7vkp: Difference between revisions

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==Crystal structure of E.coli pseudouridine kinase PsuK==

== Structural highlights ==

<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VKP FirstGlance]. <br>

<table><tr><td colspan='2'>[[7vkp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VKP 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=7vkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vkp OCA], [https://pdbe.org/7vkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vkp RCSB], [https://www.ebi.ac.uk/pdbsum/7vkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vkp ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Pseudouridine (Psi) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG) in Escherichia coli were first characterized as involved in pseudouridine degradation by catalyzing the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (PsiMP) and further hydrolyzing 5'-PsiMP to produce uracil and ribose 5'-phosphate. Recently, their homolog proteins in eukaryotes were also identified, which were named PUKI and PUMY in Arabidopsis. Here, we solved the crystal structures of apo-EcPsuK and its binary complex with Psi or N (1)-methyl-pseudouridine (m1Psi). The structure of EcPsuK showed a homodimer conformation assembled by its beta-thumb region. EcPsuK has an appropriate binding site with a series of hydrophilic and hydrophobic interactions for Psi. Moreover, our complex structure of EcPsuK-m1Psi suggested the binding pocket has an appropriate capacity for m1Psi. We also identified the monovalent ion-binding site and potential ATP-binding site. Our studies improved the understanding of the mechanism of Psi turnover.

Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK.,Li X, Li K, Guo W, Wen Y, Meng C, Wu B Front Microbiol. 2022 Jun 17;13:926099. doi: 10.3389/fmicb.2022.926099., eCollection 2022. PMID:35783380<ref>PMID:35783380</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Li KJ]]

[[Category: Li, K J]]

[[Category: Li XJ]]

[[Category: Li, X J]]

[[Category: Wu BX]]

[[Category: Wu, B X]]

[[Category: Kinase]]

[[Category: Pseudouridine]]

[[Category: Rna binding protein]]

[[Category: Yeic]]

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@@ Line 1: / Line 1: @@
 ==Crystal structure of E.coli pseudouridine kinase PsuK==
-<StructureSection load='7vkp' size='340' side='right'caption='[[7vkp]]' scene=''>
+<StructureSection load='7vkp' size='340' side='right'caption='[[7vkp]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VKP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7vkp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VKP 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=7vkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vkp OCA], [https://pdbe.org/7vkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vkp RCSB], [https://www.ebi.ac.uk/pdbsum/7vkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vkp ProSAT]</span></td></tr>
 </table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pseudouridine (Psi) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG) in Escherichia coli were first characterized as involved in pseudouridine degradation by catalyzing the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (PsiMP) and further hydrolyzing 5'-PsiMP to produce uracil and ribose 5'-phosphate. Recently, their homolog proteins in eukaryotes were also identified, which were named PUKI and PUMY in Arabidopsis. Here, we solved the crystal structures of apo-EcPsuK and its binary complex with Psi or N (1)-methyl-pseudouridine (m1Psi). The structure of EcPsuK showed a homodimer conformation assembled by its beta-thumb region. EcPsuK has an appropriate binding site with a series of hydrophilic and hydrophobic interactions for Psi. Moreover, our complex structure of EcPsuK-m1Psi suggested the binding pocket has an appropriate capacity for m1Psi. We also identified the monovalent ion-binding site and potential ATP-binding site. Our studies improved the understanding of the mechanism of Psi turnover.
+Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK.,Li X, Li K, Guo W, Wen Y, Meng C, Wu B Front Microbiol. 2022 Jun 17;13:926099. doi: 10.3389/fmicb.2022.926099., eCollection 2022. PMID:35783380<ref>PMID:35783380</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7vkp" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Li KJ]]
+[[Category: Li, K J]]
-[[Category: Li XJ]]
+[[Category: Li, X J]]
-[[Category: Wu BX]]
+[[Category: Wu, B X]]
+[[Category: Kinase]]
+[[Category: Pseudouridine]]
+[[Category: Rna binding protein]]
+[[Category: Yeic]]