [4] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedPurine 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.,Dandanell G, Szczepanowski RH, Kierdaszuk B, Shugar D, Bochtler M J Mol Biol. 2005 Apr 22;348(1):113-25. PMID:15808857[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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