7vtf
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==cytidine bound structure of Pseudouridine kinase (PUKI) from Escherichia coli strain B== | ==cytidine bound structure of Pseudouridine kinase (PUKI) from Escherichia coli strain B== | ||
| - | <StructureSection load='7vtf' size='340' side='right'caption='[[7vtf]]' scene=''> | + | <StructureSection load='7vtf' size='340' side='right'caption='[[7vtf]], [[Resolution|resolution]] 2.20Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7vtf]] is a 4 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=7VTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTF FirstGlance]. <br> |
| - | </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=7vtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtf OCA], [https://pdbe.org/7vtf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtf RCSB], [https://www.ebi.ac.uk/pdbsum/7vtf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtf ProSAT]</span></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]] 2.2020345Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</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=7vtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtf OCA], [https://pdbe.org/7vtf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtf RCSB], [https://www.ebi.ac.uk/pdbsum/7vtf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/PSUK_ECOLI PSUK_ECOLI] Catalyzes the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (PsiMP).<ref>PMID:18591240</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Pseudouridine, one major RNA modification, is catabolized into uracil and ribose-5'-phosphate by two sequential enzymatic reactions. In the first step, pseudouridine kinase (PUKI) phosphorylates pseudouridine to pseudouridine 5'-monophosphate. High-fidelity catalysis of pseudouridine by PUKI prevents possible disturbance of in vivo pyrimidine homeostasis. However, the molecular basis of how PUKI selectively phosphorylates pseudouridine over uridine with >100-fold greater efficiency despite minor differences in their Km values has not been elucidated. To investigate this selectivity, in this study we determined the structures of PUKI from Escherichia coli strain B (EcPUKI) in various ligation states. The structure of EcPUKI was determined to be similar to PUKI from Arabidopsis thaliana, including an alpha/beta core domain and beta-stranded small domain, with dimerization occurring via the beta-stranded small domain. In a binary complex, we show that Ser30 in the substrate-binding loop of the small domain mediates interactions with the hallmark N1 atom of pseudouridine nucleobase, causing conformational changes in its quaternary structure. Kinetic and fluorescence spectroscopic analyses also showed that the Ser30-mediated interaction is a prerequisite for conformational changes and subsequent catalysis by EcPUKI. Furthermore, S30A mutation or EcPUKI complexed with other nucleosides homologous to pseudouridine but lacking the pseudouridine-specific N1 atom did not induce such conformational changes, demonstrating the catalytic significance of the proposed Ser30-mediated interaction. These analyses provide structural and functional evidence for a pseudouridine-dependent conformational change of EcPUKI and its functional linkage to catalysis. | ||
| + | |||
| + | Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI.,Kim SH, Kim M, Park D, Byun S, Rhee S J Biol Chem. 2022 Mar 25:101869. doi: 10.1016/j.jbc.2022.101869. PMID:35346685<ref>PMID:35346685</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7vtf" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Escherichia coli]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Kim SH]] | [[Category: Kim SH]] | ||
[[Category: Rhee S]] | [[Category: Rhee S]] | ||
Current revision
cytidine bound structure of Pseudouridine kinase (PUKI) from Escherichia coli strain B
| |||||||||||
