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7w93

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<StructureSection load='7w93' size='340' side='right'caption='[[7w93]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='7w93' size='340' side='right'caption='[[7w93]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[7w93]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W93 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7w93]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W93 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8IZ:5-[(2S,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione'>8IZ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8IZ:5-[(2S,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione'>8IZ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=7w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w93 OCA], [https://pdbe.org/7w93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w93 RCSB], [https://www.ebi.ac.uk/pdbsum/7w93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w93 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=7w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w93 OCA], [https://pdbe.org/7w93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w93 RCSB], [https://www.ebi.ac.uk/pdbsum/7w93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w93 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0A140N873_ECOBD A0A140N873_ECOBD]
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7w93" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Li, K J]]
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[[Category: Li KJ]]
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[[Category: Li, X J]]
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[[Category: Li XJ]]
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[[Category: Wu, B X]]
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[[Category: Wu BX]]
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[[Category: Kinase]]
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[[Category: M1-pseudouridine]]
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[[Category: Mrna vaccine]]
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[[Category: Pseudouridine]]
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[[Category: Sugar]]
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[[Category: Sugar binding protein]]
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Current revision

Crystal structure of E.coli pseudouridine kinase PsuK complexed with N1-methyl-pseudouridine

PDB ID 7w93

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