4gik: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4gik]] 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=4GIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GIK FirstGlance]. <br>
<table><tr><td colspan='2'>[[4gik]] 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=4GIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GIK FirstGlance]. <br>
</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=R5P:RIBOSE-5-PHOSPHATE'>R5P</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]] 2.187&#8491;</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=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></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=4gik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gik OCA], [https://pdbe.org/4gik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gik RCSB], [https://www.ebi.ac.uk/pdbsum/4gik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gik ProSAT]</span></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=4gik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gik OCA], [https://pdbe.org/4gik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gik RCSB], [https://www.ebi.ac.uk/pdbsum/4gik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gik ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[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>  
[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 4gik" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Revision as of 15:47, 14 March 2024

Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P Adduct

4gik, resolution 2.19Å

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