3qpb

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<StructureSection load='3qpb' size='340' side='right'caption='[[3qpb]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
<StructureSection load='3qpb' size='340' side='right'caption='[[3qpb]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3qpb]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pyogenes_serotype_m6 Streptococcus pyogenes serotype m6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QPB FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3qpb]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pyogenes_serotype_M6 Streptococcus pyogenes serotype M6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QPB FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
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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]] 1.82&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">M6_Spy1599 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301450 Streptococcus pyogenes serotype M6])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R1P:RIBOSE-1-PHOSPHATE'>R1P</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </span></td></tr>
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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=3qpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qpb OCA], [https://pdbe.org/3qpb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qpb RCSB], [https://www.ebi.ac.uk/pdbsum/3qpb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qpb ProSAT]</span></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=3qpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qpb OCA], [https://pdbe.org/3qpb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qpb RCSB], [https://www.ebi.ac.uk/pdbsum/3qpb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qpb ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/Q5XA29_STRP6 Q5XA29_STRP6]] Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.[RuleBase:RU361131]
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[https://www.uniprot.org/uniprot/Q5XA29_STRP6 Q5XA29_STRP6] Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.[RuleBase:RU361131]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 A resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an alpha/beta monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is approximately 7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.
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The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases.,Tran TH, Christoffersen S, Allan PW, Parker WB, Piskur J, Serra I, Terreni M, Ealick SE Biochemistry. 2011 Aug 2;50(30):6549-6558. Epub 2011 Jul 8. PMID:21707079<ref>PMID:21707079</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3qpb" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Uridine phosphorylase 3D structures|Uridine phosphorylase 3D structures]]
*[[Uridine phosphorylase 3D structures|Uridine phosphorylase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Streptococcus pyogenes serotype m6]]
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[[Category: Streptococcus pyogenes serotype M6]]
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[[Category: Uridine phosphorylase]]
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[[Category: Christoffersen S]]
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[[Category: Christoffersen, S]]
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[[Category: Ealick SE]]
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[[Category: Ealick, S E]]
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[[Category: Parker WB]]
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[[Category: Parker, W B]]
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[[Category: Piskur J]]
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[[Category: Piskur, J]]
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[[Category: Serra I]]
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[[Category: Serra, I]]
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[[Category: Terreni M]]
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[[Category: Terreni, M]]
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[[Category: Tran TH]]
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[[Category: Tran, T H]]
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[[Category: Hexamer]]
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[[Category: Np-i superfamily]]
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[[Category: Pyrimidine salvage pathway]]
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[[Category: Transferase]]
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[[Category: Transition state]]
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Current revision

Crystal Structure of Streptococcus Pyogenes Uridine Phosphorylase Reveals a Subclass of the NP-I Superfamily

PDB ID 3qpb

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