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| | ==Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine 5'-Phosphate Adduct== | | ==Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine 5'-Phosphate Adduct== |
| - | <StructureSection load='4gil' size='340' side='right' caption='[[4gil]], [[Resolution|resolution]] 2.54Å' scene=''> | + | <StructureSection load='4gil' size='340' side='right'caption='[[4gil]], [[Resolution|resolution]] 2.54Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4gil]] is a 3 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=4GIL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GIL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4gil]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GIL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GIL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KPS:PSEUDOURIDINE+5-PHOSPHATE,+LINEAR'>KPS</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KPS:PSEUDOURIDINE+5-PHOSPHATE,+LINEAR'>KPS</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gij|4gij]], [[4gik|4gik]], [[4gim|4gim]]</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=4gil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gil OCA], [https://pdbe.org/4gil PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gil RCSB], [https://www.ebi.ac.uk/pdbsum/4gil PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gil ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2165, JW2152, psuG, yeiN ([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=4gil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gil OCA], [http://pdbe.org/4gil PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gil RCSB], [http://www.ebi.ac.uk/pdbsum/4gil PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gil ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PSUG_ECOLI PSUG_ECOLI]] Catalyzes the reversible cleavage of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil. Functions biologically in the cleavage direction, as part of a pseudouridine degradation pathway.[HAMAP-Rule:MF_01876]<ref>PMID:18591240</ref> <ref>PMID:23066817</ref> | + | [https://www.uniprot.org/uniprot/PSUG_ECOLI PSUG_ECOLI] Catalyzes the reversible cleavage of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil. Functions biologically in the cleavage direction, as part of a pseudouridine degradation pathway.[HAMAP-Rule:MF_01876]<ref>PMID:18591240</ref> <ref>PMID:23066817</ref> |
| | <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: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Begley, T P]] | + | [[Category: Large Structures]] |
| - | [[Category: Ealick, S E]] | + | [[Category: Begley TP]] |
| - | [[Category: Huang, S]] | + | [[Category: Ealick SE]] |
| - | [[Category: Mahanta, N]] | + | [[Category: Huang S]] |
| - | [[Category: Alpha-beta-alpha sandwich fold]] | + | [[Category: Mahanta N]] |
| - | [[Category: Hydrolase]]
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| Structural highlights
Function
PSUG_ECOLI Catalyzes the reversible cleavage of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil. Functions biologically in the cleavage direction, as part of a pseudouridine degradation pathway.[HAMAP-Rule:MF_01876][1] [2]
Publication Abstract from PubMed
Pseudouridine (Psi), the most abundant modification in RNA, is synthesized in situ using Psi synthase. Recently, a pathway for the degradation of Psi was described [Preumont, A., Snoussi, K., Stroobant, V., Collet, J. F., and Van Schaftingen, E. (2008) J. Biol. Chem. 283, 25238-25246]. In this pathway, Psi is first converted to Psi 5'-monophosphate (PsiMP) by Psi kinase and then PsiMP is degraded by PsiMP glycosidase to uracil and ribose 5-phosphate. PsiMP glycosidase is the first example of a mechanistically characterized enzyme that cleaves a C-C glycosidic bond. Here we report X-ray crystal structures of Escherichia coli PsiMP glycosidase and a complex of the K166A mutant with PsiMP. We also report the structures of a ring-opened ribose 5-phosphate adduct and a ring-opened ribose PsiMP adduct. These structures provide four snapshots along the reaction coordinate. The structural studies suggested that the reaction utilizes a Lys166 adduct during catalysis. Biochemical and mass spectrometry data further confirmed the existence of a lysine adduct. We used site-directed mutagenesis combined with kinetic analysis to identify roles for specific active site residues. Together, these data suggest that PsiMP glycosidase catalyzes the cleavage of the C-C glycosidic bond through a novel ribose ring-opening mechanism.
Pseudouridine monophosphate glycosidase: a new glycosidase mechanism.,Huang S, Mahanta N, Begley TP, Ealick SE Biochemistry. 2012 Nov 13;51(45):9245-55. doi: 10.1021/bi3006829. Epub 2012 Oct, 30. PMID:23066817[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Preumont A, Snoussi K, Stroobant V, Collet JF, Van Schaftingen E. Molecular identification of pseudouridine-metabolizing enzymes. J Biol Chem. 2008 Sep 12;283(37):25238-46. doi: 10.1074/jbc.M804122200. Epub 2008, Jun 30. PMID:18591240 doi:http://dx.doi.org/10.1074/jbc.M804122200
- ↑ Huang S, Mahanta N, Begley TP, Ealick SE. Pseudouridine monophosphate glycosidase: a new glycosidase mechanism. Biochemistry. 2012 Nov 13;51(45):9245-55. doi: 10.1021/bi3006829. Epub 2012 Oct, 30. PMID:23066817 doi:http://dx.doi.org/10.1021/bi3006829
- ↑ Huang S, Mahanta N, Begley TP, Ealick SE. Pseudouridine monophosphate glycosidase: a new glycosidase mechanism. Biochemistry. 2012 Nov 13;51(45):9245-55. doi: 10.1021/bi3006829. Epub 2012 Oct, 30. PMID:23066817 doi:http://dx.doi.org/10.1021/bi3006829
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