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| | ==Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2'-deoxyguanosine== | | ==Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2'-deoxyguanosine== |
| - | <StructureSection load='4da0' size='340' side='right' caption='[[4da0]], [[Resolution|resolution]] 2.95Å' scene=''> | + | <StructureSection load='4da0' size='340' side='right'caption='[[4da0]], [[Resolution|resolution]] 2.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4da0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DA0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4da0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DA0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d8v|4d8v]], [[4d8x|4d8x]], [[4d8y|4d8y]], [[4d98|4d98]], [[4d9h|4d9h]], [[4da6|4da6]], [[4da7|4da7]], [[4da8|4da8]], [[4dab|4dab]], [[4dae|4dae]], [[4dan|4dan]], [[4dao|4dao]], [[4dar|4dar]]</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=4da0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da0 OCA], [https://pdbe.org/4da0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4da0 RCSB], [https://www.ebi.ac.uk/pdbsum/4da0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4da0 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU19630, deoD, punB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </span></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=4da0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da0 OCA], [http://pdbe.org/4da0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4da0 RCSB], [http://www.ebi.ac.uk/pdbsum/4da0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4da0 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DEOD_BACSU DEOD_BACSU]] Cleavage of adenosine and its derivatives. | + | [[https://www.uniprot.org/uniprot/DEOD_BACSU DEOD_BACSU]] Cleavage of adenosine and its derivatives. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Purine nucleoside phosphorylase|Purine nucleoside phosphorylase]] | + | *[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus globigii migula 1900]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Purine-nucleoside phosphorylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Giuseppe, P O]] | + | [[Category: Giuseppe PO]] |
| - | [[Category: Martins, N H]] | + | [[Category: Martins NH]] |
| - | [[Category: Meza, A N]] | + | [[Category: Meza AN]] |
| - | [[Category: Murakami, M T]] | + | [[Category: Murakami MT]] |
| - | [[Category: Phosphorylase/hydrolase-like]]
| + | |
| - | [[Category: Transferase]]
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| Structural highlights
Function
[DEOD_BACSU] Cleavage of adenosine and its derivatives.
Publication Abstract from PubMed
The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2'deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2'deoxy)ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5' hydroxyl group of adenosine and Arg(43*) side chain contributes for the ribosyl radical to adopt an unusual C3'-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl(6) and Br(8) substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser(90) by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr(91)) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.
Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.,de Giuseppe PO, Martins NH, Meza AN, Dos Santos CR, Pereira HD, Murakami MT PLoS One. 2012;7(9):e44282. Epub 2012 Sep 5. PMID:22957058[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ de Giuseppe PO, Martins NH, Meza AN, Dos Santos CR, Pereira HD, Murakami MT. Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases. PLoS One. 2012;7(9):e44282. Epub 2012 Sep 5. PMID:22957058 doi:http://dx.doi.org/10.1371/journal.pone.0044282
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