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| | <StructureSection load='2vs1' size='340' side='right'caption='[[2vs1]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='2vs1' size='340' side='right'caption='[[2vs1]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VS1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VS1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2jjq|2jjq]]</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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [https://pdbe.org/2vs1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [https://www.ebi.ac.uk/pdbsum/2vs1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vs1 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://pdbe.org/2vs1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vs1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ATRMA_PYRAB ATRMA_PYRAB] Catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in tRNA.<ref>PMID:18069966</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vs/2vs1_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vs/2vs1_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrococcus abyssi erauso et al. 1993]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Golinelli-Pimpaneau, B]] | + | [[Category: Pyrococcus abyssi]] |
| - | [[Category: Grosjean, H]] | + | [[Category: Golinelli-Pimpaneau B]] |
| - | [[Category: Leulliot, N]] | + | [[Category: Grosjean H]] |
| - | [[Category: Walbott, H]] | + | [[Category: Leulliot N]] |
| - | [[Category: Iron]]
| + | [[Category: Walbott H]] |
| - | [[Category: Iron-sulfur]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Methyltransferase]]
| + | |
| - | [[Category: S-adenosyl-l-methionine]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Trna methyltransferase]]
| + | |
| Structural highlights
Function
ATRMA_PYRAB Catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in tRNA.[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
The 5-methyluridine is invariably found at position 54 in the TPsiC loop of tRNAs of most organisms. In Pyrococcus abyssi, its formation is catalyzed by the S-adenosyl-l-methionine-dependent tRNA (uracil-54, C5)-methyltransferase ((Pab)TrmU54), an enzyme that emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferase-like gene from bacteria to archaea. The crystal structure of (Pab)TrmU54 in complex with S-adenosyl-l-homocysteine at 1.9 A resolution shows the protein organized into three domains like Escherichia coli RumA, which catalyzes the same reaction at position 1939 of 23S rRNA. A positively charged groove at the interface between the three domains probably locates part of the tRNA-binding site of (Pab)TrmU54. We show that a mini-tRNA lacking both the D and anticodon stem-loops is recognized by (Pab)TrmU54. These results were used to model yeast tRNA(Asp) in the (Pab)TrmU54 structure to get further insights into the different RNA specificities of RumA and (Pab)TrmU54. Interestingly, the presence of two flexible loops in the central domain, unique to (Pab)TrmU54, may explain the different substrate selectivities of both enzymes. We also predict that a large TPsiC loop conformational change has to occur for the flipping of the target uridine into the (Pab)TrmU54 active site during catalysis.
The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity.,Walbott H, Leulliot N, Grosjean H, Golinelli-Pimpaneau B Nucleic Acids Res. 2008 Sep;36(15):4929-40. Epub 2008 Jul 24. PMID:18653523[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Urbonavicius J, Auxilien S, Walbott H, Trachana K, Golinelli-Pimpaneau B, Brochier-Armanet C, Grosjean H. Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer. Mol Microbiol. 2008 Jan;67(2):323-35. PMID:18069966 doi:10.1111/j.1365-2958.2007.06047.x
- ↑ Walbott H, Leulliot N, Grosjean H, Golinelli-Pimpaneau B. The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity. Nucleic Acids Res. 2008 Sep;36(15):4929-40. Epub 2008 Jul 24. PMID:18653523 doi:http://dx.doi.org/10.1093/nar/gkn437
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