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| | ==Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi== | | ==Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi== |
| - | <StructureSection load='3fyc' size='340' side='right' caption='[[3fyc]], [[Resolution|resolution]] 2.15Å' scene=''> | + | <StructureSection load='3fyc' size='340' side='right'caption='[[3fyc]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3fyc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FYC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FYC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3fyc]] is a 2 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=3FYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FYC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qyr|1qyr]], [[2h1r|2h1r]], [[1zq9|1zq9]]</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></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3fyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyc OCA], [https://pdbe.org/3fyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fyc RCSB], [https://www.ebi.ac.uk/pdbsum/3fyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fyc 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=3fyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fyc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fyc RCSB], [http://www.ebi.ac.uk/pdbsum/3fyc PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fy/3fyc_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fy/3fyc_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3fyc ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3fyc" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Methanocaldococcus jannaschii]] | | [[Category: Methanocaldococcus jannaschii]] |
| - | [[Category: Musayev, F N.]] | + | [[Category: Musayev FN]] |
| - | [[Category: Rife, J P.]] | + | [[Category: Rife JP]] |
| - | [[Category: Scarsdale, J N.]] | + | [[Category: Scarsdale JN]] |
| - | [[Category: Dimethyladenosine transferase]]
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| - | [[Category: Methyltransferase]]
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| - | [[Category: Ribosomal assembly]]
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| - | [[Category: Rna methylase]]
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| - | [[Category: Rna-binding]]
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| - | [[Category: Rossmann fold]]
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| - | [[Category: Rrna processing]]
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| - | [[Category: S-adenosyl-l-methionine]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
RSMA_METJA Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607][1] [2]
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 enzymes of the KsgA/Dim1 family are universally distributed throughout all phylogeny; however, structural and functional differences are known to exist. The well-characterized function of these enzymes is to dimethylate two adjacent adenosines of the small ribosomal subunit in the normal course of ribosome maturation, and the structures of KsgA from Escherichia coli and Dim1 from Homo sapiens and Plasmodium falciparum have been determined. To this point, no examples of archaeal structures have been reported. Here, we report the structure of Dim1 from the thermophilic archaeon Methanocaldococcus jannaschii. While it shares obvious similarities with the bacterial and eukaryotic orthologs, notable structural differences exist among the three members, particularly in the C-terminal domain. Previous work showed that eukaryotic and archaeal Dim1 were able to robustly complement for KsgA in E. coli. Here, we repeated similar experiments to test for complementarity of archaeal Dim1 and bacterial KsgA in Saccharomyces cerevisiae. However, neither the bacterial nor the archaeal ortholog could complement for the eukaryotic Dim1. This might be related to the secondary, non-methyltransferase function that Dim1 is known to play in eukaryotic ribosomal maturation. To further delineate regions of the eukaryotic Dim1 critical to its function, we created and tested KsgA/Dim1 chimeras. Of the chimeras, only one constructed with the N-terminal domain from eukaryotic Dim1 and the C-terminal domain from archaeal Dim1 was able to complement, suggesting that eukaryotic-specific Dim1 function resides in the N-terminal domain also, where few structural differences are observed between members of the KsgA/Dim1 family. Future work is required to identify those determinants directly responsible for Dim1 function in ribosome biogenesis. Finally, we have conclusively established that none of the methyl groups are critically important to growth in yeast under standard conditions at a variety of temperatures.
Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.,Pulicherla N, Pogorzala LA, Xu Z, O Farrell HC, Musayev FN, Scarsdale JN, Sia EA, Culver GM, Rife JP J Mol Biol. 2009 Sep 4;391(5):884-93. Epub 2009 Jun 9. PMID:19520088[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Pulicherla N, Pogorzala LA, Xu Z, O Farrell HC, Musayev FN, Scarsdale JN, Sia EA, Culver GM, Rife JP. Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. J Mol Biol. 2009 Sep 4;391(5):884-93. Epub 2009 Jun 9. PMID:19520088 doi:10.1016/j.jmb.2009.06.015
- ↑ O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP. Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design. Biochemistry. 2010 Mar 30;49(12):2697-704. PMID:20163168 doi:10.1021/bi901875x
- ↑ Pulicherla N, Pogorzala LA, Xu Z, O Farrell HC, Musayev FN, Scarsdale JN, Sia EA, Culver GM, Rife JP. Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. J Mol Biol. 2009 Sep 4;391(5):884-93. Epub 2009 Jun 9. PMID:19520088 doi:10.1016/j.jmb.2009.06.015
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