View source for 8k07


==Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- citrate bound K185A mutant==
<StructureSection load='8k07' size='340' side='right'caption='[[8k07]], [[Resolution|resolution]] 1.12&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8k07]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8K07 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8K07 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.121&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=8k07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8k07 OCA], [https://pdbe.org/8k07 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8k07 RCSB], [https://www.ebi.ac.uk/pdbsum/8k07 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8k07 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PUMY_ARATH PUMY_ARATH] Catalyzes the reversible cleavage of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil (PubMed:31907295). Functions biologically in the cleavage direction, as part of a pseudouridine degradation pathway (PubMed:31907295). Acts together with the pseudouridine kinase PUKI in the peroxisome to prevent toxic pseudouridine monophosphate accumulation (PubMed:31907295). Can catalyze the formation of pseudouridine 5'-phosphate (reverse reaction) in vitro, with a catalytic efficiency 4 times lower than the hydrolysis reaction (PubMed:31907295).<ref>PMID:31907295</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pseudouridine is a noncanonical C-nucleoside containing a C-C glycosidic linkage between uracil and ribose. In the two-step degradation of pseudouridine, pseudouridine 5'-monophosphate glycosylase (PUMY) is responsible for the second step and catalyses the cleavage of the C-C glycosidic bond in pseudouridine 5'-monophosphate (PsiMP) into uridine and ribose 5'-phosphate, which are recycled via other metabolic pathways. Structural features of Escherichia coli PUMY have been reported, but the details of the substrate specificity of PsiMP were unknown. Here, we present three crystal structures of Arabidopsis thaliana PUMY in different ligation states and a kinetic analysis of PsiMP degradation. The results indicate that Thr149 and Asn308, which are conserved in the PUMY family, are structural determinants for recognizing the nucleobase of PsiMP. The distinct binding modes of PsiMP and ribose 5'-phosphate also suggest that the nucleobase, rather than the phosphate group, of PsiMP dictates the substrate-binding mode. An open-to-close transition of the active site is essential for catalysis, which is mediated by two alpha-helices, alpha11 and alpha12, near the active site. Mutational analysis validates the proposed roles of the active site residues in catalysis. Our structural and functional analyses provide further insight into the enzymatic features of PUMY towards PsiMP.

Structure and function of the pseudouridine 5'-monophosphate glycosylase PUMY from Arabidopsis thaliana.,Lee J, Kim SH, Rhee S RNA Biol. 2024 Jan;21(1):1-10. doi: 10.1080/15476286.2023.2293340. Epub 2023 Dec , 20. PMID:38117089<ref>PMID:38117089</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8k07" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Kim SH]]
[[Category: Lee JY]]
[[Category: Rhee SK]]