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| - | [[Image:1yqu.gif|left|200px]] | |
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| - | <!-- | + | ==Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene== |
| - | The line below this paragraph, containing "STRUCTURE_1yqu", creates the "Structure Box" on the page.
| + | <StructureSection load='1yqu' size='340' side='right'caption='[[1yqu]], [[Resolution|resolution]] 3.10Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet) | + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1yqu]] is a 3 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=1YQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YQU FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | --> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GUN:GUANINE'>GUN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | {{STRUCTURE_1yqu| PDB=1yqu | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqu OCA], [https://pdbe.org/1yqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yqu RCSB], [https://www.ebi.ac.uk/pdbsum/1yqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yqu ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == 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/yq/1yqu_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=1yqu 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> |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | 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.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 1YQU 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=1YQU OCA].
| + | </div> |
| | + | <div class="pdbe-citations 1yqu" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | 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]
| + | *[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[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 Sat May 3 16:39:57 2008''
| + | |
| Structural highlights
Function
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.[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 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.,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 Also
References
- ↑ Buxton RS, Hammer-Jespersen K, Valentin-Hansen P. A second purine nucleoside phosphorylase in Escherichia coli K-12. I. Xanthosine phosphorylase regulatory mutants isolated as secondary-site revertants of a deoD mutant. Mol Gen Genet. 1980;179(2):331-40. PMID:7007808
- ↑ Hammer-Jespersen K, Buxton RS, Hansen TD. A second purine nucleoside phosphorylase in Escherichia coli K-12. II. Properties of xanthosine phosphorylase and its induction by xanthosine. Mol Gen Genet. 1980;179(2):341-8. PMID:7007809
- ↑ Koszalka GW, Vanhooke J, Short SA, Hall WW. Purification and properties of inosine-guanosine phosphorylase from Escherichia coli K-12. J Bacteriol. 1988 Aug;170(8):3493-8. PMID:3042752
- ↑ Dandanell G, Szczepanowski RH, Kierdaszuk B, Shugar D, Bochtler M. Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene. J Mol Biol. 2005 Apr 22;348(1):113-25. PMID:15808857 doi:http://dx.doi.org/10.1016/j.jmb.2005.02.019
- ↑ Dandanell G, Szczepanowski RH, Kierdaszuk B, Shugar D, Bochtler M. Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene. J Mol Biol. 2005 Apr 22;348(1):113-25. PMID:15808857 doi:http://dx.doi.org/10.1016/j.jmb.2005.02.019
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