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| | <StructureSection load='3a27' size='340' side='right'caption='[[3a27]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='3a27' size='340' side='right'caption='[[3a27]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a27]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A27 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3a27]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A27 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 2.005Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a25|3a25]], [[3a26|3a26]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ1557 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3a27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a27 OCA], [https://pdbe.org/3a27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a27 RCSB], [https://www.ebi.ac.uk/pdbsum/3a27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a27 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=3a27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a27 OCA], [https://pdbe.org/3a27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a27 RCSB], [https://www.ebi.ac.uk/pdbsum/3a27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a27 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/TYW2_METJA TYW2_METJA]] S-adenosyl-L-methionine-dependent transferase that acts as a component of the wyosine derivatives biosynthesis pathway. Catalyzes the transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine to 4-demethylwyosine (imG-14), forming 7-aminocarboxypropyl-demethylwyosine (wybutosine-86) at position 37 of tRNA(Phe).[HAMAP-Rule:MF_01922]<ref>PMID:19717466</ref>
| + | [https://www.uniprot.org/uniprot/TYW2_METJA TYW2_METJA] S-adenosyl-L-methionine-dependent transferase that acts as a component of the wyosine derivatives biosynthesis pathway. Catalyzes the transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine to 4-demethylwyosine (imG-14), forming 7-aminocarboxypropyl-demethylwyosine (wybutosine-86) at position 37 of tRNA(Phe).[HAMAP-Rule:MF_01922]<ref>PMID:19717466</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43067]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ishitani, R]] | + | [[Category: Methanocaldococcus jannaschii]] |
| - | [[Category: Nishimasu, H]] | + | [[Category: Ishitani R]] |
| - | [[Category: Nureki, O]] | + | [[Category: Nishimasu H]] |
| - | [[Category: Umitsu, M]] | + | [[Category: Nureki O]] |
| - | [[Category: Transferase]]
| + | [[Category: Umitsu M]] |
| - | [[Category: Wybutosine modification]]
| + | |
| Structural highlights
Function
TYW2_METJA S-adenosyl-L-methionine-dependent transferase that acts as a component of the wyosine derivatives biosynthesis pathway. Catalyzes the transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine to 4-demethylwyosine (imG-14), forming 7-aminocarboxypropyl-demethylwyosine (wybutosine-86) at position 37 of tRNA(Phe).[HAMAP-Rule:MF_01922][1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
S-adenosylmethionine (AdoMet) is a methyl donor used by a wide variety of methyltransferases, and it is also used as the source of an alpha-amino-alpha-carboxypropyl ("acp") group by several enzymes. tRNA-yW synthesizing enzyme-2 (TYW2) is involved in the biogenesis of a hypermodified nucleotide, wybutosine (yW), and it catalyzes the transfer of the "acp" group from AdoMet to the C7 position of the imG-14 base, a yW precursor. This modified nucleoside yW is exclusively located at position 37 of eukaryotic tRNA(Phe), and it ensures the anticodon-codon pairing on the ribosomal decoding site. Although this "acp" group has a significant role in preventing decoding frame shifts, the mechanism of the "acp" group transfer by TYW2 remains unresolved. Here we report the crystal structures and functional analyses of two archaeal homologs of TYW2 from Pyrococcus horikoshii and Methanococcus jannaschii. The in vitro mass spectrometric and radioisotope-labeling analyses confirmed that these archaeal TYW2 homologues have the same activity as yeast TYW2. The crystal structures verified that the archaeal TYW2 contains a canonical class-I methyltransferase (MTase) fold. However, their AdoMet-bound structures revealed distinctive AdoMet-binding modes, in which the "acp" group, instead of the methyl group, of AdoMet is directed to the substrate binding pocket. Our findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the "acp" group, and not the methyl group, from AdoMet to the nucleobase.
Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2.,Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O Proc Natl Acad Sci U S A. 2009 Aug 26. PMID:19717466[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O. Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc Natl Acad Sci U S A. 2009 Aug 26. PMID:19717466
- ↑ Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O. Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc Natl Acad Sci U S A. 2009 Aug 26. PMID:19717466
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