1yr3

From Proteopedia

(Difference between revisions)

Revision as of 08:50, 20 January 2021

Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene

Structural highlights

1yr3 is a 6 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1yqq, 1yqu
Gene:	xapA, pndA ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yr3"

@@ Line 1: / Line 1: @@
 ==Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene==
-<StructureSection load='1yr3' size='340' side='right' caption='[[1yr3]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='1yr3' size='340' side='right'caption='[[1yr3]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yr3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YR3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yr3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1YR3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XAN:XANTHINE'>XAN</scene></td></tr>
+</td></tr><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yqq|1yqq]], [[1yqu|1yqu]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yqq|1yqq]], [[1yqu|1yqu]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xapA, pndA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1yr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yr3 PDBsum], [http://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'>[http://proteopedia.org/fgij/fg.htm?mol=1yr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yr3 OCA], [http://pdbe.org/1yr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yr3 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Purine nucleoside phosphorylase|Purine nucleoside phosphorylase]]
+*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]]
 == References ==
 <references/>
@@ Line 38: / Line 38: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: Bochtler, M]]
 [[Category: Dandanell, G]]

1yr3

From Proteopedia

Revision as of 08:50, 20 January 2021

Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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