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| | <StructureSection load='3m8y' size='340' side='right'caption='[[3m8y]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='3m8y' size='340' side='right'caption='[[3m8y]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3m8y]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Baccr Baccr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M8Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3m8y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_ATCC_14579 Bacillus cereus ATCC 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M8Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.1Å</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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">[[3m8z|3m8z]], [[3m90|3m90]]</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=3m8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m8y OCA], [https://pdbe.org/3m8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m8y RCSB], [https://www.ebi.ac.uk/pdbsum/3m8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m8y ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BC_4087, deoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226900 BACCR])</td></tr>
| + | |
| - | <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> | + | |
| - | <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=3m8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m8y OCA], [http://pdbe.org/3m8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3m8y RCSB], [http://www.ebi.ac.uk/pdbsum/3m8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3m8y ProSAT]</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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baccr]] | + | [[Category: Bacillus cereus ATCC 14579]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Phosphopentomutase]]
| + | [[Category: Bachmann BO]] |
| - | [[Category: Bachmann, B O]] | + | [[Category: Iverson TM]] |
| - | [[Category: Iverson, T M]] | + | [[Category: Nannemann DP]] |
| - | [[Category: Nannemann, D P]] | + | [[Category: Panosian TD]] |
| - | [[Category: Panosian, T D]] | + | [[Category: Wadzinski B]] |
| - | [[Category: Wadzinski, B]] | + | [[Category: Watkins G]] |
| - | [[Category: Watkins, G]] | + | |
| - | [[Category: Alkaline phosphatase like core domain]]
| + | |
| - | [[Category: Di-metallo catalytic center]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Manganese]]
| + | |
| - | [[Category: Manganese binding]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| Structural highlights
3m8y is a 3 chain structure with sequence from Bacillus cereus ATCC 14579. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.1Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
DEOB_BACCR Phosphotransfer between the C1 and C5 carbon atoms of pentose (By similarity).
Publication Abstract from PubMed
Bacterial phosphopentomutases (PPMs) are alkaline phosphatase superfamily members that interconvert alpha-D-ribose-5-phosphate (ribose-5-phosphate) and alpha-D-ribose-1-phosphate (ribose-1-phosphate). We investigated the reaction mechanism of Bacillus cereus PPM using a combination of structural and biochemical studies. Four high-resolution crystal structures of B. cereus PPM revealed the active site architecture, identified binding sites for the substrate ribose-5-phosphate and the activator alpha-D-glucose-1,6-bisphosphate (glucose-1,6-bisphosphate), and demonstrated that glucose-1,6-bisphosphate increased phosphorylation of the active site residue Thr-85. The phosphorylation of Thr-85 was confirmed by Western and mass spectroscopic analyses. Biochemical assays identified Mn2+-dependent enzyme turnover and demonstrated that glucose-1,6-bisphosphate treatment increases enzyme activity. These results suggest that protein phosphorylation activates the enzyme, which supports an intermolecular transferase mechanism. We confirmed intermolecular phosphoryl transfer using an isotope relay assay in which PPM reactions containing mixtures of ribose-5-[18O3]-phosphate and 13C5-ribose-5-phosphate were analyzed by mass spectrometry. This intermolecular phosphoryl transfer is seemingly counter to what is anticipated from phosphomutases employing a general alkaline phosphatase reaction mechanism, which are reported to catalyze intramolecular phosphoryl transfer. However, the mechanism may be reconciled with intermolecular transfer if substrate encounters the enzyme at a different point in the catalytic cycle.
The Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle.,Panosian TD, Nannemann DP, Watkins G, Phelan VV, McDonald WH, Wadzinski BE, Bachmann BO, Iverson TM J Biol Chem. 2010 Dec 30. PMID:21193409[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Panosian TD, Nannemann DP, Watkins G, Phelan VV, McDonald WH, Wadzinski BE, Bachmann BO, Iverson TM. The Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle. J Biol Chem. 2010 Dec 30. PMID:21193409 doi:10.1074/jbc.M110.201350
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