3al6

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Crystal structure of Human TYW5

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 ==Crystal structure of Human TYW5==
-<StructureSection load='3al6' size='340' side='right' caption='[[3al6]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='3al6' size='340' side='right'caption='[[3al6]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3al6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AL6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AL6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3al6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AL6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3al5|3al5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">C2orf60 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3al6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3al6 OCA], [https://pdbe.org/3al6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3al6 RCSB], [https://www.ebi.ac.uk/pdbsum/3al6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3al6 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3al6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3al6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3al6 RCSB], [http://www.ebi.ac.uk/pdbsum/3al6 PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/TYW5_HUMAN TYW5_HUMAN] tRNA hydroxylase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the hydroxylation of 7-(a-amino-a-carboxypropyl)wyosine (yW-72) into undermodified hydroxywybutosine (OHyW*). OHyW* being further transformed into hydroxywybutosine (OHyW) by LCMT2/TYW4. OHyW is a derivative of wybutosine found in higher eukaryotes.<ref>PMID:20739293</ref>
-Wybutosine (yW) is a hypermodified nucleoside found in position 37 of tRNA(Phe), and is essential for correct phenylalanine codon translation. yW derivatives widely exist in eukaryotes and archaea, and their chemical structures have many species-specific variations. Among them, its hydroxylated derivative, hydroxywybutosine (OHyW), is found in eukaryotes including human, but the modification mechanism remains unknown. Recently, we identified a novel Jumonji C (JmjC)-domain-containing protein, TYW5 (tRNA yW-synthesizing enzyme 5), which forms the OHyW nucleoside by carbon hydroxylation, using Fe(II) ion and 2-oxoglutarate (2-OG) as cofactors. In this work, we present the crystal structures of human TYW5 (hTYW5) in the free and complex forms with 2-OG and Ni(II) ion at 2.5 and 2.8 A resolutions, respectively. The structure revealed that the catalytic domain consists of a beta-jellyroll fold, a hallmark of the JmjC domains and other Fe(II)/2-OG oxygenases. hTYW5 forms a homodimer through C-terminal helix bundle formation, thereby presenting a large, positively charged patch involved in tRNA binding. A comparison with the structures of other JmjC-domain-containing proteins suggested a mechanism for substrate nucleotide recognition. Functional analyses of structure-based mutants revealed the essential Arg residues participating in tRNA recognition by TYW5. These findings extend the repertoire of the tRNA modification enzyme into the Fe(II)/2-OG oxygenase superfamily.
-Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification.,Kato M, Araiso Y, Noma A, Nagao A, Suzuki T, Ishitani R, Nureki O Nucleic Acids Res. 2010 Oct 23. PMID:20972222<ref>PMID:20972222</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 == References ==
 <references/>
@@ Line 21: / Line 15: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Araiso, Y]]
+[[Category: Large Structures]]
-[[Category: Ishitani, R]]
+[[Category: Araiso Y]]
-[[Category: Kato, M]]
+[[Category: Ishitani R]]
-[[Category: Nureki, O]]
+[[Category: Kato M]]
-[[Category: Trna modification enzyme]]
+[[Category: Nureki O]]
-[[Category: Unknown function]]

3al6

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Crystal structure of Human TYW5

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