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| | ==phosphorylated Bacillus cereus phosphopentomutase soaked with glucose 1,6-bisphosphate== | | ==phosphorylated Bacillus cereus phosphopentomutase soaked with glucose 1,6-bisphosphate== |
| - | <StructureSection load='3uo0' size='340' side='right' caption='[[3uo0]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3uo0' size='340' side='right'caption='[[3uo0]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3uo0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UO0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UO0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3uo0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UO0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UO0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G16:ALPHA-D-GLUCOSE+1,6-BISPHOSPHATE'>G16</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G16:ALPHA-D-GLUCOSE+1,6-BISPHOSPHATE'>G16</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3tx0|3tx0]], [[3twz|3twz]], [[3un2|3un2]], [[3un3|3un3]], [[3un5|3un5]], [[3uny|3uny]]</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=3uo0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uo0 OCA], [https://pdbe.org/3uo0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uo0 RCSB], [https://www.ebi.ac.uk/pdbsum/3uo0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uo0 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">deoB, BC_4087 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1396 Bacillus cereus])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphopentomutase Phosphopentomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.7 5.4.2.7] </span></td></tr>
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| - | <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=3uo0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uo0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uo0 RCSB], [http://www.ebi.ac.uk/pdbsum/3uo0 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DEOB_BACCR DEOB_BACCR]] Phosphotransfer between the C1 and C5 carbon atoms of pentose (By similarity). | + | [https://www.uniprot.org/uniprot/DEOB_BACCR DEOB_BACCR] Phosphotransfer between the C1 and C5 carbon atoms of pentose (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3uo0" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bacillus cereus]] | | [[Category: Bacillus cereus]] |
| - | [[Category: Phosphopentomutase]] | + | [[Category: Large Structures]] |
| - | [[Category: Bachmann, B O]] | + | [[Category: Bachmann BO]] |
| - | [[Category: Birmingham, W R]] | + | [[Category: Birmingham WR]] |
| - | [[Category: Iverson, T M]] | + | [[Category: Iverson TM]] |
| - | [[Category: Nannemann, D P]] | + | [[Category: Nannemann DP]] |
| - | [[Category: Panosian, T D]] | + | [[Category: Panosian TD]] |
| - | [[Category: Alkaline phosphatase family]]
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| - | [[Category: Isomerase]]
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| Structural highlights
Function
DEOB_BACCR Phosphotransfer between the C1 and C5 carbon atoms of pentose (By similarity).
Publication Abstract from PubMed
Prokaryotic phosphopentomutases (PPMs) are di-Mn(2+) enzymes that catalyze the interconversion of alpha-d-ribose 5-phosphate and alpha-d-ribose 1-phosphate at an active site located between two independently folded domains. These prokaryotic PPMs belong to the alkaline phosphatase superfamily, but previous studies of Bacillus cereus PPM suggested adaptations of the conserved alkaline phosphatase catalytic cycle. Notably, B. cereus PPM engages substrates when the active site nucleophile, Thr-85, is phosphorylated. Further, the phosphoenzyme is stable throughout purification and crystallization. In contrast, alkaline phosphatase engages substrates when the active site nucleophile is dephosphorylated, and the phosphoenzyme reaction intermediate is only stably trapped in a catalytically compromised enzyme. Studies were undertaken to understand the divergence of these mechanisms. Crystallographic and biochemical investigations of the PPM(T85E) phosphomimetic variant and the neutral corollary PPM(T85Q) determined that the side chain of Lys-240 underwent a change in conformation in response to active site charge, which modestly influenced the affinity for the small molecule activator alpha-d-glucose 1,6-bisphosphate. More strikingly, the structure of unphosphorylated B. cereus PPM revealed a dramatic change in the interdomain angle and a new hydrogen bonding interaction between the side chain of Asp-156 and the active site nucleophile, Thr-85. This hydrogen bonding interaction is predicted to align and activate Thr-85 for nucleophilic addition to alpha-d-glucose 1,6-bisphosphate, favoring the observed equilibrium phosphorylated state. Indeed, phosphorylation of Thr-85 is severely impaired in the PPM(D156A) variant even under stringent activation conditions. These results permit a proposal for activation of PPM and explain some of the essential features that distinguish between the catalytic cycles of PPM and alkaline phosphatase.
Molecular Differences between a Mutase and a Phosphatase: Investigations of the Activation Step in Bacillus cereus Phosphopentomutase.,Iverson TM, Panosian TD, Birmingham WR, Nannemann DP, Bachmann BO Biochemistry. 2012 Feb 21. PMID:22329805[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Iverson TM, Panosian TD, Birmingham WR, Nannemann DP, Bachmann BO. Molecular Differences between a Mutase and a Phosphatase: Investigations of the Activation Step in Bacillus cereus Phosphopentomutase. Biochemistry. 2012 Feb 21. PMID:22329805 doi:10.1021/bi201761h
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