7c1z

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ATP bound structure of Pseudouridine kinase (PUKI) from Arabidopsis thaliana

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Categories: Arabidopsis thaliana | Large Structures | Kim SH | Rhee S

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 <StructureSection load='7c1z' size='340' side='right'caption='[[7c1z]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7c1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C1Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7c1z]] is a 2 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=7C1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C1Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.0961704&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At1g49350, F13F21.22, F13F21_22 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7c1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c1z OCA], [https://pdbe.org/7c1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c1z RCSB], [https://www.ebi.ac.uk/pdbsum/7c1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c1z ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/PUKI_ARATH PUKI_ARATH] Catalyzes the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (PsiMP) (PubMed:31907295). Catalyzes the first step in a pseudouridine degradation pathway (PubMed:31907295). Acts together with the pseudouridine 5'-phosphate glycosidase PUMY in the peroxisome to prevent toxic pseudouridine monophosphate accumulation (PubMed:31907295).<ref>PMID:31907295</ref>
-RNA modifications can regulate the stability of RNAs, mRNA-protein interactions, and translation efficiency. Pseudouridine is a prevalent RNA modification, and its metabolic fate after RNA turnover was recently characterized in eukaryotes, in the plant Arabidopsis thaliana. Here, we present structural and biochemical analyses of PSEUDOURIDINE KINASE from Arabidopsis (AtPUKI), the enzyme catalyzing the first step in pseudouridine degradation. AtPUKI, a member of the PfkB family of carbohydrate kinases, is a homodimeric alpha/beta protein with a protruding small beta-strand domain, which serves simultaneously as dimerization interface and dynamic substrate specificity determinant. AtPUKI has a unique nucleoside binding site specifying the binding of pseudourine, in particular at the nucleobase, by multiple hydrophilic interactions, of which one is mediated by a loop from the small beta-strand domain of the adjacent monomer. Conformational transition of the dimerized small beta-strand domains containing active site residues is required for substrate specificity. These dynamic features explain the higher catalytic efficiency for pseudouridine over uridine. Both substrates bind well (similar Km), but only pseudouridine is turned over efficiently. Our studies provide an example for structural and functional divergence in the PfkB family and highlight how AtPUKI avoids futile uridine phosphorylation which in vivo would disturb pyrimidine homeostasis.
-Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana.,Kim SH, Witte CP, Rhee S Nucleic Acids Res. 2021 Jan 11;49(1):491-503. doi: 10.1093/nar/gkaa1144. PMID:33290549<ref>PMID:33290549</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 7c1z" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Kim, S H]]
+[[Category: Kim SH]]
-[[Category: Rhee, S]]
+[[Category: Rhee S]]
-[[Category: Kinase]]
-[[Category: Psedouridine kinase]]
-[[Category: Pseudouridine]]
-[[Category: Puki]]
-[[Category: Rna]]

7c1z

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ATP bound structure of Pseudouridine kinase (PUKI) from Arabidopsis thaliana

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