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4gim

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Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-phosphate

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 ==Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-phosphate==
-<StructureSection load='4gim' size='340' side='right' caption='[[4gim]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='4gim' size='340' side='right'caption='[[4gim]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4gim]] 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=4GIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GIM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4gim]] 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=4GIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GIM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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]] 1.802&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gij|4gij]], [[4gik|4gik]], [[4gil|4gil]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=4gim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gim OCA], [https://pdbe.org/4gim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gim RCSB], [https://www.ebi.ac.uk/pdbsum/4gim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gim ProSAT]</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=4gim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gim OCA], [http://pdbe.org/4gim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gim RCSB], [http://www.ebi.ac.uk/pdbsum/4gim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gim ProSAT]</span></td></tr>
 </table>
 == 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;">
-== 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<ref>PMID:23066817</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4gim" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </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]]

4gim

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Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-phosphate

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